@article {pmid39800778,
year = {2025},
author = {Nyamota, R and Middlebrook, EA and Abkallo, HM and Akoko, J and Gakuya, F and Wambua, L and Ronoh, B and Lekolool, I and Mwatondo, A and Muturi, M and Bett, B and Fair, JM and Bartlow, AW},
title = {The Bacterial and pathogenic landscape of African buffalo (Syncerus caffer) whole blood and serum from Kenya.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {6},
pmid = {39800778},
issn = {2524-4671},
support = {HDTRA19-3-1960//USA, Defense Threat Reduction Agency/ ; },
abstract = {BACKGROUND: African buffalo (Syncerus caffer) is a significant reservoir host for many zoonotic and parasitic infections in Africa. These include a range of viruses and pathogenic bacteria, such as tick-borne rickettsial organisms. Despite the considerations of mammalian blood as a sterile environment, blood microbiome sequencing could become crucial for agnostic biosurveillance. This study investigated the blood microbiome of clinically healthy wild buffaloes in Kenya to determine its applicability in agnostic testing for bacteria in apparently healthy wild animals.<br><br>METHODS: Whole blood and serum samples were collected from 46 wild African buffalos from Meru National Park (30), Buffalo Springs (6) and Shaba (10) National Reserves in upper eastern Kenya. Total deoxyribonucleic acid (DNA) was extracted from these samples and subjected to amplicon-based sequencing targeting the 16&#xa0;S rRNA gene. The bacteria operational taxonomic units (OTU) were identified to species levels by mapping the generated V12 and V45 regions of 16&#xa0;S rRNA gene to the SILVA database. These OTU tables were used to infer the microbial abundance in each sample type and at the individual animal level. The sequences for the corresponding OTUs were also used to generate phylogenetic trees and thus infer evolution for the OTUs of interest.<br><br>RESULTS: Here, we demonstrate that buffaloes harbor many bacteria in their blood. We also report a diversity of 16&#xa0;S rRNA gene sequences for Anaplasma and Mycoplasma from individual animals. By sequencing both whole blood and serum in triplicate for each animal, we provide evidence of the differences in detecting bacteria in both sample types.<br><br>CONCLUSIONS: Diverse bacteria, including some potential pathogens, can be found in the blood of clinically healthy wild African buffalo. Agnostic surveillance for such pathogens can be achieved through blood microbiome sequencing. However, considerations for the question being asked for the blood microbiome in wildlife will impact the choice for using whole blood or serum for sequencing.},
}
@article {pmid39800756,
year = {2025},
author = {Russell, D and Rajabal, V and Alfonzetti, M and van der Merwe, MM and Gallagher, RV and Tetu, SG},
title = {Seed banking impacts native Acacia ulicifolia seed microbiome composition and function.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {4},
pmid = {39800756},
issn = {2524-6372},
support = {CE200100029//Australian Research Council/ ; LP200200688//Australian Research Council/ ; CE200100029//Australian Research Council/ ; },
abstract = {BACKGROUND: Seed banks are a vital resource for preserving plant species diversity globally. However, seedling establishment and survival rates from banked seeds can be poor. Despite a growing appreciation for the role of seed-associated microbiota in supporting seed quality and plant health, our understanding of the effects of conventional seed banking processes on seed microbiomes remains limited. In this study we investigated the composition and functional potential of seed-associated bacterial epiphytes associated with stored and freshly collected seeds of a native plant, Acacia ulicifolia, using both 16S rRNA gene sequencing and culture-based approaches.<br><br>RESULTS: Seeds obtained from seed banking facilities were found to host significantly less diverse bacterial populations, with substantial reductions in both low-abundance taxa and in community members commonly identified in freshly collected A. ulicifolia seeds. Bacteria with key plant growth promoting traits including IAA production, ACC deaminase activity, phosphate solubilisation, siderophore activity, and nitrogen fixation were identified in seed epiphytic communities, but these beneficial traits were less prevalent in stored seed compared to fresh seeds.<br><br>CONCLUSION: Overall, these results suggest that epiphytic seed microbiomes may undergo significant changes during the storage process, selecting for bacteria tolerant to storage conditions, and potentially reducing the population of plant-growth promoting bacteria on seeds.},
}
@article {pmid39800598,
year = {2025},
author = {Mariscal de Gante, L and Salanova, L and Valdivia Mazeyra, M and Serrano Pardo, R and Quiroga, B},
title = {Secondary hyperoxaluria: Cause and consequence of chronic kidney disease.},
journal = {Nefrologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.nefroe.2024.12.001},
pmid = {39800598},
issn = {2013-2514},
abstract = {Secondary hyperoxaluria is a metabolic disorder characterized by an increase in urinary oxalate excretion. The etiology may arise from an increase in the intake of oxalate or its precursors, decreased elimination at the digestive level, or heightened renal excretion. Recently, the role of the SLC26A6 transporter in the etiopathogenesis of this disease has been identified. This transporter is active at both the intestinal and renal levels, and its mechanism of action is disrupted during systemic inflammation and metabolic syndrome, which could explain the rising incidence of secondary hyperoxaluria in recent decades. Treatment includes hygienic dietary measures, and medications aimed at reducing intestinal absorption by increasing fecal excretion. Different immunomodulatory drugs, microbiome modifiers and SGLT2 inhibitors could constitute new therapeutic targets. Currently, specific treatments for secondary hyperoxaluria are lacking, making early diagnosis and preventive measures against kidney failure the main therapeutic strategies.},
}
@article {pmid39800212,
year = {2025},
author = {Li, P and Zhang, H and Chen, L and Gao, X and Hu, Y and Xu, Q and Liu, W and Chen, W and Chen, H and Yuan, S and Wang, M and Liu, S and Dai, M},
title = {Oral and Fecal Microbiota as Accurate Non-invasive Tools for Detection of Pancreatic Cancer in the Chinese Population.},
journal = {Cancer letters},
volume = {},
number = {},
pages = {217456},
doi = {10.1016/j.canlet.2025.217456},
pmid = {39800212},
issn = {1872-7980},
abstract = {Pancreatic cancer (PCA), a leading cause of cancer-related deaths, has limited non-invasive diagnostic methods. We aimed to identify oral and fecal microbiome biomarkers and construct diagnostic classifiers. Oral and fecal samples from 97 PCA patients and 90 healthy controls underwent 16S rRNA sequencing. Samples were randomly divided into training and validation cohorts in a 7:3 ratio. Random forest models were constructed using training cohort and validated internally and externally in Chinese, Japanese, and Spanish populations. Results revealed significant dysbiosis of the oral and fecal microbiota of PCA patients. Most of the differential taxa shared between oral and fecal samples showed similar changes. Relative abundances of Streptococcus in oral samples, and of Bifidobacterium, Klebsiella and Akkermansia in fecal samples, were enriched in PCA. The fecal Firmicutes to Bacteroidota ratio was higher in PCA patient samples. Oral and fecal microbiome classifiers based on the top 20 contributing genera were constructed, and internal validation showed that the area under the curve (AUC) values were 0.963 and 0.890, respectively. The fecal microbiome classifier performed well in the external Chinese population, with an AUC of 0.878, but poorly in the Japanese and Spanish populations. Furthermore, fecal microbiomes could predict metastasis status in PCA patients, with an AUC of 0.804. In conclusion, oral and fecal microbiota were dysbiotic in PCA patients. Fecal microbiome classifier provides a feasible, non-invasive, and cost-effective tool with high precision for PCA screening in China; oral microbiome classifier requires further validation in external populations sampled with the same simple and convenient methods.},
}
@article {pmid39800090,
year = {2025},
author = {Grosserichter-Wagener, C and Looman, KIM and Beth, SA and Radjabzadeh, D and Gill, PA and Smit, KN and Duijts, L and Kiefte-de Jong, JC and Kraaij, R and Moll, HA and van Zelm, MC},
title = {A distinct immunophenotype in children carrying the Blautia enterotype: The generation R study.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {},
number = {},
pages = {110426},
doi = {10.1016/j.clim.2025.110426},
pmid = {39800090},
issn = {1521-7035},
abstract = {OBJECTIVE: Studies in mouse models and human adults have shown that the intestinal microbiota composition can affect peripheral immune cells. We here examined whether the gut microbiota compositions affect B and T-cell subsets in children.<br><br>METHODS: The intestinal microbiota was characterized from stool samples of 344 10-year-old children from the Generation R Study by performing 16S rRNA sequencing. Bray-Curtis dissimilarity was used to cluster distinct microbiome compositions (enterotypes). B-cell and T-cell phenotypes were defined by 11-color-flow cytometry. Linear regression models with adjustment for lifestyle and child characteristics were performed to determine associations between enterotypes and immune cell numbers.<br><br>RESULTS: Three enterotypes with distinct microbiota composition were found, characterized by high abundance of Prevotella, Bacteroides and Blautia. Children with the Blautia enterotype had decreased numbers of plasmablasts, CD4[+] central memory (Tcm) T cells and follicular T-helper cells (Tfh), while Th22 cells and CD4[+] effector memory (Tem) T cells, CD27[-]IgA[+] memory B cells and CD27[-]IgE[+] memory B cells, were increased in these children. In addition, in children with the Blautia enterotype CD4[+] Tcm cell numbers expressing the &#x3b2;7 integrin, which can pair with &#x3b1;4 to mediate intestinal were also lower, while CD4[+]&#x3b2;7[+] Tem cell numbers were higher than in the other enterotypes.<br><br>CONCLUSION: The Blautia enterotype showed features beneficial for human health. Enterotypes were associated with differences in memory B- and T-cell compartments. This study is unique in the detailed analysis of the B and T-cell compartment and the intestinal microbiome in a large generic pediatric cohort, enabling correction for child and maternal covariates. These outcomes could guide further studies about the impact of intestinal microbiome intervention, for instance through diet and microbiota metabolites such as short chain fatty acid production.},
}
@article {pmid39799673,
year = {2025},
author = {Li, K and Rahman, SU and Rehman, A and Li, H and Hui, N and Khalid, M},
title = {Shaping rhizocompartments and phyllosphere microbiomes and antibiotic resistance genes: The influence of different fertilizer regimes and biochar application.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137148},
doi = {10.1016/j.jhazmat.2025.137148},
pmid = {39799673},
issn = {1873-3336},
abstract = {Understanding the impact of different soil amendments on microbial communities and antibiotic resistance genes (ARGs) dissemination is crucial for optimizing agricultural practices and mitigating environmental risks. This study investigated the effects of different fertilizer regimes and biochar on plant-associated bacterial communities and ARGs dissemination. The biochar's structural and chemical characteristics were characterized using scanning electron microscopy (SEM) and Fourier-transform infrared (FTIR) spectroscopy, revealing a porous architecture with diverse functional groups. The presence of ARGs varied significantly across groups, with manure-treated samples exhibiting the greatest diversity and abundance, raising concerns about ARGs dissemination. Soil enzyme activities responded differently to treatments; manure significantly enhanced catalase, acid phosphatase, and urease activities, whereas saccharase was most responsive to chemical fertilizer. These differences are possibly responsible for the distinct microbiome structure associated with the plant's root system. The analysis of bacterial diversity and richness across rhizocompartments and the phyllosphere highlighted that manure-treated rhizospheres and phyllospheres displayed the highest species richness and diversity. Notably, Proteobacteria dominated across most treatments, with distinct shifts in bacterial phyla and genera influenced by manure and biochar applications. The LEfSe analysis identified key indicator genera specific to each group, indicating that both fertilizer type and biochar application significantly shape microbial community composition. Co-occurrence network analysis further demonstrated that manure and biochar treatments created unique microbial networks in the rhizosphere, rhizoplane, phyllosphere, and endosphere, highlighting the role of these amendments in modulating microbial interactions in plant-associated environments. These findings suggest that manure, while enhancing microbial diversity and soil enzyme activities, also increases ARGs, whereas biochar may not contribute to the spread of ARGs and fosters distinct microbial communities, offering valuable insights for sustainable agricultural practices.},
}
@article {pmid39799656,
year = {2025},
author = {Chen, X and Zhou, Y and Mai, Z and Cheng, H and Wang, X},
title = {Mangroves increased the mercury methylation potential in the sediment by producing organic matters and altering microbial methylators community.},
journal = {The Science of the total environment},
volume = {962},
number = {},
pages = {178457},
doi = {10.1016/j.scitotenv.2025.178457},
pmid = {39799656},
issn = {1879-1026},
abstract = {Mangrove ecosystem has attracted global attention as a hotspot for mercury (Hg) methylation. Although numerous biotic and abiotic parameters have been reported to influence methylmercury (MeHg) production in sediments, the key factors determining the elevated MeHg levels in mangrove wetlands have not been well addressed. In this study, Hg levels in the sediments from different habitats (mudflats, mangrove fringe, and mangrove interior) in the Futian mangrove wetland were investigated, aiming to characterize the predominant factors affecting the MeHg production and distinguish the key microbial taxa responsible for Hg methylation. MeHg concentrations in the sediments from the mangrove interior (1.03 ± 0.34 ng g[-1] dw) were significantly higher than those in mudflats (0.26 ± 0.08 ng g[-1] dw) and mangrove fringe (0.45 ± 0.10 ng g[-1] dw). Mangrove vegetation also promoted the accumulation of organic matters in sediments, which stimulated the growth of methylators, ultimately leading to an elevated MeHg level in the sediment. The data from 16S sequencing and random forest analysis further indicated that the increased abundances of Desulfococcus and Desulfosarcina, which belong to complete-oxidizing microbes with acetyl-CoA pathway and are favored by mangrove vegetation, were the primary contributors to MeHg production. Besides, syntrophic partners of methylators (e.g. Syntrophus) also play a considerable role in MeHg production. The present findings provide a deep understanding of Hg-methylation in mangrove wetlands, and offers valuable insights into of the interactions between mangrove plants and soil microbiome in the presence of Hg contamination.},
}
@article {pmid39799645,
year = {2025},
author = {Tromas, N and Goitom, E and Chin, T and Dinh, QT and Dorner, SM and Khawasik, OS and Cristescu, ME and Burnet, JB},
title = {Impact of grazing by multiple Daphnia species on wastewater bacterial communities.},
journal = {The Science of the total environment},
volume = {962},
number = {},
pages = {178364},
doi = {10.1016/j.scitotenv.2024.178364},
pmid = {39799645},
issn = {1879-1026},
abstract = {Understanding the dynamics of fecal bacterial communities is crucial for managing public health risks and protecting drinking water resources. While extensive research exists on how abiotic factors influence the survival of fecal microbial communities in water, less attention has been paid to the impact of predation by higher organisms, such as the widely distributed grazer Daphnia. Nevertheless, Daphnia plays a significant role in regulating bacterial communities in natural aquatic ecosystems, and recent studies highlighted its potential as a biofilter in alternative tertiary wastewater treatment systems. In this study, we investigated the influence of three different Daphnia species on a wastewater bacterial community, including fecal indicator bacterium E. coli. Using a microcosm setup to simulate the discharge of untreated sewage into surface water, we conducted in-depth analysis of bacterial community dynamics through sequencing the 16S rRNA gene. Our results revealed significant changes in microbial diversity and composition following exposure to Daphnia grazing, with variations observed among the three Daphnia species. D. pulicaria exerted the most pronounced impact on microbial diversity, followed by D. middendorffiana and D. mendotae. A total of 90 taxa exhibited significantly reduced relative abundance in the presence of Daphnia, with Firmicutes phylum being the most affected. At genus level, bacteria typically associated with wastewater (e.g., Zoogloea and Arcobacter) and gut microbiome constituents (e.g., Prevotella and Akkermansia) were notably affected by Daphnia exposure. The influence of Daphnia on bacterial community composition was most pronounced for D. pulicaria, while D. middendorffiana and D. mendotae primarily impacted community structure. Furthermore, we demonstrated that the microbial response to Daphnia exposure is phylogenetically conserved, potentially reflecting a grazing resistance or grazer feeding trait. Our findings shed new light on the role of Daphnia in controlling bacterial communities in polluted water bodies and underscore its potential as biofilter in wastewater treatment and reuse contexts.},
}
@article {pmid39799515,
year = {2025},
author = {Jiang, Y and Liao, D and Zhu, Q and Lu, YY},
title = {PhyloMix: Enhancing microbiome-trait association prediction through phylogeny-mixing augmentation.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf014},
pmid = {39799515},
issn = {1367-4811},
abstract = {MOTIVATION: Understanding the associations between traits and microbial composition is a fundamental objective in microbiome research. Recently, researchers have turned to machine learning (ML) models to achieve this goal with promising results. However, the effectiveness of advanced ML models is often limited by the unique characteristics of microbiome data, which are typically high-dimensional, compositional, and imbalanced. These characteristics can hinder the models' ability to fully explore the relationships among taxa in predictive analyses. To address this challenge, data augmentation has become crucial. It involves generating synthetic samples with artificial labels based on existing data and incorporating these samples into the training set to improve ML model performance.<br><br>RESULTS: Here we propose PhyloMix, a novel data augmentation method specifically designed for microbiome data to enhance predictive analyses. PhyloMix leverages the phylogenetic relationships among microbiome taxa as an informative prior to guide the generation of synthetic microbial samples. Leveraging phylogeny, PhyloMix creates new samples by removing a subtree from one sample and combining it with the corresponding subtree from another sample. Notably, PhyloMix is designed to address the compositional nature of microbiome data, effectively handling both raw counts and relative abundances. This approach introduces sufficient diversity into the augmented samples, leading to improved predictive performance. We empirically evaluated PhyloMix on six real microbiome datasets across five commonly used ML models. PhyloMix significantly outperforms distinct baseline methods including sample-mixing-based data augmentation techniques like vanilla mixup and compositional cutmix, as well as the phylogeny-based method TADA. We also demonstrated the wide applicability of PhyloMix in both supervised learning and contrastive representation learning.<br><br>AVAILABILITY: The Apache licensed source code is available at (https://github.com/batmen-lab/phylomix).<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics.},
}
@article {pmid39799378,
year = {2025},
author = {Sakhabutdinov, IT and Chastukhina, IB and Ryazanov, EA and Ponomarev, SN and Gogoleva, OA and Balkin, AS and Korzun, VN and Ponomareva, ML and Gorshkov, VY},
title = {Variability of microbiomes in winter rye, wheat, and triticale affected by snow mold: predicting promising microorganisms for the disease control.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {3},
pmid = {39799378},
issn = {2524-6372},
support = {23-16-00086//Russian Science Foundation/ ; 124050300040-5//Government assignment for the FRC Kazan Scientific Center of RAS/ ; },
abstract = {BACKGROUND: Snow mold caused by different psychrophilic phytopathogenic fungi is a devastating disease of winter cereals. The variability of the snow mold pathocomplex (the quantitative composition of snow mold fungi) has not been evaluated across different crops or different agrocenoses, and no microbial taxa have been predicted at the whole-microbiome level as potential effective snow mold control agents. Our study aimed to assess the variability of the snow mold pathocomplex in different winter cereal crops (rye, wheat, and triticale) in different agrocenoses following the peak disease progression and to arrange a hierarchical list of microbial taxa predicted to be the main candidates to prevent or, conversely, stimulate the development of snow mold pathogens.<br><br>RESULTS: The variability of microbiomes between different crops within a particular agrocenosis was largely determined by fungal communities, whereas the variability of microbiomes of a particular crop in different agrocenoses was largely determined by bacterial communities. The snow mold pathocomplex was the most "constant" in rye, with the lowest level of between-replicate variability and between-agrocenoses variability and (similar to the triticale snow mold pathocomplex) strong dominance of Microdochium over other snow mold fungi. The wheat snow mold pathocomplex was represented by different snow mold fungi, including poorly investigated Phoma sclerotioides. To predict snow mold-control microorganisms, a conveyor of statistical methods was formed and applied; this conveyor enables considering not only the correlation between the abundance of target taxa and a phytopathogen but also the stability and fitness of taxa within plant-associated communities and the reproducibility of the predicted effect of taxa under different conditions. This conveyor can be widely used to search for biological agents against various plant infectious diseases.<br><br>CONCLUSIONS: The top indicator microbial taxa for winter wheat and rye following the winter period were Ph. sclerotioides and Microdochium, respectively, both of which are causal agents of snow mold disease. Bacteria from the Cellulomonas, Lechevalieria, and Pseudoxanthomonas genera and fungi from the Cladosporium, Entimomentora, Pseudogymnoascus, and Cistella genera are prime candidates for testing their plant-protective properties against Microdochium-induced snow mold disease and for further use in agricultural practice.},
}
@article {pmid39799366,
year = {2025},
author = {Węsierska, E and Micek, P and Adamski, MG and Gondek, K and Lis, M and Trela, M and Wojtysiak, D and Kowal, J and Wyrobisz-Papiewska, A and Kunstman, G and Mosiołek, S and Smoroń, K},
title = {Changes in the intestinal microbiota of broiler chicken induced by dietary supplementation of the diatomite-bentonite mixture.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {13},
pmid = {39799366},
issn = {1746-6148},
support = {BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Bentonite/pharmacology/administration &amp; dosage ; *Dietary Supplements ; *Animal Feed/analysis ; *Diet/veterinary ; Diatomaceous Earth/pharmacology ; Bacteria/classification/drug effects/genetics ; },
abstract = {BACKGROUND: Diatomite is a source of biologically available silicon but in feed industry its insecticide and anti-caking properties have been also widely recognized. The aim of the study was to evaluate the effect of dietary diatomite-bentonite mixture (DBM) supplementation on the quantitative and qualitative composition of the bacterial microbiome of the broiler chicken gut. The trial was carried out on 960 Ross 308 broiler chickens divided into 2 experimental groups throughout the entire rearing period lasting 6 weeks. The birds were fed complete granulated diets without (group C) or with DBM (group E) in an amount of 1% from the 11 day of life. Two nutritionally balanced diets were used, tailored to the age of the broilers: a grower diet (from day 11 to 34) and a finisher diet (from day 35 to 42 of life).<br><br>RESULTS: Diatomite used in a mixture with bentonite significantly altered the microbiome. Restricting the description to species that comprise a minimum of 1% of all analyzed sequences, 36 species in group E (with diatomite) and 30 species in group C (without diatomite) were selected. Several bacteria species were identified in intestinal contents of chickens for the first time. Thirteen species occurred only in group E: Agathobaculum butyriciproducens, Anaerobutyricum hallii, Anaerobutyricum soehngenii, Blautia producta ATCC 27,340&#x2009;=&#x2009;DSM 2950, Gordonibacter pamelaeae 7-10-1-b, Helicobacter pullorum NCTC 12,824, Lactobacillus crispatus, L. helveticus DSM 20,075&#x2009;=&#x2009;CGMCC 1.1877, Mucispirillum schaedleri, Phascolarctobacterium faecium, Phocaeicola coprocola DSM 17,136, P. massiliensis, and Ruthenibacterium lactatiformans.<br><br>CONCLUSIONS: The findings highlight the intricate and potentially consequential relationship between diet, specifically diatomite-bentonite mixture supplementation, and gut microbiota composition.},
}
@article {pmid39799316,
year = {2025},
author = {Ruiz-Muñoz, M and Ontañón, I and Cobos, R and Calvo-Peña, C and Otero-Suárez, R and Ferreira, V and Roselló, J and Coque, JJR},
title = {The microbiota of cork and yellow stain as a model for a new route for the synthesis of chlorophenols and chloroanisoles from the microbial degradation of suberin and/or lignin.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {6},
pmid = {39799316},
issn = {2049-2618},
mesh = {*Lignin/metabolism ; *Chlorophenols/metabolism ; *Microbiota ; *Wine/microbiology/analysis ; *Anisoles/metabolism ; Fungi/metabolism/classification ; Parabens/metabolism ; Quercus/microbiology ; Bacteria/metabolism/classification ; Lipids ; },
abstract = {BACKGROUND: The main application of cork is the production of stoppers for wine bottles. Cork sometimes contains 2,4,6-trichloroanisole, a compound that, at a concentration of ng/L, produces an unpleasant musty odor that destroys the organoleptic properties of wine and results in enormous economic losses for wineries and cork industries. Cork can exhibit a defect known as yellow stain, which is associated with high levels of 2,4,6-trichloroanisole. We describe how the microbiota of cork and yellow stain define a novel mechanism that explains the formation of chlorophenols and chloroanisoles (including 2,4,6-trichloroanisole) from p-hydroxybenzoate produced during lignin and/or suberin breakdown.<br><br>RESULTS: Electron microscopy revealed that cork affected by yellow stain exhibited significant structural degradation. This deterioration was attributed to the presence of higher microbial populations compared to those found in standard cork. Cork microbiota is rich in filamentous fungi able to metabolize lignin. A metataxonomic analysis confirmed that yellow stain contained significantly greater populations of fungal species belonging to Absidia, Geomyces, Mortierella, Mucor, Penicillium, Pseudogymnoascus, Talaromyces, and Umbelopsis. It also contained significantly greater amounts of bacteria belonging to Enterobacterales, Streptosporangiales, Tepidisphaerales, Pseudomonas, and several members of Burkholderiaceae, particularly species of the Burkholderia-Caballeronia-Paraburkholderia group. The extraction of aromatic compounds from cork samples allowed the identification of several compounds typically observed following lignin depolymerization. Notably, p-hydroxybenzoic acid and phenol were detected. Two strains of the genus Streptomyces isolated from yellow stain were able to biotransform p-hydroxybenzoate into phenol in resting cell assays. Phenol could be efficiently chlorinated in vitro to produce 2,4,6-trichlorophenol by a fungal chloroperoxidase, an enzymatic activity commonly found in filamentous fungi isolated from cork. Finally, as has been widely demonstrated before, 2,4,6-trichlorophenol can be efficiently O-methylated to 2,4,6-trichloroanisole by many of fungi that inhabit cork.<br><br>CONCLUSIONS: Chlorophenols and chloroanisoles can be produced de novo in cork from p-hydroxybenzoate generated by the microbial biodegradation of lignin and/or suberin through the participation of different types of microorganisms present in cork. The natural origin of these compounds, which are of great interest for the chlorine cycle and represent a new source of environmental contamination that differs from that caused by human activity, is described. Video Abstract.},
}
@article {pmid39799280,
year = {2025},
author = {Tabardillo, JA and Juinio-Meñez, MA and Reitzel, AM and Ravago-Gotanco, R},
title = {Differences in gut microbial diversity and composition between growth phenotypes of farmed juvenile sandfish, Holothuria scabra.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {14},
pmid = {39799280},
issn = {1471-2180},
support = {ECWRG 2019-10-R//University of the Philippines/ ; ECWRG 2019-10-R//University of the Philippines/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Holothuria/microbiology/growth &amp; development ; *RNA, Ribosomal, 16S/genetics ; *Aquaculture ; *Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; *Feces/microbiology ; Phylogeny ; Biodiversity ; Phenotype ; DNA, Bacterial/genetics ; },
abstract = {BACKGROUND: The observed growth variability of different aquaculture species in captivity hinders its large-scale production. For the sandfish Holothuria scabra, a tropical sea cucumber species, there is a scarcity of information on its intestinal microbiota in relation to host growth, which could provide insights into the processes that affect growth and identify microorganisms with probiotic or biochemical potential that could improve current production strategies. To address this gap, this study used 16 S rRNA amplicon sequencing to characterize differences in gut and fecal microbiota among large and small juveniles reared in floating ocean nurseries.<br><br>RESULTS: We recovered 5915 amplicon sequence variants and diversity indices revealed significant differences between large and small juveniles (p&#x2009;<&#x2009;0.05). Gut microbiota of large juveniles had lower bacterial diversity than its smaller counterparts. The genus cluster Burkholderia-Caballeronia-Paraburkholderia (BCP) is the most common and abundant taxa found in the gut for both size categories but less abundant in fecal samples. Small juveniles had a higher abundance of members from the Roseobacter clade (Rhodobacteriaceae) such as Ruegeria, Shimia, Psuedoruegeria and Marivita among others while the genus Schlegelella (Caldimonas) and Bosea were primarily found in larger juveniles. Predicted physiological functions identified signatures of metabolism, biosynthesis, and biodegradation pathways unique for each size category. Significant differences in diversity and composition were also exhibited between the pooled fecal and gut sample types.<br><br>CONCLUSIONS: The bacterial composition in the intestinal tract of the sandfish H. scabra is an important factor in the observed growth variability in aquaculture. The results show differences in diversity, composition and predicted physiological functions between the size groups, despite being from the same cohort and environment. It was also evident that the fecal microbiota differs from the gut and does not correspond to size category, warranting caution in using the fecal matter as a proxy to infer microbial composition and interactions in the gastrointestinal tract. Understanding the roles that these microorganisms play in sandfish growth could support the development of strategies to manage size variation in captive-bred sea cucumbers, or for the promotion and selection for faster-growing individuals.},
}
@article {pmid39799140,
year = {2025},
author = {Wu, C and Li, M and Chen, Z and Feng, S and Deng, Q and Duan, R and Liu, TC and Yang, L},
title = {Remote photobiomodulation ameliorates behavioral and neuropathological outcomes in a rat model of repeated closed head injury.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {8},
pmid = {39799140},
issn = {2158-3188},
support = {32300959//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100918//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Rats ; *Disease Models, Animal ; *Low-Level Light Therapy/methods ; Male ; *Head Injuries, Closed/complications/radiotherapy ; *Behavior, Animal ; *Rats, Sprague-Dawley ; Microglia ; Astrocytes ; Social Interaction ; },
abstract = {Repeated closed-head injuries (rCHI) from activities like contact sports, falls, military combat, and traffic accidents pose a serious risk due to their cumulative impact on the brain. Often, rCHI is not diagnosed until symptoms of irreversible brain damage appear, highlighting the need for preventive measures. This study assessed the prophylactic efficacy of remote photobiomodulation (PBM) targeted at the lungs against rCHI-induced brain injury and associated behavioral deficits. Utilizing the "Marmarou" weight-drop model, rCHI was induced in rats on days 0, 5, and 10. Remote PBM, employing an 808 nm continuous wave laser, was administered daily in 2-min sessions per lung side over 20 days. Behavioral deficits were assessed through three-chamber social interaction, forced swim, grip strength, open field, elevated plus maze, and Barnes maze tests. Immunofluorescence staining and 3D reconstruction evaluated neuronal damage, apoptosis, degeneration, and the morphology of microglia and astrocytes, as well as astrocyte and microglia-mediated excessive synapse elimination. Additionally, 16S rDNA amplicon sequencing analyzed changes in the lung microbiome following remote PBM treatment. Results demonstrated that remote PBM significantly improved depressive-like behaviors, motor dysfunction, and social interaction impairment while enhancing grip strength and reducing neuronal damage, apoptosis, and degeneration induced by rCHI. Analysis of lung microbiome changes revealed an enrichment of lipopolysaccharide (LPS) biosynthesis pathways, suggesting a potential link to neuroprotection. Furthermore, remote PBM mitigated hyperactivation of cortical microglia and astrocytes and significantly reduced excessive synaptic phagocytosis by these cells, highlighting its potential as a preventive strategy for rCHI with neuroprotective effects.},
}
@article {pmid39798925,
year = {2025},
author = {Aleksandrova, RR and Nieuwenhuis, LM and Karmi, N and Zhang, S and Swarte, JC and Björk, JR and Gacesa, R and Blokzijl, H and Connelly, MA and Weersma, RK and Lisman, T and Festen, EAM and de Meijer, VE and , },
title = {Gut microbiome dysbiosis is not associated with portal vein thrombosis in patients with end-stage liver disease: a cross-sectional study.},
journal = {Journal of thrombosis and haemostasis : JTH},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtha.2024.12.036},
pmid = {39798925},
issn = {1538-7836},
abstract = {BACKGROUND: Portal vein thrombosis (PVT) is a common complication in patients with end-stage liver disease (ESLD). The portal vein in ESLD patients is proposedly an inflammatory vascular bed due to translocation of endotoxins and cytokines from the gut. We hypothesized that a pro-inflammatory gut microbiome and elevated trimethylamine N-oxide (TMAO), a driver of thrombosis, may contribute to PVT development.<br><br>OBJECTIVES: We investigated whether gut microbiome diversity, bacterial species, metabolic pathways, and TMAO levels are associated with PVT in ESLD patients.<br><br>METHODS: Fecal samples, plasma samples and data from ESLD patients and healthy controls were collected through the TransplantLines Biobank and Cohort Study. PVT was defined as a thrombus in the portal vein within a year prior to or after fecal sample collection. Fecal samples were analyzed using Shotgun Metagenomic Sequencing, and TMAO levels were measured in plasma using a Vantera&#xae; Clinical Analyzer.<br><br>RESULTS: 102 ESLD patients, of which 23 with PVT, and 246 healthy controls were included. No significant difference in gut microbiome diversity was found between patients with PVT and without PVT (P=0.18). Both ESLD groups had significantly lower alpha-diversity compared with controls. Bacteroides fragilis and three Clostridiales species were increased in patients with PVT compared to without PVT. TMAO levels between the three groups were not significantly different.<br><br>CONCLUSION: We observed profound differences in gut microbiota between ESLD patients and controls, but minimal differences between ESLD patients with or without PVT. In our cohort, a gut-derived pro-inflammatory state was not associated with presence of PVT in ESLD patients.},
}
@article {pmid39798661,
year = {2025},
author = {Liu, R and Wei, G and Yang, Y and Wang, J and Zhao, S and Zhang, B and Hao, X and Liu, K and Shao, Z},
title = {Discovery of potentially degrading microflora of different types of plastics based on long-term in-situ incubation in the deep sea.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120812},
doi = {10.1016/j.envres.2025.120812},
pmid = {39798661},
issn = {1096-0953},
abstract = {Plastic waste that ends up in the deep sea is becoming an increasing concern. However, it remains unclear whether there is any microflora capable of degrading plastic within this vast ecosystem. In this study, we investigated the bacterial communities associated with different types of plastic-polyamide-nylon 4, 6 (PA), polyethylene (PE), polyethylene terephthalate (PET), and polystyrene (PS)-after one year of in situ incubation in the pelagic deep sea of the Western Pacific. The study was conducted via a submarine mooring system, anchored at four sites with water depths ranging from 1,167 to 1,735 meters in an area of seamounts. High-throughput 16S rRNA gene sequencing revealed distinct bacterial diversities associated with specific plastic types and locations. The family Gordoniaceae was enriched by PS and PE plastics, while the abundance of Methyloligellaceae was significantly increased in the presence of PET. In the case of PA, Bdellovibrionaceae was enriched. Additionally, all plastic types promoted the relative abundance of Rhodobacteraceae and Sulfurimonadaceae families. Plastics appeared to stimulate bacterial communities involved in nitrate and sulfur cycling in seawater, suggesting that nitrogen and sulfur potentially play significant roles in plastic degradation in deep-sea environments. The dominant family Kordiimonadaceae was identified as a significantly different taxon in non-plastic seawater. Furthermore, the addition of plastics enhanced negative interactions among the bacterial communities in the surrounding seawater, with Proteobacteria and Bdellovibrionota selected for the core microbiome. Overall, this in situ deep-sea incubation revealed the response of indigenous microflora to man-made polymeric materials and highlighted the bacterial communities that may be involved in plastic degradation in oceanic areas.},
}
@article {pmid39798621,
year = {2025},
author = {Heckmann, ND and Culler, M and Mont, MA and Lieberman, JR and Parvizi, J},
title = {Emerging Concepts in Periprosthetic Joint Infection Research: The Human Microbiome.},
journal = {The Journal of arthroplasty},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arth.2025.01.001},
pmid = {39798621},
issn = {1532-8406},
abstract = {Microorganisms, including bacteria, fungi, and viruses, that reside on and within the human body are collectively known as the human microbiome. Dysbiosis, or disruption in the microbiome, has been implicated in several disease processes, including asthma, obesity, autoimmune diseases, and numerous other conditions. While the Human Microbiome Project (HMP) and the generation of descriptive studies it inspired established correlations between characteristic patterns in the composition of the microbiome and specific disease phenotypes, current research has begun to focus on elucidating the causal role of the microbiome in disease pathogenesis. Within the field of orthopaedic surgery, researchers have proposed the concept of a "gut-joint axis" by which the intestinal microbiome influences joint health and the development of diseases such as osteoarthritis and periprosthetic joint infection (PJI). It is theorized that intestinal dysbiosis increases gut permeability, leading to the translocation of bacteria and their metabolic products into the systemic circulation and the stimulation of proinflammatory response cascades throughout the body, including within the joints. While correlative studies have identified patterns of dysbiotic derangement associated with osteoarthritis and PJI, translational research is needed to clarify the precise mechanisms by which these changes influence disease processes. Additionally, an emerging body of literature has challenged the previously held belief that certain body sites are sterile and do not possess a microbiome, with studies identifying distinct microbial genomic signatures and a core microbiome that varies between anatomic sites. A more thorough characterization of the joint microbiome may have profound implications for our understanding of PJI pathogenesis and our ability to stratify patients based on risk. The purpose of this review was to outline our current understanding of the human microbiome, to describe the gut-joint axis and its role in specific pathologies, including PJI, and to highlight the potential of microbiome-based therapeutic interventions in the field of orthopaedics.},
}
@article {pmid39798533,
year = {2025},
author = {Mao, X and Yin, X and Yang, Y and Gao, F and Li, S and Shi, X and Deng, Y and Li, L and Leung, KMY and Zhang, T},
title = {Longitudinal metagenomic analysis on antibiotic resistome, mobilome, and microbiome of river ecosystems in a sub-tropical metropolitan city.},
journal = {Water research},
volume = {274},
number = {},
pages = {123102},
doi = {10.1016/j.watres.2025.123102},
pmid = {39798533},
issn = {1879-2448},
abstract = {Rivers play an important role as reservoirs and sinks for antibiotic resistance genes (ARGs). However, it remains underexplored for the resistome and associated mobilome in river ecosystems, and hosts of riverine ARGs particularly the pathogenic ones are rarely studied. This study for the first time conducted a longitudinal metagenomic analysis to unveil the resistome, mobilome, and microbiome in river water, by collecting samples from 16 rivers in Hong Kong over a three-year period and using both short-read and long-read sequencing. Results revealed that aminoglycoside, bacitracin, β-lactam, macrolide lincosamide-streptogramin, and sulfonamide were the predominant ARG types in the river water samples. Riverine ARGs exhibited high spatial variations in abundance and diversity. Environmental factors such as fecal coliform count, Escherichia coli count, 5-day biochemical oxygen demand (BOD5), dissolved oxygen (DO), and total organic carbon (TOC) had a significant correlation to the absolute concentrations of ARGs. Nanopore sequencing was used to reveal the physical genetic linkage of mobile genetic elements (MGEs) with ARGs in river water samples. The results showed that qacEdelta, transposase, integrase, and Tn916 had a high prevalence in ARG-carrying long reads. Host tracking using ARG-carrying reads identified 23 pathogenic bacteria species that harbored ARGs. Some ARGs were shared by different bacterial groups. This study presented a nuanced insight of resistome in river water by a longitudinal metagenomic analysis and deepened our understanding of common and divergent riverine antimicrobial resistant risk across the regional patterns.},
}
@article {pmid39798503,
year = {2024},
author = {Nagi, R and Kumar, SS and Sheth, M and Deshpande, A and Khan, J},
title = {Association between oral microbiome dysbiosis and Sjogren Syndrome. A systematic review of clinical studies.},
journal = {Archives of oral biology},
volume = {172},
number = {},
pages = {106167},
doi = {10.1016/j.archoralbio.2024.106167},
pmid = {39798503},
issn = {1879-1506},
abstract = {OBJECTIVES: This systematic review investigates the association of oral microbiome dysbiosis with Sjogren Syndrome (SS).<br><br>MATERIALS AND METHODS: Indexed databases (PubMed/Medline, EMBASE, OVID, Web of Science, and Scopus) were independently searched for relevant manuscripts published until August 2024. Clinical studies on oral microbial flora count and diversity in SS patients were included. Risk of bias across individual studies was performed using the Risk of Bias in Nonrandomized Studies of Interventions tool.<br><br>RESULTS: Out of the initial 295 studies, 15 clinical studies met the selection criteria. The protocols were similar across the studies but varied in diagnostic criteria for SS, salivary flow estimation methods, dental and periodontal status findings, and the type of oral microbes observed. Out of 15 studies, 14 showed an alteration in the oral microbiome and differences in microbial diversity in SS patients. Higher oral microbial counts of Prevotella, Viellonella, and Firmicutes in SS were reported, whereas a higher prevalence of caries-associated bacteria Streptococcus, Lactobacillus, and Viellonella was found in SS patients. Overall, the studies had a low risk of bias.<br><br>CONCLUSIONS: The findings of the present review have shown the existence of significant oral microbial dysbiosis and differences in microbial diversity in SS patients compared to healthy subjects. Future well-designed longitudinal studies are needed to validate the results.},
}
@article {pmid39798398,
year = {2025},
author = {Jokisch, F and Geyer, LJM and Janssen, KP},
title = {Liver regeneration in fatty liver disease: can metabolomics shed light on the contribution of the gut microbiome?.},
journal = {EBioMedicine},
volume = {112},
number = {},
pages = {105552},
doi = {10.1016/j.ebiom.2024.105552},
pmid = {39798398},
issn = {2352-3964},
}
@article {pmid39798223,
year = {2025},
author = {Larsson, SC and Ericson, U and Dekkers, KF and Arage, G and Rašo, LM and Sayols-Baixeras, S and Hammar, U and Baldanzi, G and Nguyen, D and Nielsen, HB and Holm, JB and Risérus, U and Michaëlsson, K and Sundström, J and Smith, JG and Engström, G and Ärnlöv, J and Orho-Melander, M and Fall, T and Ahmad, S},
title = {Meat intake in relation to composition and function of gut microbiota.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {45},
number = {},
pages = {124-133},
doi = {10.1016/j.clnu.2024.12.034},
pmid = {39798223},
issn = {1532-1983},
abstract = {OBJECTIVE: Meat intake is suggested to affect gut microbiome composition and the risk of chronic diseases. We aimed to identify meat-associated gut microbiome features and their association with host factors.<br><br>DESIGN: Gut microbiota species were profiled by deep shotgun metagenomics sequencing in 9669 individuals. Intake of white meat, unprocessed red meat, and processed red meat was assessed using a food frequency questionnaire. The associations of meat intake with alpha-diversity and relative abundance of gut microbiota species were tested using linear regression models with adjustment for dietary fiber intake, body mass index, and other potential confounders. Meat-associated species were further assessed for association with enrichment of microbial gene function, meat-associated plasma metabolites, and clinical biomarkers.<br><br>RESULTS: Higher intake of processed red meat was associated with reduced alpha microbial diversity. White meat, unprocessed, and processed red meat intakes were associated with 36, 14, and 322 microbiota species, respectively. Species associated with processed red meat were enriched for bacterial pathways like amino acid degradation, while those negatively linked were enriched for pathways like homoacetogenesis. Furthermore, species positively associated with processed red meat were to a large extent associated with reduced trimethylamine N-oxide and glutamine levels but increased creatine and carnitine metabolites, fasting insulin and glucose, C-reactive protein, apolipoprotein A1, and triglyceride levels and higher blood pressure.<br><br>CONCLUSION: This largest to date population-based study on meat and gut microbiota suggests that meat intake, particularly processed red meat, may modify the gut microbiota composition, functional capacity, and health-related biomarkers.},
}
@article {pmid39798078,
year = {2025},
author = {Harindranath, S and Desai, D},
title = {Wearable technology in inflammatory bowel disease: current state and future direction.},
journal = {Expert review of medical devices},
volume = {},
number = {},
pages = {},
doi = {10.1080/17434440.2025.2453561},
pmid = {39798078},
issn = {1745-2422},
abstract = {INTRODUCTION: Wearables are electronic devices worn on the body to collect health data. These devices, like smartwatches and patches, use sensors to gather information on various health parameters. This review highlights current use and the potential benefit of wearable technology in patients with inflammatory bowel disease (IBD).<br><br>AREAS COVERED: In this review we explore the current use of wearable technology in healthcare and the studies applying this technology in patients with IBD. We also discuss the limitations of using digital health data in general and wearable technology in particular in the current clinical paradigm and predict a path forward in how to rationally and effectively apply this technology to improve the care of patients with IBD. A comprehensive search of all suitable studies was conducted using the databases of PubMed, MEDLINE, EMBASE, and Scopus from inception to August 2024.<br><br>EXPERT OPINION: Currently, wearable technology is applied in the monitoring of IBD and prediction of flares using devices and sensors. Future applications include early disease detection using biosensors, advanced data collection through ingestible devices, gut microbiome monitoring, and integration with machine learning. These advancements promise to revolutionize disease management, including IBD, by enabling early diagnosis, personalized treatment, and improved patient outcomes.},
}
@article {pmid39797944,
year = {2025},
author = {Zhang, Y and Yuan, F and Liu, Z and Huang, X and Hong, J and Chang, F and Wu, D},
title = {Rare constituents of the nasal microbiome contribute to the acute exacerbation of chronic rhinosinusitis.},
journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]},
volume = {74},
number = {1},
pages = {14},
pmid = {39797944},
issn = {1420-908X},
support = {82000954//Natural Science Foundation of China/ ; Z201100006820086//Beijing Science and Technology Nova Program/ ; QML20190617//Beijing Hospitals Authority Youth Program/ ; XMLX202136//Beijing Hospitals Authority Clinical Medicine Development of Special Funding/ ; BYSYZD2023029//Key clinical projects of Peking University Third Hospital/ ; },
mesh = {Humans ; *Rhinitis/microbiology ; Male ; *Sinusitis/microbiology ; Female ; Middle Aged ; *Microbiota ; Adult ; Cross-Sectional Studies ; Chronic Disease ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; Aged ; Bacteria/classification/genetics ; Prospective Studies ; Nasal Cavity/microbiology ; Rhinosinusitis ; },
abstract = {BACKGROUND: Dysbiosis of the nasal microbiome is considered to be related to the acute exacerbation of chronic rhinosinusitis (AECRS). The microbiota in the nasal cavity of AECRS patients and its association with disease severity has rarely been studied. This study aimed to characterize nasal dysbiosis in a prospective cohort of patients with AECRS.<br><br>METHODS: We performed a cross-sectional study of 28 patients with AECRS, 20 patients with chronic rhinosinusitis (CRS) without acute exacerbation (AE), and 29 healthy controls using 16S rRNA gene sequencing. Subjective and objective assessments of CRS disease severity during AE were also collected.<br><br>RESULTS: Compared to healthy controls and patients with CRS without AE, AECRS presented with a substantial decrease of the Corynebacterium_1 and a significant increase of Ralstonia and Acinetobacter at the genus level (LDA score&#x2009;>&#x2009;2.0 [P&#x2009;<&#x2009;0.05]). Furthermore, genera with a mean relative abundance (MRA) of less than 1% were defined as rare components based on published studies, then 29 genera with a substantial alteration in AECRS were rare constituents of the microbiome, of which 18 rare genera were highly associated with subjective and objective disease severity. Moreover, a combination of 15 genera could differentiate patients with AECRS with an area under the curve of 0.870 (95% CI&#x2009;=&#x2009;0.784-0.955). Prediction of microbial functional pathways involved significantly enhanced lipopolysaccharide biosynthesis pathways and significantly decreased folate biosynthesis, sulfur relay system, and cysteine and methionine metabolism pathways in patients with AECRS.<br><br>CONCLUSIONS: The rare nasal microbiota (MRA&#x2009;<&#x2009;1%) correlated with disease status and disease severity in patients with AECRS. The knowledge about the pattern of the nasal microbiome and its metabolomic pathway may contribute to the fundamental understanding of AECRS pathophysiology.},
}
@article {pmid39797823,
year = {2025},
author = {Chen, B and Liu, M and Zhang, Z and Lv, B and Yu, Y and Zhang, Q and Xu, N and Yang, Z and Lu, T and Xia, S and Chen, J and Qian, H},
title = {Data-Driven Approach for Designing Eco-Friendly Heterocyclic Compounds for the Soil Microbiome.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c09664},
pmid = {39797823},
issn = {1520-5851},
abstract = {Soil microbiota plays crucial roles in maintaining the health, productivity, and nutrient cycling of terrestrial ecosystems. The persistence and prevalence of heterocyclic compounds in soil pose significant risks to soil health. However, understanding the links between heterocyclic compounds and microbial responses remains challenging due to the complexity of microbial communities and their various chemical structures. This study developed a machine-learning approach that integrates the properties of chemical structures with the diversity of soil bacteria and functions to predict the impact of heterocyclic compounds on the microbial community and improve the design of eco-friendly heterocyclic compounds. We screened the key chemical structures of heterocyclic compounds─particularly those with topological polar surface areas (<74.2 Å[2] or 111.3-154.1 Å[2]), carboxyl groups, and dissociation constant, which maintained high soil bacterial diversity and functions, revealing threshold effects where specific structural parameters dictated microbial responses. These eco-friendly compounds stabilize communities and increase beneficial carbon and nitrogen cycle functions. By applying these design parameters, we quantitatively assessed the eco-friendliness scores of 811 heterocyclic compounds, providing a robust foundation for guiding future applications. Our study disentangles the critical chemical structure-related properties that influence the soil microbial community and establishes a computational framework for designing eco-friendly compounds with ecological benefits from an ecological perspective.},
}
@article {pmid39797809,
year = {2025},
author = {Vasquez, R and Song, JH and Mendoza, RM and Hwang, IC and Bagon, BB and Engstrand, L and Valeriano, VD and Kang, DK},
title = {Oral Immunisation With Non-GMO Surface Displayed SARS-CoV-2 Spike Epitopes on Bacteria-Like Particles Provokes Robust Humoral and Cellular Immune Responses, and Modulated the Gut Microbiome in Mice.},
journal = {Microbial biotechnology},
volume = {18},
number = {1},
pages = {e70073},
doi = {10.1111/1751-7915.70073},
pmid = {39797809},
issn = {1751-7915},
support = {NRF-RS-2023-00275307//National Research Foundation of Korea/ ; 321035052HD040//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry (IPET)/ ; 2020-06320//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; },
mesh = {Animals ; *Spike Glycoprotein, Coronavirus/immunology ; Mice ; Male ; Administration, Oral ; *Gastrointestinal Microbiome ; *SARS-CoV-2/immunology ; *Mice, Inbred C57BL ; *Immunity, Humoral ; *COVID-19/prevention &amp; control/immunology ; Immunity, Cellular ; Limosilactobacillus fermentum/immunology ; Epitopes/immunology ; COVID-19 Vaccines/immunology/administration &amp; dosage ; Antibodies, Viral/blood/immunology ; Immunoglobulin G/blood ; Interferon-gamma/metabolism/immunology ; Antibodies, Neutralizing/blood/immunology ; },
abstract = {The coronavirus disease 2019 (COVID-19) is a fatal disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). To date, several vaccines have been developed to combat the spread of this virus. Mucosal vaccines using food-grade bacteria, such as Lactobacillus spp., are promising strategies for developing safe and effective vaccines against SARS-CoV-2. In this study, we designed a non-GMO surface-displayed SARS-CoV-2 spike S1 epitope on Limosilactobacillus fermentum-derived bacteria-like particles (BLPs). After that, we evaluated its efficacy to induce immune responses in immunocompetent mice. Moreover, we examined the influence of oral immunisation on the gut microbiome and microbiota metabolites. Twenty-eight 6-week-old male C57BL/6 mice were orally immunised with the following: PBS (control), Lm. fermentum-derived BLPs only, BLPs displaying SARS-CoV-2 spike S1-2, or BLPs displaying SARS-CoV-2 spike S1-3 epitopes. Our results showed that mucosal immunisation of mice with surface-displayed SARS-CoV-2 spike epitopes provoked high-level secretory IgA and systemic IgG production. Moreover, the immunisation exhibited a Th1-like immune response, characterised by an elevated IgG2a-to-IgG1 ratio and high antiviral IFN-γ production. In addition, we observed gut microbiome modulation and increased butyrate production in immunised mice. Overall, the use of Lm. fermentum-derived BLPs and the anchor CshA to display SARS-CoV-2 spike S1epitopes is a promising novel strategy in developing a cost-effective, non-GMO mucosal vaccine alternative against SARS-CoV-2.},
}
@article {pmid39797569,
year = {2025},
author = {Rogers, AB and Kale, V and Baldi, G and Alberdi, A and Gilbert, MTP and Gupta, D and Limborg, MT and Li, S and Payne, T and Petersen, B and Rasmussen, JA and Richardson, L and Finn, RD},
title = {HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
doi = {10.1093/database/baae112},
pmid = {39797569},
issn = {1758-0463},
mesh = {Animals ; *Chickens/microbiology ; Host Microbial Interactions/genetics ; Salmon/microbiology ; Microbiota ; Databases, Genetic ; Gastrointestinal Microbiome ; },
abstract = {The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.},
}
@article {pmid39797472,
year = {2025},
author = {Chong-Nguyen, C and Yilmaz, B and Coles, B and Sokol, H and MacPherson, A and Siepe, M and Reineke, D and Mosbahi, S and Tomii, D and Nakase, M and Atighetchi, S and Ferro, C and Wingert, C and Gräni, C and Pilgrim, T and Windecker, S and Blasco, H and Dupuy, C and Emond, P and Banz, Y and Losmanovà, T and Döring, Y and Siontis, GCM},
title = {A scoping review evaluating the current state of gut microbiota and its metabolites in valvular heart disease physiopathology.},
journal = {European journal of clinical investigation},
volume = {},
number = {},
pages = {e14381},
doi = {10.1111/eci.14381},
pmid = {39797472},
issn = {1365-2362},
abstract = {BACKGROUND: The human microbiome is crucial in regulating intestinal and systemic functions. While its role in cardiovascular disease is better understood, the link between intestinal microbiota and valvular heart diseases (VHD) remains largely unexplored.<br><br>METHODS: Peer-reviewed studies on human, animal or cell models analysing gut microbiota profiles published up to April 2024 were included. Eligible studies used 16S rRNA or shotgun sequencing, metabolite profiling by mass spectrometry, and examined osteogenesis or fibrosis signalling in valve cells. Methods and findings were qualitatively analysed, with data charted to summarize study design, materials and outcomes.<br><br>RESULTS: Thirteen studies were included in the review: five human, three animal and five in&#xa0;vitro. Of the nine studies on calcific aortic stenosis (CAS), elevated trimethylamine N-oxide (TMAO) levels were linked to an increased risk of cardiovascular events in cohort studies, with CAS patients showing higher levels of Bacteroides plebeius, Enterobacteriaceae, Veillonella dispar and Prevotella copri. In&#xa0;vivo, TMAO promoted aortic valve fibrosis, while tryptophan derivatives stimulated osteogenic differentiation and interleukin-6 secretion in valvular interstitial cells. Two studies on rheumatic mitral valve disease found altered microbiota profiles and lower short-chain fatty acid levels, suggesting potential impacts on immune regulation. Two studies on Barlow's mitral valve disease in animal models revealed elevated TMAO levels in dogs with congestive heart failure, reduced Paraprevotellaceae, increased Actinomycetaceae and dysbiosis involving Turicibacter and E.&#x2009;coli.<br><br>CONCLUSIONS: TMAO has been mainly identified as a prognostic marker in VHD. Gut microbiota dysbiosis has been observed in various forms of VHD and deserve further study.},
}
@article {pmid39797462,
year = {2025},
author = {Huo, DY and Li, YF and Song, LJ and Zhang, WX and Li, XD and Zhang, J and Ren, S and Wang, Z and Li, W},
title = {Colon-Targeted Ginseng Polysaccharides-Based Microspheres for Improving Ulcerative Colitis via Anti-Inflammation and Gut Microbiota Modulation.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e2404122},
doi = {10.1002/adhm.202404122},
pmid = {39797462},
issn = {2192-2659},
support = {2023YFD1601600//National Key Research and Development Program/ ; },
abstract = {Natural plant-derived polysaccharides exhibit substantial potential for treating ulcerative colitis (UC) owing to their anti-inflammatory and antioxidant properties and favorable safety profiles. However, their practical application faces several challenges, including structural instability in gastric acid, imprecise targeting of inflamed regions, and limited intestinal retention times. To address these limitations, pH-responsive, colon-targeting microspheres (pWGPAC MSs) are developed for delivering phosphorylated wild ginseng polysaccharides (pWGP) to alleviate UC. These pWGPAC MSs are fabricated by incorporating pWGP into calcium-crosslinked alginate microspheres with subsequent chitosan surface modification to enhance mucosal adhesion. These pWGPAC MSs demonstrated exceptional stability under acidic conditions while enabling targeted release in the colon. In a mouse model of UC, the pWGPAC MSs effectively mitigated mucosal injury, attenuated inflammation, and restored intestinal barrier function. Further mechanistic investigations revealed that these pWGPAC MSs modulated the TLR4/MYD88 signaling pathway and promoted M2 macrophage polarization. Integrated microbiome and metabolome analyses demonstrated that these pWGPAC MSs regulated the gut microbiota composition and decreased pro-inflammatory metabolite levels. In addition, these microspheres demonstrated promising safety profiles. Collectively, these findings establish pWGPAC MSs as a promising therapeutic strategy for the treatment of UC and provide a solid foundation for future clinical applications.},
}
@article {pmid39797321,
year = {2025},
author = {Azzolina, D and Auricchio, S and Greco, L and Auricchio, R},
title = {Bayesian Sequential Pragmatic Cluster Randomized Clinical Trial Design for PrEventive Effect of MEditerranean Diet in Children: PEMED Trial Research Protocol.},
journal = {Journal of clinical medicine},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/jcm14010240},
pmid = {39797321},
issn = {2077-0383},
abstract = {Background: Childhood nutrition plays an important role in the promotion of long-term health. Introducing solid foods in alignment with the Mediterranean Diet during weaning fosters a preference for healthy foods early in life. However, access to nutritious diets remains a challenge in underserved communities. Scampia, a socioeconomically disadvantaged district in Naples, Italy, exemplifies a community where barriers to healthy eating persist. This research reports a trial protocol that plans for a study to evaluate the impact of the Mediterranean Diet on child health and to establish preventive strategies for chronic diseases. Methods: The PEMED (PrEventive effect of MEditerranean Diet in Children) trial is a Bayesian Sequential Pragmatic Cluster Randomized Clinical Trial. Family Pediatricians (FPs) are randomized to deliver either Mediterranean Diet-based dietary guidance starting at weaning or standard dietary practices using typical baby foods. Children will be followed up for six years, with regular assessments of growth, microbiome composition, and adherence to the Mediterranean Diet, using validated tools. Interim analyses will be conducted at three-year intervals to evaluate the efficacy and monitor adverse events. Saliva and stool samples will be collected for genetic and microbiome analyses, and adherence will be monitored through quarterly dietary recalls and biomarkers. Results: This trial will consider Italy's established FP network for implementing innovative dietary intervention in a real-world setting. Conclusions: This study will address nutritional disparities in the underserved Scampia community and provide a scalable model for early dietary interventions. The results will shed light on the role of the Mediterranean Diet in improving childhood health and informing public health strategies globally.},
}
@article {pmid39797221,
year = {2024},
author = {Pueschel, L and Nothacker, S and Kuhn, L and Wedemeyer, H and Lenzen, H and Wiestler, M},
title = {Exploring Dietary- and Disease-Related Influences on Flatulence and Fecal Odor Perception in Inflammatory Bowel Disease.},
journal = {Journal of clinical medicine},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/jcm14010137},
pmid = {39797221},
issn = {2077-0383},
support = {DFG, ME 3696/3-1//Deutsche Forschungsgemeinschaft/ ; HiLF-1//Hochschulinterne Leistungsf&#xf6;rderung" (HiLF-1) of the Hannover Medical School/ ; },
abstract = {Background/Objectives: Inflammatory bowel disease (IBD) affects gastrointestinal function and may alter fecal and flatulence odor (intestinal odor) due to changes in inflammation, the gut microbiome, and metabolism. Investigating the relationship between dietary habits and intestinal odor in IBD is critical given the relationship between diet, gut health, and microbiome diversity. Methods: We performed a cohort analysis of a monocentric, cross-sectional study at a tertiary referral center and compared the perception of fecal and flatulence odor in 233 IBD patients (n = 117 women) with that of 96 healthy controls (HCs) (n = 67 women). In addition to a short screening questionnaire on highly processed foods (sQ-HPF), dietary behavior (Food Frequency Questionnaire (FFQ)), clinical (HBI, PMS) and biochemical (CRP, fecal calprotectin) parameters of disease activity, and adherence to a Mediterranean diet were assessed. Results: A notable predisposition towards elevated levels of intestinal malodor was identified in the IBD cohort when compared to the HC group. The analysis of dietary behavior in conjunction with intestinal malodor revealed more pronounced associations in the HC collective than in the IBD collective. The data further indicated that, in comparison to those in remission, IBD individuals with an active disease status exhibited a higher prevalence of intestinal malodor. In an adjusted logistic regression analysis of the influence of disease- and diet-specific factors on flatulence and fecal malodor in IBD, male sex was identified as a significant risk factor. Conclusions: This study highlights the significance of dietary factors in the management of IBD symptoms, with a particular focus on flatulence and fecal odor. Individuals with IBD demonstrated a higher propensity for intestinal malodor compared to HC, with active disease status further amplifying this prevalence. Dietary behavior showed stronger associations with malodor in the HC group than in IBD individuals, suggesting distinct interaction patterns between diet and gut health in these populations.},
}
@article {pmid39796688,
year = {2024},
author = {Nardo, G and Pantziarka, P and Conti, M},
title = {Synergistic Potential of Antibiotics with Cancer Treatments.},
journal = {Cancers},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/cancers17010059},
pmid = {39796688},
issn = {2072-6694},
abstract = {Intratumoral microbiota, the diverse community of microorganisms residing within tumor tissues, represent an emerging and intriguing field in cancer biology. These microbial populations are distinct from the well-studied gut microbiota, offering novel insights into tumor biology, cancer progression, and potential therapeutic interventions. Recent studies have explored the use of certain antibiotics to modulate intratumoral microbiota and enhance the efficacy of cancer therapies, showing promising results. Antibiotics can alter intratumoral microbiota's composition, which may have a major role in promoting cancer progression and immune evasion. Certain bacteria within tumors can promote immunosuppression and resistance to therapies. By targeting these bacteria, antibiotics can help create a more favorable environment for chemotherapy, targeted therapy, and immunotherapy to act effectively. Some bacteria within the tumor microenvironment produce immunosuppressive molecules that inhibit the activity of immune cells. The combination of antibiotics and other cancer therapies holds significant promise for creating a synergistic effect and enhancing the immune response against cancer. In this review, we analyze several preclinical studies that have been conducted to demonstrate the synergy between antibiotics and other cancer therapies and discuss possible clinical implications.},
}
@article {pmid39796619,
year = {2025},
author = {Johnson, AJ and Alvear, A and Knights, D and Chow, LS and Bantle, AE},
title = {A Randomized Pilot Study of Time-Restricted Eating Shows Minimal Microbiome Changes.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/nu17010185},
pmid = {39796619},
issn = {2072-6643},
support = {KL2TR002492//National Institutes of Health, National Center of Advancing Translational Sciences/ ; UL1TR002494//National Institutes of Health, National Center for Advancing Translational Sciences/ ; K23DK115906/DK/NIDDK NIH HHS/United States ; 17SFR-2YR50LC//Healthy Foods, Healthy Lives Institute at the University of Minnesota/ ; },
mesh = {Humans ; Pilot Projects ; *Gastrointestinal Microbiome ; Male ; *Feces/microbiology ; Female ; Adult ; Obesity/microbiology ; Middle Aged ; Body Composition ; Fasting ; Time Factors ; },
abstract = {OBJECTIVE: TRE is an emerging approach in obesity treatment, yet there is limited data on how it influences gut microbiome composition in humans. Our objective was to characterize the gut microbiome of human participants before and after a TRE intervention. This is a secondary analysis of a previously published clinical trial examining the effects of time-restricted eating (TRE).<br><br>METHODS: In a previously published, 12-week randomized controlled trial, Chow et al. evaluated the effects of an 8-h TRE intervention on body composition in human participants. Chow et al. demonstrated significant reductions in weight, lean mass, and visceral fat in the TRE group compared to those following time-unrestricted eating (non-TRE). Stool samples were collected by a subset of those participants using home kits at both baseline and post-intervention for shotgun metagenomic sequencing for this secondary analysis. Microbiome community composition was compared before and after intervention as alpha and beta diversity.<br><br>RESULTS: Sixteen participants provided stool samples (eight in the TRE group and eight in the non-TRE group). Stool samples were collected from all participants at at least one time point, but both pre- and post-treatment samples were available from only five participants who completed both baseline and post-treatment collections. In alignment with the findings of Chow et al., the participants in the TRE group of the secondary analysis who collected microbiome sample(s) successfully reduced their eating window from an average of 15.3 &#xb1; 0.8 h at baseline to 9.3 &#xb1; 1.7 h during the intervention (mean &#xb1; SD, p < 0.001) and the non-TRE group's eating window remained unchanged. While the TRE group lost weight and visceral fat mass, no effect of the TRE intervention was observed on alpha diversity (Shannon index, Simpson index, and number of taxa, linear mixed models), beta diversity (Bray-Curtis, PERMANOVA), even after controlling for weight and visceral fat changes.<br><br>CONCLUSIONS: Our analysis did not detect any significant differences in gut microbiome composition or diversity indices between participants undergoing a TRE intervention and those in the control group. The study's findings are limited by a small sample size, short duration, and the collection of stool samples at only two time points. Future studies with larger sample sizes, longer durations, and more frequent sampling, and collection of detailed dietary data are needed to better understand the relationship between TRE and gut microbiome dynamics.},
}
@article {pmid39796584,
year = {2024},
author = {Firrman, J and Deyaert, S and Mahalak, KK and Liu, L and Baudot, A and Joossens, M and Poppe, J and Cameron, SJS and Van den Abbeele, P},
title = {The Bifidogenic Effect of 2'Fucosyllactose Is Driven by Age-Specific Bifidobacterium Species, Demonstrating Age as an Important Factor for Gut Microbiome Targeted Precision Medicine.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/nu17010151},
pmid = {39796584},
issn = {2072-6643},
support = {8072-41000-102-00D//United States Department of Agriculture/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Trisaccharides/pharmacology ; *Bifidobacterium/drug effects ; Infant ; *Feces/microbiology ; Aged ; Adult ; Child, Preschool ; *Precision Medicine ; Middle Aged ; Child ; Female ; Male ; Age Factors ; Young Adult ; Adolescent ; Milk, Human/chemistry ; Oligosaccharides/pharmacology ; Lactose ; },
abstract = {BACKGROUND: The human gut microbiota develops in concordance with its host over a lifetime, resulting in age-related shifts in community structure and metabolic function. Little is known about whether these changes impact the community's response to microbiome-targeted therapeutics. Providing critical information on this subject, faecal microbiomes of subjects from six age groups, spanning from infancy to 70-year-old adults (n = six per age group) were harvested. The responses of these divergent communities to treatment with the human milk oligosaccharide 2'-fucosyllactose (2'FL), fructo-oligosaccharides (FOS), and lactose was investigated using the Ex vivo SIFR[®] technology that employs bioreactor fermentation and is validated to be predictive of clinical findings. Additionally, it was evaluated whether combining faecal microbiomes of a given age group into a single pooled microbiome produced similar results as the individual microbiomes.<br><br>RESULTS: First, marked age-dependent changes in community structure were identified. Bifidobacterium levels strongly declined as age increased, and Bifidobacterium species composition was age-dependent: B. longum, B. catenulatum/pseudocatenulatum, and B. adolescentis were most prevalent for breastfed infants, toddlers/children, and adults, respectively. Metabolomic analyses (LA-REIMS) demonstrated that these age-dependent differences particularly impacted treatment effects of 2'FL (more than FOS/lactose). Further analysis revealed that while 2'FL enhanced production of short-chain fatty acids (SCFAs) and exerted potent bifidogenic effects, regardless of age, the specific Bifidobacterium species enhanced by 2'FL, as well as subsequent cross-feeding interactions, were highly age-dependent. Furthermore, single-pooled microbiomes produced results that were indicative of the average treatment response for each age group. Nevertheless, pooled microbiomes had an artificially high diversity, thus overestimating treatment responses (especially for infants), did not recapitulate interindividual variation, and disallowed for the correlative analysis required to unravel mechanistic actions.<br><br>CONCLUSIONS: Age is an important factor in shaping the gut microbiome, with the dominant taxa and their metabolites changing over a lifetime. This divergence affects the response of the microbiota to therapeutics, demonstrated in this study using 2'FL. These results evidence the importance of screening across multiple age groups separately to provide granularity of how therapeutics impact the microbiome and, consequently, human health.},
}
@article {pmid39796578,
year = {2024},
author = {Zaramella, A and Arcidiacono, D and Duci, M and Benna, C and Pucciarelli, S and Fantin, A and Rosato, A and De Re, V and Cannizzaro, R and Fassan, M and Realdon, S},
title = {Predictive Value of a Gastric Microbiota Dysbiosis Test for Stratifying Cancer Risk in Atrophic Gastritis Patients.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/nu17010142},
pmid = {39796578},
issn = {2072-6643},
support = {(IOV-IRCCS) 2018-2021//Ricerca Corrente Istituto Oncologico Veneto (IOV-IRCCS) 2018-2021/ ; (CRO-IRCCS) 2021-2022//Ricerca Corrente Istituto Oncologico Veneto (CRO-IRCCS) 2021-2022/ ; Grant number RF-2016-02363566//Ricerca Finalizzata/ ; },
mesh = {Humans ; *Gastritis, Atrophic/microbiology ; *Stomach Neoplasms/microbiology ; *Dysbiosis/microbiology ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Predictive Value of Tests ; Disease Progression ; Helicobacter Infections/microbiology/complications/diagnosis ; Risk Assessment ; Risk Factors ; Adult ; Helicobacter pylori/isolation &amp; purification/genetics ; Stomach/microbiology/pathology ; },
abstract = {BACKGROUND/OBJECTIVES: Gastric cancer (GC) incidence remains high worldwide, and the survival rate is poor. GC develops from atrophic gastritis (AG), associated with Helicobacter pylori (Hp) infection, passing through intestinal metaplasia and dysplasia steps. Since Hp eradication does not exclude GC development, further investigations are needed. New data suggest the possible role of unexplored gastric microbiota beyond Hp in the progression from AG to GC. Aimed to develop a score that could be used in clinical practice to stratify GC progression risk, here was investigate gastric microbiota in AG Hp-negative patients with or without high-grade dysplasia (HGD) or GC.<br><br>METHODS: Consecutive patients undergoing upper endoscopy within an endoscopic follow-up for AG were considered. The antrum and corpus biopsies were used to assess the microbiota composition along the disease progression by sequencing the 16S ribosomal RNA gene. Statistical differences between HGD/GC and AG patients were included in a multivariate analysis.<br><br>RESULTS: HGD/GC patients had a higher percentage of Bacillus in the antrum and a low abundance of Rhizobiales, Weeksellaceae and Veillonella in the corpus. These data were used to calculate a multiparametric score (Resident Gastric Microbiota Dysbiosis Test, RGM-DT) to predict the risk of progression toward HGD/GC. The performance of RGM-DT in discriminating patients with HGD/GC showed a specificity of 88.9%.<br><br>CONCLUSIONS: The microbiome-based risk prediction model for GC could clarify the role of gastric microbiota as a cancer risk biomarker to be used in clinical practice. The proposed test might be used to personalize follow-up program thanks to a better cancer risk stratification.},
}
@article {pmid39796547,
year = {2024},
author = {Saarinen, MT and Forssten, SD and Evans, K and Airaksinen, K and Telving, R and Hornshøj, BH and Jensen, HM and Jokkala, J and Hanhineva, K and Tiihonen, K},
title = {Effects of Betaine and Polydextrose on Intestinal Microbiota and Liver Ergothioneine in a High-Fat Diet-Fed Mouse Model and a Human Colonic Simulation Model.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/nu17010109},
pmid = {39796547},
issn = {2072-6643},
mesh = {Animals ; *Betaine/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Diet, High-Fat/adverse effects ; *Ergothioneine/pharmacology ; Humans ; *Liver/metabolism/drug effects ; *Colon/microbiology/metabolism/drug effects ; Male ; *Mice, Inbred C57BL ; Mice ; *Glucans/pharmacology ; Dietary Supplements ; Disease Models, Animal ; Feces/microbiology ; Obesity/microbiology/metabolism ; },
abstract = {BACKGROUND/OBJECTIVES: Ergothioneine (EGT) is an effective antioxidant that animals cannot produce and has an important anti-inflammatory role in cell protection, which can help lower the risk of various diseases. In this study, we investigated the potential role of gut microbiota in the production of EGT, which was found to increase in the mouse liver after dietary supplementation with betaine (BET) or polydextrose (PDX).<br><br>METHODS: The effects of BET and PDX on the gut microbiota and tissue EGT content were investigated using a diet-induced obese mouse model and simulated fermentation in the human colon. Male C57BL/6J mice were fed a high-fat diet (HFD) for 8 weeks to induce obesity and related metabolic disorders, and for the last 4 weeks of this study, the mice continued on the same diet, supplemented with BET, PDX, or their combination. The potential function of BET and PDX in microbial EGT production was further studied in an in vitro human colon model.<br><br>RESULTS: The quantity of Bifidobacterium spp. and Bacteroidota were significantly higher in the feces of mice on diets supplemented with PDX or BET + PDX, and Enterobacteriaceae levels were significantly higher in PDX-supplemented mice than in HFD-fed mice. Untargeted metabolomic analysis of the liver revealed a significant increase in EGT in mice fed HFDs with BET or BET + PDX. Microbial analysis from samples collected from the human in vitro model showed significant changes in Neglecta timonensis, Blautia faecis, Lachnospiracea incertae sedis, Faecalibacillus, and Stenotrophomonas maltophilia species, along with an increase in microbial metabolites, namely, acetic, propionic and butyric acids, and a decrease in 2-methylbutyric acid.<br><br>CONCLUSIONS: Although PDX and BET or their combination affected microbial composition and metabolites in the human colon simulation model, the model used was not able to detect a significant change in microbiota-based EGT production and, therefore, could not explain the increase in EGT in the liver of betaine-fed mice.},
}
@article {pmid39796536,
year = {2024},
author = {Cuffaro, F and Lamminpää, I and Niccolai, E and Amedei, A},
title = {Nutritional and Microbiota-Based Approaches in Amyotrophic Lateral Sclerosis: From Prevention to Treatment.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/nu17010102},
pmid = {39796536},
issn = {2072-6643},
support = {PNRR-MAD-2022-12375798//Ministero della Salute/ ; PE0000006//Ministry of University and Research (MUR)/ ; },
mesh = {*Amyotrophic Lateral Sclerosis/therapy ; Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/therapy ; Probiotics/therapeutic use ; Brain-Gut Axis/physiology ; Fecal Microbiota Transplantation ; Fatty Acids, Omega-3 ; Prebiotics/administration &amp; dosage ; Oxidative Stress ; Nutritional Status ; Diet, Mediterranean ; Antioxidants ; },
abstract = {Metabolic alterations, including hypermetabolism, lipid imbalances, and glucose dysregulation, are pivotal contributors to the onset and progression of Amyotrophic Lateral Sclerosis (ALS). These changes exacerbate systemic energy deficits, heighten oxidative stress, and fuel neuroinflammation. Simultaneously, gastrointestinal dysfunction and gut microbiota (GM) dysbiosis intensify disease pathology by driving immune dysregulation, compromising the intestinal barrier, and altering gut-brain axis (GBA) signaling, and lastly advancing neurodegeneration. Therapeutic and preventive strategies focused on nutrition offer promising opportunities to address these interconnected pathophysiological mechanisms. Diets enriched with antioxidants, omega-3 fatty acids, and anti-inflammatory compounds-such as the Mediterranean diet-have shown potential in reducing oxidative stress and systemic inflammation. Additionally, microbiota-targeted approaches, including probiotics, prebiotics, postbiotics, and fecal microbiota transplantation, are emerging as innovative tools to restore microbial balance, strengthen gut integrity, and optimize GBA function. This review highlights the critical need for personalized strategies integrating immunonutrition and microbiota modulation to slow ALS progression, improve quality of life, and develop preventive measures for neurodegenerative and neuroinflammatory diseases. Future research should prioritize comprehensive dietary and microbiota-based interventions to uncover their therapeutic potential and establish evidence-based guidelines for managing ALS and related disorders.},
}
@article {pmid39796518,
year = {2024},
author = {Vega-Rojas, A and Haro, C and Molina-Abril, H and Guil-Luna, S and Santos-Marcos, JA and Gutierrez-Mariscal, FM and Garcia-Fernandez, H and Caballero-Villarraso, J and Rodriguez-Ariza, A and Lopez-Miranda, J and Perez-Martinez, P and Hervas, A and Camargo, A},
title = {Gut Microbiota Interacts with Dietary Habits in Screenings for Early Detection of Colorectal Cancer.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/nu17010084},
pmid = {39796518},
issn = {2072-6643},
support = {PI-0055-2021//Consejer&#xed;a de Salud y Consumo/ ; PI-0156-2016//Consejer&#xed;a de Salud y Consumo/ ; AGL2015-67896-P//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; n.a.//European Union/ ; CP14/00114//Instituto de Salud Carlos III/ ; PI19/00299//Instituto de Salud Carlos III/ ; DTS19/00007//Instituto de Salud Carlos III/ ; PI22/00925//Instituto de Salud Carlos III/ ; C1-0001-2022//Andalusian Health Service/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/diagnosis ; *Gastrointestinal Microbiome ; *Early Detection of Cancer/methods ; Male ; Female ; Middle Aged ; *Feeding Behavior ; *Colonoscopy ; Aged ; Adenocarcinoma/microbiology ; Occult Blood ; Diet ; Colonic Polyps/microbiology/diagnosis ; Feces/microbiology ; },
abstract = {BACKGROUND/OBJECTIVES: Gut microbiota interacts with nutrients, which may be relevant to assigning a microbial signature to colorectal cancer (CRC). We aim to evaluate the potential of gut microbiota combined with dietary habits in the early detection of pathological findings related to CRC in the course of a screening program.<br><br>METHODOLOGY: The colonoscopy performed on 152 subjects positive for fecal occult blood test showed that 6 subjects had adenocarcinoma, 123 had polyps, and 23 subjects had no pathological findings. Gut microbiota was analyzed by 16S metagenomic. Caret package was used to build the classification models in R.<br><br>RESULTS: Random forest (RF) classifier models were used to test the potential of gut microbiota alone or combined with dietary habits as a biomarker to discern between individuals with CRC-related lesions (polyps or adenocarcinoma) versus individuals without pathological findings. RF classifier models yielded an area under the curve of 0.790 using gut microbiota data, 0.710 using dietary habits data, and 0.804 in the combined model including gut microbiota and dietary habits data. The abundance of Suterella, Oscillospirales, Proteobacteria, and Burkholderiales was highly discriminant between groups, together with the consumption of fruit and vegetables and the consumption of carbonated and/or sweetened beverages.<br><br>CONCLUSIONS: Our results suggest that the interaction between gut microbiota and dietary habits is relevant when a microbial signature is used as a marker in CRC. Moreover, gut microbiota signature and information about the dietary habits of the individuals seem to be important for improving screening programs for the early detection of CRC.},
}
@article {pmid39796514,
year = {2024},
author = {Barry, DJ and Wu, SSX and Cooke, MB},
title = {The Relationship Between Gut Microbiota, Muscle Mass and Physical Function in Older Individuals: A Systematic Review.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/nu17010081},
pmid = {39796514},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Sarcopenia ; Aged ; Female ; *Muscle, Skeletal/physiology ; Male ; Body Composition ; Muscle Strength ; Physical Functional Performance ; Aged, 80 and over ; Middle Aged ; },
abstract = {BACKGROUND: Recent evidence suggests that sarcopenia and subsequent changes in muscle mass and functional outcomes are linked to disruption to the gastrointestinal microbiota composition and/or function via the microbiota-gut-muscle axis. Despite growing interest, few studies have systemically analysed (1) the relationship between the gut microbiota, muscle mass and physical performance and (2) the effects of gut-modulating dietary interventions on these outcomes within older individuals with or without sarcopenia.<br><br>METHODS: Four electronic databases (PubMed, MEDLINE, Embase and Scopus) were searched for articles published from the year 2004 until July 2023. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) were followed. Revised Cochrane Risk of Bias (RoB 2.0) and Joanna Briggs Institute (JBI) critical appraisal checklist were utilised to evaluate the risk of bias within intervention and observational studies, respectively.<br><br>RESULTS: A total of 20 studies (14 observational and 6 interventional) involving 4071 older participants (mean age 69.9 years, 51.6% female) were included. There was significant heterogeneity regarding interventions and outcome measures used in these studies. Correlations between microbiota diversity and composition and sarcopenia-related functional outcomes were observed. Interventional studies targeting the gut microbiota resulted in improved muscle strength, body composition or physical function in some, but not all, studies.<br><br>CONCLUSIONS: Despite limitations in the studies reviewed, the findings provide further evidence that the development of sarcopenia is likely influenced by an altered gut microbial environment and that interventions targeting the microbiome could hold therapeutic potential for the treatment or management of sarcopenia.},
}
@article {pmid39796508,
year = {2024},
author = {Deskur, A and Ambrożkiewicz, F and Samborowska, E and Błogowski, W and Sulikowski, T and Białek, A and Zawada, I and Dąbkowski, K and Mitrus, J and Karczmarski, J and Cybula, P and Paziewska, A and Starzyńska, T},
title = {Plasma Bacterial Metabolites in Crohn's Disease Pathogenesis and Complications.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/nu17010074},
pmid = {39796508},
issn = {2072-6643},
support = {Funding: This work was supported by the Medical Pomeranian University in Szczecin.//Funding: This work was supported by the Medical Pomeranian University in Szczecin./ ; },
mesh = {Humans ; *Crohn Disease/blood/microbiology ; Female ; Male ; Adult ; *Gastrointestinal Microbiome ; Middle Aged ; Bacteria ; Fatty Acids, Volatile/blood ; Methylamines/blood ; Biomarkers/blood ; Young Adult ; Case-Control Studies ; Choline/blood ; Dysbiosis/blood/microbiology ; },
abstract = {BACKGROUND/OBJECTIVES: Crohn's disease is known for being associated with an abnormal composition of the bacterial flora, dysbiosis and intestinal function disorders. Metabolites produced by gut microbiota play a pivotal role in the pathogenesis of CD, and the presence of unspecific extraintestinal manifestations.<br><br>METHODS: The aim of this study was a determination of the level of bacterial metabolites in blood plasma in patients with Crohn's disease. CD patients (29) and healthy individuals (30) were recruited for this study. Bacterial metabolites (SCFAs and TMAO panel) were measured by a liquid chromatography-mass spectrometry system.<br><br>RESULTS: A significant correlation (p-value < 0.05) between CD and bacterial metabolites was obtained for three of eight tested SCFAs; acetic acid (reduced in CD; FC 1.7; AUC = 0.714), butyric acid (increased; FC 0.68; AUC = 0.717), 2MeBA (FC 1.168; AUC = 0.702), and indoxyl (FC 0.624). The concentration of CA (FC 0.82) and choline (FC 0.78) in plasma was significantly disturbed according to the biological treatment. Choline level (FC 1.28) was also significantly disturbed in the patients treated with glucocorticoids. In total, 68.97% of Crohn's patients presented extraintestinal manifestations (EIMs) of Crohn's disease, mainly osteoarticular complications. The level of BA was statistically significantly elevated in patients with extraintestinal (FC 0.602) manifestations, while in the group of patients with osteoarticular complications, a significant difference in the level of betaine (FC 1.647) was observed.<br><br>CONCLUSIONS: The analyzed bacterial metabolites of plasma may significantly help in the diagnostic process, and in the monitoring of the disease course and treatment, in a lowly invasive way, as biomarkers after additional research on a larger group of patients.},
}
@article {pmid39796496,
year = {2024},
author = {Czerwińska-Ledwig, O and Nowak-Zaleska, A and Żychowska, M and Meyza, K and Pałka, T and Dzidek, A and Szlachetka, A and Jurczyszyn, A and Piotrowska, A},
title = {The Positive Effects of Training and Time-Restricted Eating in Gut Microbiota Biodiversity in Patients with Multiple Myeloma.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/nu17010061},
pmid = {39796496},
issn = {2072-6643},
support = {022/RID/2018/19//Ministry of Science and Higher Education (Poland)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Multiple Myeloma/microbiology ; Middle Aged ; Aged ; Male ; Female ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; Walking ; Bacteria/classification/genetics/isolation &amp; purification ; Feces/microbiology ; },
abstract = {BACKGROUND: The physical activity of different groups of individuals results in the rearrangement of microbiota composition toward a symbiotic microbiota profile. This applies to both healthy and diseased individuals. Multiple myeloma (MM), one of the more common hematological malignancies, predominantly affects older adults. Identifying an appropriate form of physical activity for this patient group remains a challenge. The aim of this study was to investigate the impact of a 6-week Nordic walking (NW) training program combined with a 10/14 time-restricted eating regimen on the gut microbiota composition of multiple myeloma patients.<br><br>METHODS: This study included healthy individuals as the control group (n = 16; mean age: 62.19 &#xb1; 5.4) and patients with multiple myeloma in remission (MM group; n = 16; mean age: 65.00 &#xb1; 5.13; mean disease duration: 57 months). The training intervention was applied to the patient group and consisted of three moderate-intensity sessions per week, individually tailored to the estimated physical capacity of each participant. The taxonomic composition was determined via 16S rRNA sequencing (V3-V9 regions). The microbiota composition was compared between the patient group and the control group.<br><br>RESULTS: The alpha and beta diversity metrics for species and genus levels differed significantly between the control and patient groups before the implementation of the NW program. In contrast, no differences were observed between the control and patient groups after the training cycle, indicating that the patients' microbiota changed toward the pattern of the control group. This is confirmed by the lowest values of average dissimilarity between the MMB groups and the control at all taxonomic levels, as well as the highest one between the control group and the MMA patient group. The gut microbiota of the patients was predominantly represented by the phyla Firmicutes, Actinobacteria, Verrucomicrobia, Proteobacteria, and Bacteroidetes.<br><br>CONCLUSIONS: The training, combined with time-restricted eating, stimulated an increase in the biodiversity and taxonomic rearrangement of the gut microbiota species.},
}
@article {pmid39796488,
year = {2024},
author = {Salvado, R and Lugones-Sánchez, C and Santos-Minguez, S and González-Sánchez, S and Quesada, JA and Benito, R and Rodríguez-Sánchez, E and Gómez-Marcos, MA and Guimarães-Cunha, P and Hernandez-Rivas, JM and Mira, A and García-Ortiz, L and Mivas Investigators, },
title = {Sex Differences in Gut Microbiota and Their Relation to Arterial Stiffness (MIVAS Study).},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/nu17010053},
pmid = {39796488},
issn = {2072-6643},
support = {RD21/0016/0010//Instituto de Salud Carlos III/ ; PI20/00321//European Union-Next Generation EU, Facility for Recovery and Resilience (MRR)/ ; GRS: 2505/B/22, GRS: 2305/B/21, GRS 2148/B/2020//Government of Castilla y Le&#xf3;n/ ; },
mesh = {Humans ; *Vascular Stiffness ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Middle Aged ; Cross-Sectional Studies ; Aged ; Sex Factors ; Spain ; Cardiovascular Diseases/microbiology ; Feces/microbiology ; Pulse Wave Analysis ; Sex Characteristics ; },
abstract = {BACKGROUND: Recent research highlights the potential role of sex-specific variations in cardiovascular disease. The gut microbiome has been shown to differ between the sexes in patients with cardiovascular risk factors.<br><br>OBJECTIVES: The main objective of this study is to analyze the differences between women and men in the relationship between gut microbiota and measures of arterial stiffness.<br><br>METHODS: We conducted a cross-sectional study in Spain, selecting 180 subjects (122 women, 58 men) aged between 45 and 74. Subjects with arterial stiffness were identified by the presence of at least one of the following: carotid-femoral pulse wave velocity (cf-PWV) above 12 mm/s, cardio-ankle vascular index (CAVI) above nine, or brachial-ankle pulse wave velocity (ba-PWV) above 17.5 m/s. All other cases were considered subjects without arterial stiffness. The composition of the gut microbiome in fecal samples was determined by 16S rRNA sequencing.<br><br>RESULTS: We found that women have a more diverse microbiome than men (Shannon, p < 0.05). There is also a significant difference in gut microbiota composition between sexes (Bray-Curtis, p < 0.01). Dorea, Roseburia, and Agathobacter, all of them short-chain fatty-acid producers, were more abundant in women's microbiota (log values > 1, p-value and FDR < 0.05). Additionally, Blautia was more abundant in women when only the subjects with arterial stiffness were considered. According to logistic regression, Roseburia was negatively associated with arterial stiffness in men, while Bifidobacterium and Subdoligranulum were positively related to arterial stiffness.<br><br>CONCLUSIONS: In the Spanish population under study, women had higher microbiome diversity and potentially protective genera. The host's gender determines the influence of the same bacteria on arterial stiffness.<br><br>TRIAL REGISTRATION NUMBER: NCT03900338.},
}
@article {pmid39796476,
year = {2024},
author = {Andersen, CJ and Fernandez, ML},
title = {Emerging Biomarkers and Determinants of Lipoprotein Profiles to Predict CVD Risk: Implications for Precision Nutrition.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/nu17010042},
pmid = {39796476},
issn = {2072-6643},
mesh = {Humans ; *Cardiovascular Diseases/blood/prevention &amp; control ; *Biomarkers/blood ; *Lipoproteins/blood ; Precision Medicine/methods ; Risk Factors ; Heart Disease Risk Factors ; Nutritional Status ; Risk Assessment ; },
abstract = {Biomarkers constitute a valuable tool to diagnose both the incidence and the prevalence of chronic diseases and may help to inform the design and effectiveness of precision nutrition interventions. Cardiovascular disease (CVD) continues to be the foremost cause of death all over the world. While the reasons that lead to increased risk for CVD are multifactorial, dyslipidemias, plasma concentrations of specific lipoproteins, and dynamic measures of lipoprotein function are strong biomarkers to predict and document coronary heart disease incidence. The aim of this review is to provide a comprehensive evaluation of the biomarkers and emerging approaches that can be utilized to characterize lipoprotein profiles as predictive tools for assessing CVD risk, including the assessment of traditional clinical lipid panels, measures of lipoprotein efflux capacity and inflammatory and antioxidant activity, and omics-based characterization of lipoprotein composition and regulators of lipoprotein metabolism. In addition, we discuss demographic, genetic, metagenomic, and lifestyle determinants of lipoprotein profiles-such as age, sex, gene variants and single-nucleotide polymorphisms, gut microbiome profiles, dietary patterns, physical inactivity, obesity status, smoking and alcohol intake, and stress-which are likely to be essential factors to explain interindividual responses to precision nutrition recommendations to mitigate CVD risk.},
}
@article {pmid39796469,
year = {2024},
author = {Wu, F and Guo, Y and Wang, Y and Sui, X and Wang, H and Zhang, H and Xin, B and Yang, C and Zhang, C and Jiang, S and Qu, L and Feng, Q and Dai, Z and Shi, C and Li, Y},
title = {Effects of Long-Term Fasting on Gut Microbiota, Serum Metabolome, and Their Association in Male Adults.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/nu17010035},
pmid = {39796469},
issn = {2072-6643},
support = {2022SY54B0506, BJH22WS1J002, 18035020103//the Advanced Space Medico-Engineering Research Project of China/ ; SMFA22Q03, SMFA22B04//The State Key Laboratory of Space Medicine, China Astronaut Research and Training Center/ ; HYZHXM01002//the Space Medical Experiment Project of China Manned Space Program/ ; JCYJ20200109110630285//he Shenzhen Science and Technology Innovation Commission 2020 Basic Research Project/ ; 2022YFA1604504//National Key R&amp;D Program of China/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/physiology ; *Fasting/blood ; *Metabolome ; Pilot Projects ; Adult ; Animals ; Obesity/microbiology/blood ; Bacteria/classification ; Diet, High-Fat ; },
abstract = {BACKGROUND: Long-term fasting demonstrates greater therapeutic potential and broader application prospects in extreme environments than intermittent fasting.<br><br>METHOD: This pilot study of 10-day complete fasting (CF), with a small sample size of 13 volunteers, aimed to investigate the time-series impacts on gut microbiome, serum metabolome, and their interrelationships with biochemical indices.<br><br>RESULTS: The results show CF significantly affected gut microbiota diversity, composition, and interspecies interactions, characterized by an expansion of the Proteobacteria phylum (about six-fold) and a decrease in Bacteroidetes (about 50%) and Firmicutes (about 34%) populations. Notably, certain bacteria taxa exhibited complex interactions and strong correlations with serum metabolites implicated in energy and amino acid metabolism, with a particular focus on fatty acylcarnitines and tryptophan derivatives. A key focus of our study was the effect of Ruthenibacterium lactatiformans, which was highly increased during CF and exhibited a strong correlation with fat metabolic indicators. This bacterium was found to mitigate high-fat diet-induced obesity, glucose intolerance, dyslipidemia, and intestinal barrier dysfunction in animal experiments. These effects suggest its potential as a probiotic candidate for the amelioration of dyslipidemia and for mediating the benefits of fasting on fat metabolism.<br><br>CONCLUSIONS: Our pilot study suggests that alterations in gut microbiota during CF contribute to the shift of energy metabolic substrate and the establishment of a novel homeostatic state during prolonged fasting.},
}
@article {pmid39796301,
year = {2024},
author = {Galazka, S and Vigl, V and Kuffner, M and Dielacher, I and Spettel, K and Kriz, R and Kreuzinger, N and Vierheilig, J and Woegerbauer, M},
title = {Prevalence of Antibiotic Resistance Genes in Differently Processed Smoothies and Fresh Produce from Austria.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/foods14010011},
pmid = {39796301},
issn = {2304-8158},
support = {BMASGK-74602/0005-IX/B/15/2019//Austrian Federal Ministry of Social Affairs, Health, Care and Consumer Protection (BMASGK)/ ; },
abstract = {Plant-derived foods are potential vehicles for microbial antibiotic resistance genes (ARGs), which can be transferred to the human microbiome if consumed raw or minimally processed. The aim of this study was to determine the prevalence and the amount of clinically relevant ARGs and mobile genetic elements (MGEs) in differently processed smoothies (freshly prepared, cold-pressed, pasteurized and high-pressure processed) and fresh produce samples (organically and conventionally cultivated) to assess potential health hazards associated with their consumption. The MGE ISPps and the class 1 integron-integrase gene intI1 were detected by probe-based qPCR in concentrations up to 10[4] copies/mL in all smoothies, lettuce, carrots and a single tomato sample. The highest total (2.2 × 10[5] copies/mL) and the most diverse ARG and MGE loads (16/26 targets) were observed in freshly prepared and the lowest prevalences (5/26) and concentrations (4.1 × 10[3] copies/mL) in high-pressure-processed (HPP) smoothies. BlaCTX-M-1-15 (1.2 × 10[5] c/mL) and strB (6.3 × 10[4] c/mL) were the most abundant, and qacEΔ1 (95%), blaTEM1 (85%), ermB and sul1 (75%, each) were the most prevalent ARGs. QnrS, vanA, sat-4, blaKPC, blaNDM-1 and blaOXA-10 were never detected. HPP treatment reduced the microbial loads by ca. 5 logs, also destroying extracellular DNA potentially encoding ARGs that could otherwise be transferred by bacterial transformation. The bacterial microbiome, potential pathogens, bacterial ARG carriers and competent bacteria able to take up ARGs were identified by Illumina 16S rRNA gene sequencing. To reduce the risk of AMR spread from smoothies, our data endorse the application of DNA-disintegrating processing techniques such as HPP.},
}
@article {pmid39796296,
year = {2024},
author = {Lee, JH and Son, H and Subramaniyam, S and Lim, HJ and Park, S and Choi, RY and Kim, IW and Seo, M and Kweon, HY and Kim, Y and Kim, SW and Choi, JS and Shin, Y},
title = {Impact of Edible Insect Polysaccharides on Mouse Gut Microbiota: A Study on White-Spotted Flower Chafer Larva (Protaetia brevitarsis seulensis) and Silkworm Pupa (Bombyx mori).},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/foods14010006},
pmid = {39796296},
issn = {2304-8158},
support = {PJ01673101//the Cooperative Research Program for Agriculture Science and Technology Development (Project no. PJ01673101)/ ; },
abstract = {The increasing global population and the environmental consequences of meat consumption have led to the exploration of alternative sources of protein. Edible insects have gained attention as a sustainable and nutritionally rich meat alternative. We investigated the effects of two commonly consumed insects, Protaetia brevitarsis seulensis larva and Bombyx mori pupa, on beneficial gut microbiota growth, using whole 16s metagenome sequencing to assess diet-associated changes. Seven-week-old female C57BL/6J mice were administered the edible insects, along with fracto-oligosaccharide (FOS) as a positive control and sham (phosphate buffer saline (PBS)) as a negative control, to assess the relative abundance of insect-diet-associated gut microbes. In total, 567 genera and 470 species were observed, and among these, 15 bacterial genera were differentially abundant in all three groups. These results show that among the two insects, Bombyx mori pupa polysaccharides have a greater ability to regulate beneficial probiotics and next-generation probiotics. In particular, Lactococcus garvieae, which has promising effects on the gastrointestinal tracts of humans and animals, was significantly enriched in both Protaetia brevitarsis seulensis larva and Bombyx mori pupa polysaccharides, similar to fracto-oligosaccharide. The results suggest that the consumption of these insects, particularly polysaccharides, can enhance the growth of beneficial gut microbes, potentially leading to improved overall health in healthy populations.},
}
@article {pmid39795998,
year = {2024},
author = {May, MS and Park, H and Moallem, DH and Seeram, D and Dajiang, S and Hibshoosh, H and Jamison, JK and Uhlemann, AC and Manji, GA},
title = {Low Bacterial Biomass in Human Pancreatic Cancer and Adjacent Normal Tissue.},
journal = {International journal of molecular sciences},
volume = {26},
number = {1},
pages = {},
doi = {10.3390/ijms26010140},
pmid = {39795998},
issn = {1422-0067},
mesh = {Humans ; *Pancreatic Neoplasms/microbiology/pathology/drug therapy ; Female ; Male ; Aged ; Middle Aged ; *Carcinoma, Pancreatic Ductal/microbiology/pathology/drug therapy ; *Deoxycytidine/analogs &amp; derivatives/therapeutic use ; *Gemcitabine ; RNA, Ribosomal, 16S/genetics ; Neoadjuvant Therapy ; Gammaproteobacteria/genetics/isolation &amp; purification ; Biomass ; DNA, Bacterial/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; Gastrointestinal Microbiome ; },
abstract = {The gut microbiome plays an important role in the carcinogenesis of luminal gastrointestinal malignancies and response to antineoplastic therapy. Preclinical studies have suggested a role of intratumoral gammaproteobacteria in mediating response to gemcitabine-based chemotherapy in pancreatic ductal adenocarcinoma (PDAC). To our knowledge, this is the first study to evaluate the impact of the PDAC microbiome on chemotherapy response using samples from human pancreatic tumor resections. We performed 16S rRNA gene amplification and sequencing on both formalin-fixed paraffin-embedded (FFPE) and fresh frozen human PDAC resection samples. We analyzed frozen samples from 26 patients with resected PDAC and examined tumor and tumor-adjacent normal tissue. These patients represented nine long-term survivors (LTS) and nine short-term survivors (STS) after neoadjuvant gemcitabine therapy and eight control patients who did not receive any neoadjuvant therapy prior to resection. We also included FFPE samples from five patients, including tumor samples (3 samples per patient), tumor-adjacent normal tissue (2 per patient) and tumor-adjacent paraffin (1 per patient). Within frozen tissue, total DNA yields were high, but bacterial DNA was generally low, comparable to those seen in negative controls. In FFPE tissue, DNA yields were low and bacterial abundances were comparable in paraffin, tumor and normal PDAC samples. Gammaproteobacteria concentrations did not correlate with outcomes in patients treated with neoadjuvant gemcitabine-based chemotherapy. Our study found low microbial biomass in pancreatic tumor tissue, with no detectable association between bacterial taxa and chemotherapy outcomes. These results suggest a limited role of the microbiome in gemcitabine-based chemotherapy response in PDAC. Preclinical studies have implicated the pancreatic tumor microbiome in driving response to therapy. Cytidine deaminase, an enzyme produced by gammaproteobacteria, can metabolize gemcitabine and has been hypothesized to inhibit pancreatic tumor response to chemotherapy. Several clinical trials have evaluated the role of the tumor microbiome in pancreatic cancer treatment. We evaluated the impact of the pancreatic tumor microbiome on chemotherapy response using samples from human pancreatic tumor resections. We found a low microbial load that is partially attributable to contaminants and that gammaproteobacteria levels did not correlate with outcomes in patients with pancreatic cancer treated with gemcitabine-based chemotherapy.},
}
@article {pmid39795933,
year = {2024},
author = {Danova, S and Dobreva, L and Mancheva, K and Atanasov, G and Simeonova, L and Vilhelmova-Ilieva, N},
title = {Lactobacilli-Derived Postmetabolites Are Broad-Spectrum Inhibitors of Herpes Viruses In Vitro.},
journal = {International journal of molecular sciences},
volume = {26},
number = {1},
pages = {},
doi = {10.3390/ijms26010074},
pmid = {39795933},
issn = {1422-0067},
mesh = {*Antiviral Agents/pharmacology ; *Lactobacillus/drug effects ; *Herpesvirus 1, Human/drug effects/physiology ; Animals ; Chlorocebus aethiops ; Vero Cells ; Humans ; Virus Replication/drug effects ; Herpesviridae/drug effects ; },
abstract = {Herpes viruses are highly contagious agents affecting all classes of vertebrates, thus causing serious health, social, and economic losses. Within the One Health concept, novel therapeutics are extensively studied for both veterinary and human control and management of the infection, but the optimal strategy has not been invented yet. Lactic acid bacteria are key components of the microbiome that are known to play a protective role against pathogens as one of the proposed mechanisms involves compounds released from their metabolic activity. Previously, we reported the anti-herpes effect of postmetabolites isolated from Lactobacilli, and here, we confirm the inhibitory properties of another nine products against the phylogenetically distant human Herpes simplex virus-1 (HSV-1) and fish Koi Herpes virus (KHV) in cell cultures. Cytotoxicity, cytopathic effect inhibition, virucidal effect, the influence on the adsorption stage of the virus to the cells, as well as the protective effect of the postmetabolites on healthy cells were evaluated. The inhibitory effect was more pronounced against HSV-1 than against KHV at all studied viral cycle stages. Regarding the intracellular replicative steps, samples S7, S8, and S9 (Mix group) isolated from Ligilactobacillus salivarius (vaginal strain) demonstrated the most distinct effect with calculated selective indices (SIs) in the range between 69.4 and 77.8 against HSV-1, and from 62.2 to 68.4 against KHV. Bioactive metabolites from various LAB species significantly inhibit extracellular HSV-1 and, to a lesser extent, KHV virions. The blockage of viral adsorption to the host cells was remarkable, as recorded by a decrease in the viral titer with Δlg ≥ 5 in the Mix group for both herpes viruses. The remaining postmetabolites also significantly inhibited viral adsorption to varying degrees with Δlg ≥ 3. Most metabolites also exerted a protective effect on healthy MDBK and CCB cells to subsequent experimental viral infection. Our results reveal new horizons for the application of LAB and their postbiotic products in the prevention and treatment of herpes diseases.},
}
@article {pmid39795926,
year = {2024},
author = {Dymova, AA and Kovalev, MA and Silantyev, AS and Borzykh, AA and Osipova, PJ and Poddubko, SV and Mitkevich, VA and Karpov, DS and Kostina, NV},
title = {Unusual Genomic and Biochemical Features of Paenarthrobacter lasiusi sp. nov-A Novel Bacterial Species Isolated from Lasius niger Anthill Soil.},
journal = {International journal of molecular sciences},
volume = {26},
number = {1},
pages = {},
doi = {10.3390/ijms26010067},
pmid = {39795926},
issn = {1422-0067},
support = {no. 075-10-2021-113, project ID: RF----193021X0001//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Soil Microbiology ; *Genome, Bacterial ; *Ants/microbiology/genetics ; Animals ; *Phylogeny ; Genomics/methods ; Nitrogen Fixation/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The black garden ant (Lasius niger) is a widely distributed species across Europe, North America, and North Africa, playing a pivotal role in ecological processes within its diverse habitats. However, the microbiome associated with L. niger remains poorly investigated. In the present study, we isolated a novel species, Paenarthrobacter lasiusi, from the soil of the L. niger anthill. The genome of P. lasiusi S21 was sequenced, annotated, and searched for groups of genes of physiological, medical, and biotechnological importance. Subsequently, a series of microbiological, physiological, and biochemical experiments were conducted to characterize P. lasiusi S21 with respect to its sugar metabolism, antibiotic resistance profile, lipidome, and capacity for atmospheric nitrogen fixation, among others. A notable feature of the P. lasiusi S21 genome is the presence of two prophages, which may have horizontally transferred host genes involved in stress responses. P. lasiusi S21 synthesizes a number of lipids, including mono- and digalactosyldiacylglycerol, as well as steroid compounds that are typically found in eukaryotic organisms rather than prokaryotes. P. lasiusi S21 exhibits resistance to penicillins, lincosamides, fusidins, and oxazolidinones, despite the absence of specific genes conferring resistance to these antibiotics. Genomic data and physiological tests indicate that P. lasiusi S21 is nonpathogenic to humans. The genome of P. lasiusi S21 contains multiple operons involved in heavy metal metabolism and organic compound inactivation. Consequently, P. lasiusi represents a novel species with an intriguing evolutionary history, manifesting in distinctive genomic, metabolomic, and physiological characteristics. This species may have potential applications in the bioaugmentation of contaminated soils.},
}
@article {pmid39795621,
year = {2025},
author = {Srivastava, A and Shete, O and Gulia, A and Aggarwal, S and Ghosh, TS and Ahuja, V and Anand, S},
title = {Role of Gut and Urinary Microbiome in Children with Urinary Tract Infections: A Systematic Review.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/diagnostics15010093},
pmid = {39795621},
issn = {2075-4418},
support = {DDR/IIRP23/1895//Indian Council of Medical Research/ ; },
abstract = {Background: The complex interaction between the gut and urinary microbiota underscores the importance of understanding microbial dysbiosis in pediatric urinary tract infection (UTI). However, the literature on the gut-urinary axis in pediatric UTIs is limited. This systematic review aims to summarize the current literature on the roles of gut and urinary dysbiosis in pediatric UTIs. Methods: This systematic review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. A comprehensive literature search was performed across four databases, including PubMed, Web of Science, Scopus, and EMBASE. All studies published between January 2003 and December 2023 utilizing 16S rRNA sequencing to profile the gut or urinary microbiome in children with UTIs were included. Heat map visualization was used to compare microbial profiles between UTI and control cohorts. The methodological quality assessment was performed using the Newcastle-Ottawa scale (NOS). Results: Eight studies were included in this review. While five studies compared the microbiota signatures between patients and controls, three studies focused solely on the UTI cohort. Also, the gut and urinary microbiome profiles were investigated by four studies each. The consistent loss of microbiome alpha-diversity with an enrichment of specific putative pathobiont microbes was observed among the included studies. Escherichia coli consistently emerged as the predominant uropathogen in pediatric UTIs. In addition to this, Escherichia fergusonii, Klebsiella pneumoniae, and Shigella flexneri were isolated in the urine of children with UTIs, and enrichment of Escherichia, Enterococcus, Enterobacter, and Bacillus was demonstrated in the gut microbiota of UTI patients. On the contrary, certain genera, such as Achromobacter, Alistipes, Ezakiella, Finegoldia, Haemophilus, Lactobacillus, Massilia, Prevotella, Bacteroides, and Ureaplasma, were isolated from the controls, predominantly in the fecal samples. The methodological quality of the included studies was variable, with total scores (NOS) ranging from 5 to 8. Conclusions: The enrichment of specific pathobionts, such as Escherichia coli, in the fecal or urinary samples of the UTI cohort, along with the presence of core microbiome-associated genera in the non-UTI population, underscores the critical role of the gut-urinary axis in pediatric UTI pathogenesis. These findings highlight the potential for microbiome-based strategies in pediatric UTIs. Further studies with larger cohorts, standardized healthy controls, and longitudinal profiling are essential to validate these observations and translate them into clinical practice.},
}
@article {pmid39795230,
year = {2025},
author = {Hernández-Ruiz, RG and Olivares-Ochoa, XC and Salinas-Varela, Y and Guajardo-Espinoza, D and Roldán-Flores, LG and Rivera-Leon, EA and López-Quintero, A},
title = {Phenolic Compounds and Anthocyanins in Legumes and Their Impact on Inflammation, Oxidative Stress, and Metabolism: Comprehensive Review.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {1},
pages = {},
doi = {10.3390/molecules30010174},
pmid = {39795230},
issn = {1420-3049},
mesh = {*Anthocyanins/pharmacology/chemistry ; *Oxidative Stress/drug effects ; Humans ; *Inflammation/metabolism/drug therapy ; *Phenols/pharmacology/chemistry ; *Fabaceae/chemistry ; *Antioxidants/pharmacology ; Animals ; Gastrointestinal Microbiome/drug effects ; Insulin Resistance ; },
abstract = {Inflammation, oxidative stress, and metabolic diseases are intricately linked in a complex, self-reinforcing relationship. Inflammation can induce oxidative stress, while oxidative stress can trigger inflammatory responses, creating a cycle that contributes to the development and progression of metabolic disorders; in addition, these effects can be observed at systemic and local scales. Both processes lead to cellular damage, mitochondrial dysfunction, and insulin resistance, particularly affecting adipose tissue, the liver, muscles, and the gastrointestinal tract. This results in impaired metabolic function and energy production, contributing to conditions such as type 2 diabetes, obesity, and metabolic syndrome. Legumes are a good source of phenolic compounds and anthocyanins that exert an antioxidant effect-they directly neutralize reactive oxygen species and free radicals, reducing oxidative stress. In vivo, in vitro, and clinical trial studies demonstrate that these compounds can modulate key cellular signaling pathways involved in inflammation and metabolism, improving insulin sensitivity and regulating lipid and glucose metabolism. They also exert anti-inflammatory effects by inhibiting proinflammatory enzymes and cytokines. Additionally, anthocyanins and phenolics may positively influence the gut microbiome, indirectly affecting metabolism and inflammation.},
}
@article {pmid39795014,
year = {2024},
author = {Insawake, K and Songserm, T and Songserm, O and Theapparat, Y and Adeyemi, KD and Rassmidatta, K and Ruangpanit, Y},
title = {Flavonoids, Isoquinoline Alkaloids, and Their Combinations Affect Growth Performance, Inflammatory Status, and Gut Microbiome of Broilers Under High Stocking Density and Heat Stress.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/ani15010071},
pmid = {39795014},
issn = {2076-2615},
support = {ARDA-2019//Agricultural Research Development Agency, Thailand/ ; },
abstract = {High stocking density (HSD) and heat stress (HS) challenge broiler production. While antibiotics can mitigate the adverse effects of HS and HSD, their restricted use underscores the need to explore phytochemicals, particularly their combined effects under such conditions. This study investigated the influence of flavonoids, isoquinoline alkaloids, and their combinations as alternatives to bacitracin on growth performance, inflammatory status, gut morphology, and ceca microbiome in broilers raised under HSD and HS. A total of 2100 one-day-old male Ross 308 broiler chicks were distributed into 70 replicates, randomly assigned to one of seven dietary treatments and raised during the summer for 37 days. The treatments included normal stocking density (NSD, 10 birds/m[2]); HSD (15 birds/m[2]); HSD + 50 ppm of bacitracin (BCT); HSD + 300 ppm of flavonoids (FVNs); HSD + 80 ppm of isoquinoline alkaloids (IQAs); HSD + FVNs (1-10 days) and IQAs (11-37 days) (FVN-IQA); and HSD + IQAs (1-10 days) and FVNs (11-37 days) (IQA-FVN). The HS index reached or exceeded 160 during most of the experimental period. From 11 to 24 days of age, the HSD and BCT birds had lower body weight gain. The FVNs, IQAs, and their combinations decreased the corticosterone, IL-6, malondialdehyde, and heterophil-lymphocytes ratio compared to the HSD. Jejunal, ileal, and duodenal villi height/crypt depth ratio was lower in HSD than in other treatments except BCT. The α- and β-diversity, microbiota composition, and metabolic pathways were affected by treatment groups. Overall, FVNs, IQAs, and their combinations improved the growth performance, anti-inflammatory response, and gut health in broilers under HSD and HS, with the combinations exerting synergistic effects.},
}
@article {pmid39795013,
year = {2024},
author = {Chen, T and Zhao, M and Chen, M and Tang, X and Qian, Y and Li, X and Wang, Y and Liao, X and Wu, Y},
title = {High Concentrations of Tilmicosin Promote the Spread of Multidrug Resistance Gene tolC in the Pig Gut Microbiome Through Mobile Genetic Elements.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/ani15010070},
pmid = {39795013},
issn = {2076-2615},
support = {32172781, 32402820//National Natural Science Foundation of China/ ; 2023A1515011643//Natural Science Foundation of Guangdong Province/ ; GZC20240506//Postdoctoral Fellowship Program of CPSF/ ; 2024M750962//China Postdoctoral Science Foundation/ ; 2023B0202060001//Key-Area Research and Development Program of Guangdong Province/ ; 2021TDQD002//Start-up Research Project of Maoming Laboratory/ ; },
abstract = {The impact of antibiotic therapy on the spread of antibiotic resistance genes (ARGs) and its relationship to gut microbiota remains unclear. This study investigated changes in ARGs, mobile genetic elements (MGEs), and gut microbial composition following tilmicosin administration in pigs. Thirty pigs were randomly divided into control (CK), low-concentration (0.2 g/kg; L), and high-concentration (0.4 g/kg; H) groups. Tilmicosin concentration in manure peaked on day 16 of dosing and dropped below detectable levels by day 13 of the withdrawal period. While tilmicosin did not significantly affect the total abundance of macrolide resistance genes (MRGs) (p > 0.05), it significantly increased the abundance of the multidrug resistance gene tolC in the H group compared with the L and CK groups during the withdrawal period (p < 0.05). This increase was associated with a coincidental rise in the abundance of MGEs (e.g., int1 and int2) and the growth of potential tolC-hosting bacteria such as Paenalcaligenes and Proteiniclasticum. Redundancy analysis showed gut microbial composition as the primary driver of MRG abundance, with MGEs, tilmicosin concentration, and manure physicochemical properties playing secondary roles. These findings suggest that high-dose tilmicosin may alter the gut microbiota and promote ARG spread via MGE-mediated transfer.},
}
@article {pmid39794952,
year = {2024},
author = {Yu, L and Qiu, G and Yu, X and Zhao, J and Liu, J and Wang, H and Dong, L},
title = {Terpinen-4-ol Improves the Intestinal Barrier Function of the Colon in Immune-Stressed Weaning Piglets.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/ani15010009},
pmid = {39794952},
issn = {2076-2615},
abstract = {The aim of this study was to investigate the effects of terpinen-4-ol (TER) supplementation on the intestinal barrier function of pigs. Five groups of fifty 28-day-old piglets with comparable body weights were randomly assigned to the following groups: the control group (CON), the lipopolysaccharide group (LPS), the low TER group (PLT), the middle TER group (PMT), and the high TER group (PHT). The basal diet was given to the CON and LPS groups, and 30, 60, or 90 mg/kg TER was added to the basal diet for the TER groups. After the 21-day trial period, piglets in the LPS and TER groups received an intraperitoneal injection of 100 μg/kg body weight of LPS, whereas the piglets in the CON group received an injection of 0.9% normal saline solution. The results showed that LPS stimulation resulted in a decrease (p < 0.05) in the depth of colonic crypts in piglets, which was greater (p < 0.05) in the TER group. Compared with those in the CON group, the number of goblet cells and MUC2 expression were decreased in the colon of piglets in the LPS group, while these parameters were increased in the PMT group (p < 0.05). The malondialdehyde (MDA) content was greater in the colon of the LPS group than in that of the CON group, while the activities of glutathione peroxidase (GSH-Px), superoxide dismutase (SOD), and catalase (CAT) were lower in the colon of the LPS group; conversely, the MDA content was lower in the colons of the PLT and PMT groups than in those of the LPS group (p < 0.05). TER also reduced (p < 0.05) LPS-induced upregulation of IL-1β and TNF-α expression, along with the relative gene expression of NLRP3, ASC, and caspase-1 in the colon of piglets (p < 0.05). Compared with those in the CON group, the abundances of Firmicutes and UCG-005 in the LPS group were lower (p < 0.05), and those in the TER group were significantly greater than those in the LPS group. Compared with those in the CON group, the abundance of Proteobacteria in the LPS group increased (p < 0.05), while the abundance of Actinobacteria and Phascolarctobacterium increased (p < 0.05) in the colon of the PHT group compared with that in the LPS group. In conclusion, TER effectively improved the intestinal barrier function of the colon in weaning piglets. Based on the results of this study, the appropriate dose of TER in the diets of weaning piglets was 60 mg/kg.},
}
@article {pmid39794871,
year = {2025},
author = {Samodova, D and Stankevic, E and Søndergaard, MS and Hu, N and Ahluwalia, TS and Witte, DR and Belstrøm, D and Lubberding, AF and Jagtap, PD and Hansen, T and Deshmukh, AS},
title = {Salivary proteomics and metaproteomics identifies distinct molecular and taxonomic signatures of type-2 diabetes.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {5},
pmid = {39794871},
issn = {2049-2618},
support = {74550801//European Foundation for the Study of Diabetes/ ; NNF18CC0034900; NNF23SA0084103//Novo Nordisk Fonden/ ; NNF18CC0034900; NNF23SA0084103//Novo Nordisk Fonden/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; *Saliva/microbiology ; *Proteomics/methods ; Male ; Middle Aged ; Female ; *Microbiota ; Biomarkers/metabolism ; Bacterial Proteins/genetics ; Adult ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Computational Biology/methods ; Salivary Proteins and Peptides/metabolism ; Case-Control Studies ; Aged ; },
abstract = {BACKGROUND: Saliva is a protein-rich body fluid for noninvasive discovery of biomolecules, containing both human and microbial components, associated with various chronic diseases. Type-2 diabetes (T2D) imposes a significant health and socio-economic burden. Prior research on T2D salivary microbiome utilized methods such as metagenomics, metatranscriptomics, 16S rRNA sequencing, and low-throughput proteomics.<br><br>RESULTS: We conducted ultrafast, in-depth MS-based proteomic and metaproteomic profiling of saliva from 15 newly diagnosed T2D individuals and 15 age-/BMI-matched healthy controls (HC). Using state-of-the-art proteomics, over 4500 human and bacterial proteins were identified in a single 21-min run. Bioinformatic analysis revealed host signatures of altered immune-, lipid-, and glucose-metabolism regulatory systems, increased oxidative stress, and possible precancerous changes in T2D saliva. Abundance of peptides for bacterial genera such as Neisseria and Corynebacterium were altered showing biomarker potential, offering insights into disease pathophysiology and microbial applications for T2D management.<br><br>CONCLUSIONS: This study presents a comprehensive mapping of salivary proteins and microbial communities, serving as a foundational resource for enhancing understanding of T2D pathophysiology. The identified biomarkers hold promise for advancing diagnostics and therapeutic approaches in T2D and its associated long-term complication Video Abstract.},
}
@article {pmid39794404,
year = {2025},
author = {Prajapati, SK and Wang, S and Mishra, SP and Jain, S and Yadav, H},
title = {Protection of Alzheimer's disease progression by a human-origin probiotics cocktail.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1589},
pmid = {39794404},
issn = {2045-2322},
support = {W81XWH-18-PRARP AZ180098//U.S. Department of Defense/ ; W81XWH-18-PRARP AZ180098//U.S. Department of Defense/ ; W81XWH-18-PRARP AZ180098//U.S. Department of Defense/ ; W81XWH-18-PRARP AZ180098//U.S. Department of Defense/ ; R56AG069676/NH/NIH HHS/United States ; R56AG069676/NH/NIH HHS/United States ; R56AG069676, R56AG064075, R01AG071762, R21AG072379, U01AG076928 and R21AG082164/NH/NIH HHS/United States ; R56AG069676/NH/NIH HHS/United States ; 22A17//Florida Department of Health/ ; 22A17//Florida Department of Health/ ; },
mesh = {*Alzheimer Disease/microbiology/therapy/prevention &amp; control ; Animals ; *Probiotics/pharmacology/administration &amp; dosage ; Mice ; Humans ; Female ; *Disease Models, Animal ; *Gastrointestinal Microbiome ; *Disease Progression ; *Blood-Brain Barrier/metabolism ; Male ; Mice, Transgenic ; Dysbiosis/microbiology/therapy ; Brain/pathology/metabolism ; },
abstract = {Microbiome abnormalities (dysbiosis) significantly contribute to the progression of Alzheimer's disease (AD). However, the therapeutic efficacy of microbiome modulators in protecting against these ailments remains poorly studied. Herein, we tested a cocktail of unique probiotics, including 5 Lactobacillus and 5 Enterococcus strains isolated from infant gut with proven microbiome modulating capabilities. We aimed to determine the probiotics cocktail's efficacy in ameliorating AD pathology in a humanized AD mouse model of APP/PS1 strains. Remarkably, feeding mice with 1 × 10[11] CFU per day in drinking water for 16 weeks significantly reduced cognitive decline (measured by the Morris Water Maze test) and AD pathology markers, such as Aβ aggregation, microglia activation, neuroinflammation, and preserved blood-brain barrier (BBB) tight junctions. The beneficial effects were linked to a reduced inflammatory microbiome, leading to decreased gut permeability and inflammation in both systemic circulation and the brain. Although both male and female mice showed overall improvements in cognition and biological markers, females did not exhibit improvements in specific markers related to inflammation and barrier permeability, suggesting that the underlying mechanisms may differ depending on sex. In conclusion, our results suggest that this unique probiotics cocktail could serve as a prophylactic agent to reduce the progression of cognitive decline and AD pathology. This is achieved by beneficially modulating the microbiome, improving intestinal tight junction proteins, reducing permeability in both gut and BBB, and decreasing inflammation in the gut, blood circulation, and brain, ultimately mitigating AD pathology and cognitive decline.},
}
@article {pmid39794320,
year = {2025},
author = {Kasahara, K and Kerby, RL and Aquino-Martinez, R and Evered, AH and Cross, TL and Everhart, J and Ulland, TK and Kay, CD and Bolling, BW and Bäckhed, F and Rey, FE},
title = {Gut microbes modulate the effects of the flavonoid quercetin on atherosclerosis.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {12},
pmid = {39794320},
issn = {2055-5008},
support = {HL144651//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HL148577//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HL007936//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; 17CVD01//Fondation Leducq/ ; 17CVD01//Fondation Leducq/ ; },
mesh = {*Quercetin/pharmacology ; Animals ; *Atherosclerosis/prevention &amp; control/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects ; Mice ; Hydroxybenzoates/pharmacology ; Mice, Knockout ; Metabolomics/methods ; Disease Models, Animal ; Bacteria/classification/drug effects/genetics/isolation &amp; purification ; Male ; Mice, Knockout, ApoE ; Apolipoproteins E/genetics/deficiency ; Dietary Supplements ; },
abstract = {Gut bacterial metabolism of dietary flavonoids results in the production of a variety of phenolic acids, whose contributions to health remain poorly understood. Here, we show that supplementation with the commonly consumed flavonoid quercetin impacted gut microbiome composition and resulted in a significant reduction in atherosclerosis burden in conventionally raised (ConvR) Apolipoprotein E (ApoE) knockout (KO) mice but not in germ-free (GF) ApoE KO mice. Metabolomic analysis revealed that consumption of quercetin significantly increased plasma levels of benzoylglutamic acid, 3,4 dihydroxybenzoic acid (3,4-DHBA) and its sulfate-conjugated form in ConvR mice, but not in GF mice supplemented with the flavonoid. Levels of these metabolites were negatively associated with atherosclerosis burden. Furthermore, we show that 3,4-DHBA prevented lipopolysaccharide (LPS)-induced decrease in transendothelial electrical resistance (TEER). These results suggest that the effects of quercetin on atherosclerosis are influenced by gut microbes and are potentially mediated by bacterial metabolites derived from the flavonoid.},
}
@article {pmid39793868,
year = {2025},
author = {Yuan, Y and Zhang, L and Zhang, Y and Lee, K and Liu, Y},
title = {Resilience and Response of Anaerobic Digestion Systems to Short-term Hydraulic Loading Shocks: Focusing on Total and Active Microbial Community Dynamics.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120801},
doi = {10.1016/j.envres.2025.120801},
pmid = {39793868},
issn = {1096-0953},
abstract = {Anaerobic digestion is known to be sensitive to operational changes, such as hydraulic loading shock, yet the impact on the microbiome, particularly the active RNA-based community, has not been fully understood. This study aimed to investigate the performance of anaerobic reactors and their microbial communities under short-term hydraulic loading shocks. Using synthetic wastewater, the reactor was subjected to 24-hour shocks at three-fold and seven-fold the baseline loading rate, followed by DNA and RNA analyses to assess the system's resiliency and microbial responses. The research focused on shifts in major microbial groups and their functions, paying close attention to the active RNA community during loading shock events to better reflect the system's immediate condition. Findings indicated that although the microbial community structure, particularly among the archaea, was altered, the reactor quickly regained its balance. Differences were observed between DNA and RNA profiles and between regular and shock loadings; however, the alpha diversity and functions of the overall community were sustained. This study offers important insights for the design and operation of wastewater treatment plants, with the goal of achieving stable and efficient anaerobic digestion systems.},
}
@article {pmid39793775,
year = {2025},
author = {Li, X and Ning, L and Zhao, H and Gu, C and Han, Y and Xu, W and Si, Y and Xu, Y and Wang, R and Ren, Q},
title = {Jiawei Ermiao Granules (JWEMGs) clear persistent HR-HPV infection though improving vaginal microecology.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {119342},
doi = {10.1016/j.jep.2025.119342},
pmid = {39793775},
issn = {1872-7573},
abstract = {Jiawei Ermiao Granules (JWEMGs), a traditional Chinese herbal formulation, has been widely used in China for the treatment of human papillomavirus (HPV) infections. However, the underlying mechanisms through which it exerts its antiviral effects remain poorly understood.<br><br>AIM OF THE STUDY: This study aimed to investigate the potential mechanisms by which JWEMGs modulate vaginal microecology and clear HPV infections, utilizing clinical trials, metagenomic sequencing, and in vitro models.<br><br>MATERIALS AND METHODS: Clinical indicators related to vaginal microecology, such as vaginal pH, cleanliness, Nugent score, Donders score, catalase, neuraminidase, and leukocyte esterase, were evaluated in 65 patients with high-risk HPV (HR-HPV) infection. The study examined the impact of two courses of oral JWEMGs on these clinical parameters. Additionally, metagenomic sequencing was performed on vaginal lavage samples from 33 patients to assess the alteration of the vaginal microbiome following JWEMGs treatment. Immunohistochemistry was used to detect ALPK1 expression in cervical exfoliated cells, and ELISA was employed to measure cytokine levels in vaginal lavage fluid. JWEMGs intervention was applied to HaCaT-HPV E6/E7 cells to evaluate its effects on restoring &#x3b1;-kinase 1 (ALPK1) expression and promoting the secretion of cytokines and chemokines.<br><br>RESULTS: Treatment with JWEMGs significantly improved several clinical indicators, including cleanliness, pH, Nugent score, Donders score, catalase, neuraminidase, and leukocyte esterase, in HR-HPV-infected patients. Furthermore, JWEMGs therapy led to an increased abundance of Lactobacillus species, especially Lactobacillus crispatus, and a marked reduction in Gardnerella species. JWEMGs treatment also significantly promoted ALPK1 expression in cervical exfoliated cells and augmented the secretion of key cytokines, including IL-6, IL-8, and TNF-&#x3b1;. In parallel, in vitro results showed that JWEMGs substantially enhanced IL-6, IL-8, TNF-&#x3b1;, CCL2, CCL5, and CCL7 secretion in HaCaT-HPV E6/E7 cells, which correlated with the activation of the ALPK1/NF-&#x3ba;B signaling pathway.<br><br>CONCLUSION: In conclusion, JWEMGs treatment effectively remodels the vaginal microbiota and bolsters mucosal immunity in the lower genital tract, thereby improving the vaginal microecology in HR-HPV-infected individuals. In vitro findings further demonstrated that JWEMGs promote cytokine and chemokine expression, activating the ALPK1/NF-&#x3ba;B pathway.},
}
@article {pmid39793467,
year = {2025},
author = {Cardacino, A and Turco, S and Balestra, GM},
title = {Seasonal dynamics of kiwifruit microbiome: A case study in a KVDS-affected orchard.},
journal = {Microbiological research},
volume = {292},
number = {},
pages = {128044},
doi = {10.1016/j.micres.2024.128044},
pmid = {39793467},
issn = {1618-0623},
abstract = {Over the past decade, Italian kiwifruit orchards and overall production have faced a significant threat from Kiwifruit Vine Decline Syndrome (KVDS). Despite the insights gained from metagenomics studies into the microbial communities associated with the disease, unanswered questions still remain. In this study, the evolution of bacterial, fungal, and oomycetes communities in soil and root endosphere at three different time points during the vegetative season was investigated for the first time in a KVDS-affected orchard in the Lazio Region. The fungal and oomycetes genera previously associated with the syndrome, including Fusarium, Ilyonectria, Thelonectria, Phytophthora, Pythium and Globisporangium, were identified in both groups. In contrast, the characterization of bacterial communities revealed the first instance of the presence of the genus Ralstonia in soil and root samples. The microbiome composition shifts between KVDS-affected and asymptomatic plants were significant as evidenced by the results, particularly after a temperature increase. This temperature change coincided with the onset of severe disease symptoms and may indicate a key role in the progression of KVDS.},
}
@article {pmid39793444,
year = {2025},
author = {Verheijden, RJ and van Eijs, MJM and Paganelli, FL and Viveen, MC and Rogers, MRC and Top, J and May, AM and van de Wijgert, JHHM and Suijkerbuijk, KPM and , },
title = {Gut microbiome and immune checkpoint inhibitor toxicity.},
journal = {European journal of cancer (Oxford, England : 1990)},
volume = {216},
number = {},
pages = {115221},
doi = {10.1016/j.ejca.2025.115221},
pmid = {39793444},
issn = {1879-0852},
abstract = {BACKGROUND: Multiple studies have suggested that gut microbiome may influence immune checkpoint inhibitor (ICI) efficacy, but its association with immune-related adverse events (irAEs) is less well studied. In this prospective cohort study, we assessed whether gut microbiome composition at start, or changes during ICI, are associated with severe irAEs.<br><br>METHODS: Stool samples of cancer patients treated with anti-PD-1&#x202f;&#xb1;&#x202f;anti-CTLA-4 were analyzed using 16S rRNA gene sequencing and metagenomic shotgun sequencing. Differences in alpha and beta diversity between patients with and without severe irAE were assessed, as well as differential relative abundance (RA) of taxa, MetaCyc pathways, and seven prespecified literature-based bacterial groups including pathobionts and Ruminococcaceae.<br><br>FINDINGS: We analyzed 497 samples of 195 patients before and soon after starting ICI, at severe irAE onset and after starting immunosuppression. Mean RA of the pathobionts group was significantly higher in patients who developed a severe irAE (8.2&#x202f;%) compared to those who did not (4.8&#x202f;%; odds ratio 1.40; 95&#x202f;%CI 1.07-1.87) at baseline, and also early during ICI treatment and at severe irAE onset. A significantly stronger decrease in RA of Ruminococcaceae after starting ICI was observed in patients who developed a severe irAE compared to those who did not. RAs of Ruminococcaceae, the genus Ruminococcus, and the species R. bromii and R. callidus were significantly lower at severe irAE onset compared to other time points.<br><br>INTERPRETATION: Gut microbiome dysbiosis signaled by higher RA of pathobionts and decrease in RA of Ruminococcaceae may predispose to severe irAEs.},
}
@article {pmid39793233,
year = {2025},
author = {Xu, K and Tan, J and Lin, D and Jiang, H and Chu, Y and Zhou, L and Zhang, J and Lu, Y},
title = {Gut microbes of the cecum versus the colon drive more severe lethality and multi-organ damage.},
journal = {International immunopharmacology},
volume = {147},
number = {},
pages = {114029},
doi = {10.1016/j.intimp.2025.114029},
pmid = {39793233},
issn = {1878-1705},
abstract = {Intestinal perforations lead to a high risk of sepsis-associated morbidity and multi-organ dysfunctions. A perforation allows intestinal contents (IC) to enter the peritoneal cavity, causing abdominal infections. Right- and left-sided perforations have different prognoses in humans, but the mechanisms associated with different cecum and colon perforations remain unclear. This study investigates how gut flora influences outcomes from perforations at different sites in mice. Using fecal-induced peritonitis mouse model, isolated IC from the cecum or colon was injected peritoneally at 2 mg/kg. Bacterial burden was quantified with quantitative PCR, and microbial communities were analyzed using 16S rRNA gene sequencing. Survival rates were monitored, and blood biochemical indices, histological changes, cytokines expression, immunological signaling and multiple-organ damage were assessed at 16 h post-injections. The results showed cecum IC developed more severe sepsis than colon IC, with shorter median survival time and greater multi-organ damage. Mice treated with cecum IC displayed elevated tissue damage markers in the liver, heart, and kidneys, contributing to worsened pathology. This was likely driven by systematic inflammatory cytokines production and lung inflammation. Mechanistically, cecum IC triggered stronger cGAS-STING and TBK1-NF-κB signaling, promoting systemic inflammation compared to the colon IC. Moreover, bacterial analysis demonstrated that cecum IC carry a higher bacterial burden than colon IC and exhibit a different microbial community. A detailed microbiome comparison revealed an increased abundance of potentially pathogenic bacteria in the cecum IC. These findings suggest that the site of intestinal perforation influences sepsis severity, with the cecum being associated with a higher bacterial burden and a relatively increased abundance of potentially pathogenic bacteria compared to the colon. Our findings first compared the lethality associated with the microbial composition of the cecum and colon, indicating the perforation site could help providers predict the severity of sepsis, thereby introducing a novel perspective to microbiology and sepsis research.},
}
@article {pmid39794474,
year = {2025},
author = {Yin, Q and da Silva, AC and Zorrilla, F and Almeida, AS and Patil, KR and Almeida, A},
title = {Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39794474},
issn = {2058-5276},
support = {MR/W016184/1//RCUK | Medical Research Council (MRC)/ ; },
abstract = {Gut bacteria from the Enterobacteriaceae family are a major cause of opportunistic infections worldwide. Given their prevalence among healthy human gut microbiomes, interspecies interactions may play a role in modulating infection resistance. Here we uncover global ecological patterns linked to Enterobacteriaceae colonization and abundance by leveraging a large-scale dataset of 12,238 public human gut metagenomes spanning 45 countries. Machine learning analyses identified a robust gut microbiome signature associated with Enterobacteriaceae colonization status, consistent across health states and geographic locations. We classified 172 gut microbial species as co-colonizers and 135 as co-excluders, revealing a genus-wide signal of colonization resistance within Faecalibacterium and strain-specific co-colonization patterns of the underexplored Faecalimonas phoceensis. Co-exclusion is linked to functions involved in short-chain fatty acid production, iron metabolism and quorum sensing, while co-colonization is linked to greater functional diversity and metabolic resemblance to Enterobacteriaceae. Our work underscores the critical role of the intestinal environment in the colonization success of gut-associated opportunistic pathogens with implications for developing non-antibiotic therapeutic strategies.},
}
@article {pmid39794303,
year = {2025},
author = {Zhang, Y and Chen, XX and Chen, R and Li, L and Ju, Q and Qiu, D and Wang, Y and Jing, PY and Chang, N and Wang, M and Zhang, J and Chen, ZN and Wang, K},
title = {Lower respiratory tract microbiome dysbiosis impairs clinical responses to immune checkpoint blockade in advanced non-small-cell lung cancer.},
journal = {Clinical and translational medicine},
volume = {15},
number = {1},
pages = {e70170},
doi = {10.1002/ctm2.70170},
pmid = {39794303},
issn = {2001-1326},
support = {82273226//National Natural Science Foundation of China/ ; 82473215//National Natural Science Foundation of China/ ; 2020QNRC001//Young Elite Scientist Sponsorship Program by China Association for Science and Technology/ ; 2021LC2115//Clinical Booster Project of Fourth Military Medical University/ ; },
mesh = {*Carcinoma, Non-Small-Cell Lung/drug therapy/immunology/pathology ; Humans ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Lung Neoplasms/drug therapy/immunology/pathology ; Male ; *Dysbiosis/immunology/microbiology ; Female ; Middle Aged ; Aged ; Bronchoalveolar Lavage Fluid/microbiology/immunology ; Microbiota/drug effects ; },
abstract = {BACKGROUND: Gut microbiome on predicting clinical responses to immune checkpoint inhibitors (ICIs) has been discussed in detail for decades, while microecological features of the lower respiratory tract within advanced non-small-cell lung cancer (NSCLC) are still relatively vague.<br><br>METHODS: During this study, 26 bronchoalveolar lavage fluids (BALF) from advanced NSCLC participants who received immune checkpoint inhibitor monotherapy were performed 16S rRNA sequencing and untargeted metabolome sequencing to identify differentially abundant microbes and metabolic characteristics. Additionally, inflammatory cytokines and chemokines were also launched in paired BALF and serum samples by immunoassays to uncover their underlying correlations. The omics data were separately analyzed and integrated by using multiple correlation coefficients. Multiplex immunohistochemical staining was then used to assess the immune cell infiltration after immune checkpoint blockade therapy.<br><br>RESULTS: Lower respiratory tract microbiome diversity favoured preferred responses to ICIs. Microbial markers demonstrated microbial diversity overweight a single strain in favoured response to ICI therapy, where Bacillus matters. Sphingomonas and Sediminibacterium were liable to remodulate lipid and essential amino acid degradations to embrace progression after immunotherapies. Microbiome-derived metabolites reshaped the immune microenvironment in the lower respiratory tract by releasing inflammatory cytokines and chemokines, which was partially achieved by metabolite-mediated tumoral inflammatory products and reduction of CD8[+] effective T cells and M1 phenotypes macrophages in malignant lesions.<br><br>CONCLUSIONS: This study provided a microecological landscape of the lower respiratory tract with advanced NSCLC to ICI interventions and presented a multidimensional perspective with favoured outcomes that may improve the predictive capacity of the localized microbiome in clinical practices.<br><br>HIGHLIGHTS: Alterations of the lower respiratory tract microbiome indicate different clinical responses to ICB within advanced NSCLC. Reduced microbial diversity of lower respiratory tracts impairs anti-tumoral performances. Microbe-derived metabolites perform as a dominant regulator to remodify the microecological environment in lower respiratory tracts. Multi-omics sequencings of the lower respiratory tract possess the potential to predict the long-term clinical responses to ICB among advanced NSCLC.},
}
@article {pmid39793933,
year = {2025},
author = {Sabarathinam, S and Jayaraman, A and Venkatachalapathy, R},
title = {Gut Microbiome-Derived Metabolites and Their Impact on Gene Regulatory Networks in Gestational Diabetes.},
journal = {The Journal of steroid biochemistry and molecular biology},
volume = {},
number = {},
pages = {106674},
doi = {10.1016/j.jsbmb.2025.106674},
pmid = {39793933},
issn = {1879-1220},
abstract = {This study explored the therapeutic potential of gut microbiota metabolites in managing Gestational Diabetes Mellitus (GDM). Using network pharmacology, molecular docking, and dynamics simulations, we identified key targets and pathways involved in GDM. We screened 135 gut-derived metabolites, with 8 meeting drug-likeness and pharmacokinetic criteria. Analysis revealed significant overlap with GDM-related targets, including AKT1, IL6, TNF, and STAT3. Functional enrichment analysis highlighted the AGE-RAGE signaling and inflammatory pathways as crucial in GDM pathogenesis.Molecular docking and dynamics simulations showed strong binding affinities and stable interactions between two metabolites, luteolin and naringenin chalcone, and the target protein AKT1. These findings suggest that gut microbiota-derived metabolites, particularly luteolin and naringenin chalcone, may effectively modulate key pathways in GDM, offering promising avenues for novel treatment strategies.},
}
@article {pmid39793468,
year = {2025},
author = {Sun, X and Pei, Z and Wang, H and Zhao, J and Chen, W and Lu, W},
title = {Bridging dietary polysaccharides and gut microbiome: How to achieve precision modulation for gut health promotion.},
journal = {Microbiological research},
volume = {292},
number = {},
pages = {128046},
doi = {10.1016/j.micres.2025.128046},
pmid = {39793468},
issn = {1618-0623},
abstract = {Dietary polysaccharides function not only as indispensable nutrients and energy sources for the host organism but also as critical substrates for the gut microbiota. Gut microorganisms possess the ability to selectively degrade and metabolize specific dietary polysaccharides, thus fostering their proliferation and yielding crucial bioactive metabolites that potentially influence host metabolic and immune pathways. Dysbiosis of the gut microbiota has been extensively documented to be closely linked with the onset and progression of various diseases; in this regard, the precision modulation strategy of the gut microbiome via dietary polysaccharides holds substantial potential to enhance human health. Here, we delve into the therapeutic potential of dietary polysaccharides for the precision modulation of specific gut microorganisms via dietary interventions, with particular emphasis on their implications for the prevention and management of metabolic and inflammatory disorders. Given the complexity of the human gut microbiome and the varying degrees to which different bacterial members utilize carbohydrates, we conduct an in-depth analysis of the differential utilization of dietary polysaccharides by key gut microbiome, with particular emphasis on the role of carbohydrate-active enzymes in these processes. Furthermore, we elucidate the pivotal role of carbohydrate utilization within microbial cross-feeding networks and its significance in maintaining gut homeostasis. In summary, this review investigates the precision modulation of gut microbiota through dietary polysaccharides, with the aim of establishing a theoretical foundation for the development of personalized nutritional interventions. These strategies hold substantial potential for enhancing human health and offer valuable opportunities for the prevention and treatment of microbiota-associated diseases.},
}
@article {pmid39793111,
year = {2025},
author = {Zhang, C and Zhou, H and He, K and Xiao, Y and Chen, M and Zuo, Z and Shu, R and Geng, Y and Jin, S and Mei, Y and He, B and Li, F},
title = {The interaction of Serratia bacteria and harmonine in harlequin ladybird confers an interspecies competitive edge.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {2},
pages = {e2417873121},
doi = {10.1073/pnas.2417873121},
pmid = {39793111},
issn = {1091-6490},
support = {2021YFD1400100 2021YFD1400101//MOST | National Key Research and Development Program of China (NKPs)/ ; 32102271//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022T150579//China Postdoctoral Science Foundation (China Postdoctoral Foundation Project)/ ; },
mesh = {Animals ; *Coleoptera/microbiology ; *Serratia/genetics ; Predatory Behavior ; Penicillins ; },
abstract = {The harlequin ladybird, Harmonia axyridis, is a predatory beetle used globally to control pests such as aphids and scale insects. Originating from East Asia, this species has become highly invasive since its introduction in the late 19th century to Europe and North America, posing a threat to local biodiversity. Intraguild predation is hypothesized to drive the success of this invasive species, but the underlying mechanisms remain unknown. In this study, a feeding assay revealed that while harlequin ladybirds survive feeding on seven-spotted ladybird eggs, the reverse is not true. However, seven-spotted ladybirds that had fed on harlequin ladybird eggs were able to survive the feeding assay when treated with penicillin. Microbiome sequencing and whole genome analysis of harlequin ladybird eggs revealed a newly discovered pathogenic bacterium strain named Serratia harmoniae. The median lethal concentration (LC50) of S. harmoniae was found to be 2.1 × 10[5] times higher in the harlequin ladybird compared to the seven-spotted ladybird. The high tolerance observed in harlequin ladybirds was attributed to harmonine, specifically produced in the fat body of this species. Silencing three key genes in the harmonine biosynthesis pathway-Spidey, Sca2, and Desat-reduced the production of the compound, leading to increased S. harmoniae levels and higher mortality. Treating RNAi-altered individuals with penicillin reversed this effect, successfully reducing S. harmoniae presence and increasing insect survival. Taken together, these findings demonstrate that S. harmoniae, a newly identified pathogenic bacterium carried by harlequin ladybirds, interacts with harmonine to confer an interspecies competitive advantage over native ladybird species in nonnative regions.},
}
@article {pmid39793044,
year = {2025},
author = {Putumbaka, S and Schut, GJ and Thorgersen, MP and Poole, FL and Shao, N and Rodionov, DA and Adams, MWW},
title = {Tungsten is utilized for lactate consumption and SCFA production by a dominant human gut microbe Eubacterium limosum.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {1},
pages = {e2411809121},
doi = {10.1073/pnas.2411809121},
pmid = {39793044},
issn = {1091-6490},
support = {R01 GM136885/GM/NIGMS NIH HHS/United States ; },
mesh = {*Eubacterium/metabolism/genetics ; Humans ; *Gastrointestinal Microbiome/physiology ; *Lactic Acid/metabolism ; *Tungsten/metabolism ; *Fatty Acids, Volatile/metabolism ; Bacterial Proteins/metabolism/genetics ; Gene Expression Regulation, Bacterial ; },
abstract = {Eubacterium limosum is a dominant member of the human gut microbiome and produces short-chain fatty acids (SCFAs). These promote immune system function and inhibit inflammation, making this microbe important for human health. Lactate is a primary source of gut SCFAs but its utilization by E. limosum has not been explored. We show that E. limosum growing on lactate takes up added tungstate rather than molybdate and produces the SCFAs acetate and butyrate, but not propionate. The genes encoding an electron bifurcating, tungsten-containing oxidoreductase (WOR1) and a tungsten-containing formate dehydrogenase (FDH), along with an electron bifurcating lactate dehydrogenase (LCT), lactate permease, and enzymes of the propanediol pathway, are all up-regulated on lactate compared to growth on glucose. Lactate metabolism is controlled by a GntR-family repressor (LctR) and two global regulators, Rex and CcpA, where Rex in part controls W storage and tungstopyranopterin (Tuco) biosynthesis. Tuco-dependent riboswitches, along with CcpA, also control two iron transporters, consistent with the increased iron demand for many iron-containing enzymes, including WOR1 and FDH, involved in SCFA production. From intracellular aldehyde concentrations and the substrate specificity of WOR1, we propose that WOR1 is involved in detoxifying acetaldehyde produced during lactate degradation. Lactate to SCFA conversion by E. limosum is clearly highly tungstocentric and tungsten might be an overlooked micronutrient in the human microbiome and in overall human health.},
}
@article {pmid39792908,
year = {2025},
author = {Luangphiphat, W and Prombutara, P and Jamjuree, P and Chantarangkul, C and Vitheejongjaroen, P and Muennarong, C and Fukfon, K and Onwan, M and Taweechotipatr, M},
title = {The efficacy of Lacticaseibacillus paracasei MSMC39-1 and Bifidobacterium animalis TA-1 probiotics in modulating gut microbiota and reducing the risk of the characteristics of metabolic syndrome: A randomized, double-blinded, placebo-controlled study.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0317202},
doi = {10.1371/journal.pone.0317202},
pmid = {39792908},
issn = {1932-6203},
mesh = {Humans ; *Metabolic Syndrome/microbiology/therapy ; *Probiotics/therapeutic use/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Double-Blind Method ; Male ; Female ; Adult ; *Bifidobacterium animalis ; Middle Aged ; *Lacticaseibacillus paracasei ; },
abstract = {Modern treatment, a healthy diet, and physical activity routines lower the risk factors for metabolic syndrome; however, this condition is associated with all-cause and cardiovascular mortality worldwide. This investigation involved a randomized controlled trial, double-blind, parallel study. Fifty-eight participants with risk factors of metabolic syndrome according to the inclusion criteria were randomized into two groups and given probiotics (Lacticaseibacillus paracasei MSMC39-1 and Bifidobacterium animalis TA-1) (n = 31) or a placebo (n = 27). The participants had a mean age of 42.29 ± 7.39 and 43.89 ± 7.54 years in the probiotics and placebo groups, respectively. Stool samples, anthropometric data, and blood chemistries were taken at baseline and at 12 weeks. The primary outcome was achieved by the probiotics group as their low-density lipoprotein-cholesterol level dramatically lowered compared to the placebo group (the difference was 39.97 ± 26.83 mg/dl, p-value <0.001). Moreover, significant reductions in body weight, body mass index, waist circumference, systolic blood pressure, and total cholesterol were observed in the volunteers treated with probiotics compared to the placebo. In the gut microbiome analysis, the results showed statistically significant differences in the beta diversity in the post-intervention probiotics group. Blautia, Roseburia, Collinsella, and Ruminococcus were among the gut microbiomes that were more prevalent in the post-intervention probiotics group. In addition, this group exhibited increases in the predicted functional changes in ATP-binding cassette (ABC) transporters, as well as ribonucleic acid transport, the biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, and pyruvate metabolism. In conclusion, this research demonstrated that the probiotics L. paracasei MSMC39-1 and B. animalis TA-1 have the efficacy to lower risk factors associated with metabolic syndrome.},
}
@article {pmid39792897,
year = {2025},
author = {Lee, S and Aasmets, O and Arffman, RK and Laru, J and Rossi, HR and Salumets, A and Piltonen, TT and Org, E},
title = {The reproductive tract microbiome in women with polycystic ovary syndrome and across different menstrual cycle phases.},
journal = {Human reproduction (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/humrep/deae270},
pmid = {39792897},
issn = {1460-2350},
support = {315921//Research Council of Finland/ ; },
abstract = {STUDY QUESTION: Do polycystic ovary syndrome (PCOS), menstrual cycle phases, and ovulatory status affect reproductive tract (RT) microbiome profiles?<br><br>SUMMARY ANSWER: We identified microbial features associated with menstrual cycle phases in the upper and lower RT microbiome, but only two specific differences in the upper RT according to PCOS status.<br><br>WHAT IS KNOWN ALREADY: The vaginal and uterine microbiome profiles vary throughout the menstrual cycle. Studies have reported alterations in the vaginal microbiome among women diagnosed with PCOS.<br><br>STUDY DESIGN, SIZE, DURATION: This prospective case-control study included a cohort of 37 healthy control women and 52 women diagnosed with PCOS. Microbiome samples were collected from the vagina as vaginal swabs (VS) and from the uterus as endometrial flushing (EF) aspirate samples, and compared according to PCOS diagnosis, the menstrual cycle phases, and ovulatory status, at Oulu University Hospital (Oulu, Finland) from January 2017 to March 2020.<br><br>A total of 83 VS samples and 80 EF samples were collected. Age and body mass index (BMI) were matched between women with and without PCOS. Clinical characteristics were assessed using blood samples collected between cycle days 2 and 8, and microbial DNA was sequenced on the Ion Torrent platform. Microbial alpha diversity (i.e. the observed number of unique genera and Shannon diversity index) was analysed across sample types, PCOS diagnosis and menstrual cycle phases. Linear mixed-effects models were utilised to identify microbial features in relation to PCOS and the menstrual cycle phases. Associations between the beta diversity of the RT microbiome and PCOS- and cycle-related clinical features were calculated using PERMANOVA.<br><br>Microbial alpha diversity showed no difference with PCOS (VS: Pobserved feature = 0.836, Pshannon = 0.998; EF: Pobserved feature = 0.366, Pshannon = 0.185), but varied with menstrual cycle phases (VS: Pobserved feature = 0.001, Pshannon = 0.882; EF: Pobserved feature = 0.026, Pshannon = 0.048). No difference was observed in beta diversity based on either PCOS or the menstrual cycle phases (VS: PPCOS = 0.280, Pcycle = 0.115; EF: PPCOS = 0.234, Pcycle = 0.088). In the endometrial flushing samples, we identified two novel microbial features, characterised by the ratio of differential abundance of two genera, associated with PCOS (FDR &#x2264; 0.1) and 13 novel features associated with the menstrual cycle phases (FDR &#x2264; 0.1).<br><br>Although this was the first study to simultaneously analyse, the lower and upper RT microbiome in women with and without PCOS, the limited sample size of anovulatory cases may hinder the detection of differences related to PCOS and ovulatory status.<br><br>The main finding suggests that PCOS and the menstrual cycle phases are associated with specific microbial features in the upper RT, indicating that the analysis of the upper RT microbiome can potentially identify biomarkers for both PCOS and menstrual cycle phases.<br><br>This research was funded by the Research Council of Finland (grants no. 315921, 321763, 336449), the Sigrid Jus&#xe9;lius Foundation, Novo Nordisk Foundation (grant no. NNF21OC0070372), and the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant (MATER, grant no. 813707). This research was also funded by the Estonian Research Council (grants no. PRG1076, PRG1414), the Horizon Europe grant (NESTOR, grant no. 101120075) of the European Commission, and EMBO Installation Grant (grant no. 3573). The funders did not participate in any processes of the study. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.<br><br>TRIAL REGISTRATION NUMBER: N/A.},
}
@article {pmid39792643,
year = {2025},
author = {Gu, P and Wei, R and Liu, R and Yang, Q and He, Y and Guan, J and He, W and Li, J and Zhao, Y and Xie, L and He, J and Guo, Q and Hu, J and Bao, J and Wang, W and Guo, J and Zeng, Z and Chen, Z and Jiang, Y and Liu, Z and Chen, P},
title = {Aging-induced Alternation in the Gut Microbiota Impairs Host Antibacterial Defense.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2411008},
doi = {10.1002/advs.202411008},
pmid = {39792643},
issn = {2198-3844},
support = {2022YFA0806400//National Key R&amp;D Program of China/ ; 2022B1515120024//Guang Dong Basic and Applied Basic Research Foundation/ ; 2022A1515110070//Guang Dong Basic and Applied Basic Research Foundation/ ; 32071124//National Natural Science Foundation of China/ ; 32271230//National Natural Science Foundation of China/ ; 81971859//National Natural Science Foundation of China/ ; 82130063//National Natural Science Foundation of China/ ; 82241061//National Natural Science Foundation of China/ ; },
abstract = {Older individuals experience increased susceptibility and mortality to bacterial infections, but the underlying etiology remains unclear. Herein, it is shown that aging-associated reduction of commensal Parabacteroides goldsteinii (P. goldsteinii) in both aged mice and humans critically contributes to worse outcomes of bacterial infection. The colonization of live P. goldsteinii conferred protection against aging-associated bacterial infections. Metabolomic profiling reveals a protective compound, apigenin, generated by P. goldsteinii, antagonizes bacterial clearance defects in aged mice. AMP-binding protein (ampB) is identified as a key gene involved in apigenin synthesis in P. goldsteinii using homologous recombination in bacteria. Mechanistically, apigenin binds directly to the potential sites on Fgr (M341 and D404), preventing its inhibitory role on Vav1 phosphorylation, and therefore promoting the activation of Cdc42/Rac1, Arp2/3 expression and subsequent actin reorganization, which contributes to the enhanced phagocytosis of macrophages to bacteria. Collectively, the findings suggest that dysbiosis of the gut microbiota may impair host defense mechanisms and increase susceptibility to bacterial infections in older adults and highlight the microbiota-apigenin-Fgr axis as a possible route to ameliorate aging-associated antibacterial defects.},
}
@article {pmid39792461,
year = {2025},
author = {Tan, G and LeCates, CN and Simpson, A and Holtzen, S and Parris, DJ and Stewart, FJ and Stockton, A and , },
title = {Amplicon Sequencing Reveals Diversity in Spatially Separated Microbial Communities in the Icelandic Mars Analog Environment Mælifellssandur.},
journal = {Astrobiology},
volume = {},
number = {},
pages = {},
doi = {10.1089/ast.2023.0124},
pmid = {39792461},
issn = {1557-8070},
abstract = {Exploration missions to Mars rely on landers or rovers to perform multiple analyses over geographically small sampling regions, while landing site selection is done using large-scale but low-resolution remote-sensing data. Utilizing Earth analog environments to estimate small-scale spatial and temporal variation in key geochemical signatures and biosignatures will help mission designers ensure future sampling strategies meet mission science goals. Icelandic lava fields can serve as Mars analog sites due to conditions that include low nutrient availability, temperature extremes, desiccation, and isolation from anthropogenic contamination. This work reports analysis of samples collected using methods analogous to those of planetary missions to characterize microbial communities at different spatial scales in Mælifellssandur, Iceland, an environment with homogeneity at "remote imaging" resolution (overall temperature, apparent moisture content, and regolith grain size). Although microbial richness did not vary significantly among samples, the phylogenetic composition of the sediment microbiome differed significantly among sites separated by 100 m, which suggests distinct microbial signatures despite apparent homogeneity from remote observations. This work highlights the importance of considering microenvironments in future life-detection missions to extraterrestrial planetary bodies.},
}
@article {pmid39792407,
year = {2024},
author = {Shi, Y and Guo, Z and Wang, Q and Deng, H},
title = {Prognostic value of tumor-infiltrating lymphocyte subtypes and microorganisms in triple-negative breast cancer.},
journal = {Journal of cancer research and therapeutics},
volume = {20},
number = {7},
pages = {1983-1990},
doi = {10.4103/jcrt.jcrt_41_24},
pmid = {39792407},
issn = {1998-4138},
mesh = {Humans ; *Lymphocytes, Tumor-Infiltrating/immunology/metabolism ; *Triple Negative Breast Neoplasms/immunology/pathology/mortality ; Prognosis ; Female ; *Tumor Microenvironment/immunology ; *Biomarkers, Tumor/metabolism ; Gastrointestinal Microbiome/immunology ; },
abstract = {Tumor-infiltrating lymphocytes (TILs) are key components of the tumor microenvironment (TME) and serve as prognostic markers for breast cancer. Patients with high TIL infiltration generally experience better clinical outcomes and extended survival compared to those with low TIL infiltration. However, as the TME is highly complex and TIL subtypes perform distinct biological functions, TILs may only provide an approximate indication of tumor immune status, potentially leading to biased prognostic results. Therefore, we reviewed the interactions between immune-infiltrating subtypes and tumor cells throughout the entire TME. By examining the antitumor or protumor effects of each TIL subtype, we aimed to better characterize the tumor immune landscape, offering more accurate and comprehensive insights for guiding triple-negative breast cancer (TNBC) treatment. In addition, this approach could lead to the development of new therapeutic targets, enabling tailored treatment strategies and precision medicine. Accumulating evidence suggests that the intestinal microbiome and its metabolites influence antitumor responses by modulating innate and adaptive immunity, with specific bacteria potentially serving as biomarkers for predicting clinical responses. Various studies have identified microorganisms in breast tissue, previously considered sterile, revealing differences in breast microbial composition between patients with breast cancer and controls, as well as associations between specific breast microorganisms and clinicopathologic features, including immune correlations. The aim of this review was to provide a more comprehensive set of prognostic markers for TNBC and to tap into potential-specific therapeutic targets.},
}
@article {pmid39792346,
year = {2025},
author = {Kwon, CY},
title = {Similar but Different Three Major Traditional Medicines in East Asia: A Bibliometric Analysis.},
journal = {Chinese journal of integrative medicine},
volume = {},
number = {},
pages = {},
pmid = {39792346},
issn = {1993-0402},
abstract = {OBJECTIVE: Traditional medicine (TM) has played a key role in the health care system of East Asian countries, including China, Japan and South Korea. This bibliometric study analyzes the recent research status of these three TMs, including traditional Chinese medicine (TCM), traditional Korean medicine (TKM), and Kampo medicine (KM).<br><br>METHODS: Research topics of studies published for recent 10 years (2014 to 2023), through a search on MEDLINE via PubMed, was analyzed. Medical Subject Headings were used to distinguish between the three TMs researches. Bibliographic information was analyzed through VOSViewer version. Total 10,151 documents were included: TCM studies (n=9,630); TKM studies (n=256); and KM studies (n=295).<br><br>RESULTS: Comparing the three co-occurrence analysis maps, TCM studies generally overwhelm the quantitative scale of TKM and KM studies. In the trend of the latest research of TCM, not only corona virus disease 2019 (COVID-19), but also clinical research topics such as gastrointestinal microbiome and diabetes mellitus have emerged, with in silico research approaches being actively applied. In the case of TKM, obesity and cooperative treatment with Western medicine are gaining attention. In KM, COVID-19 and Scutellaria baicalensis were recent research focuses. Unique features that distinguished from the other two TM research trends included 'gut microbiota', 'diabetes mellitus', 'clinical trials', 'disease models', and 'quality control' in the TCM map; 'prospective studies', 'cell line, tumor', and 'panax' in the TKM map; and 'aged, 80 and over', 'retrospective studies', 'glycyrrhiza', 'panax', and 'paeonia' in the KM map. Also, some quantitative and qualitative differences were found in author co-operation maps in each TM.<br><br>CONCLUSIONS: This analysis revealed that there were clear quantitative and qualitative differences among TCM, TKM, and KM. Although these medicines have a common root, they may have become distinct due to factors such as the size of research funds, cultural differences, and the medical licensing system.},
}
@article {pmid39792234,
year = {2025},
author = {Patel, JJ and Barash, M},
title = {The Gut in Critical Illness.},
journal = {Current gastroenterology reports},
volume = {27},
number = {1},
pages = {1-9},
pmid = {39792234},
issn = {1534-312X},
mesh = {Humans ; *Critical Illness/therapy ; *Gastrointestinal Microbiome/physiology ; Intestinal Mucosa/microbiology ; Animals ; },
abstract = {PURPOSE OF REVIEW: The purpose of this narrative review is to describe the mechanisms for gut dysfunction during critical illness, outline hypotheses of gut-derived inflammation, and identify nutrition and non-nutritional therapies that have direct and indirect effects on preserving both epithelial barrier function and gut microbiota during critical illness.<br><br>RECENT FINDINGS: Clinical and animal model studies have demonstrated that critical illness pathophysiology and interventions breach epithelial barrier function and convert a normally commensal gut microbiome into a pathobiome. As a result, the gut has been postulated to be the "motor" of critical illness and numerous hypotheses have been put forward to explain how it contributes to systemic inflammation and drives multiple organ failure. Strategies to ameliorate gut dysfunction have focused on maintaining gut barrier function and promoting gut microbiota commensalism. The trajectory of critical illness may be closely related to gut epithelial barrier function, the gut microbiome and interventions that may contribute towards a deleterious pathobiome with immune dysregulation.},
}
@article {pmid39792141,
year = {2024},
author = {Hastie, E and Srivatsa, MS and Gianella, S and Cottrell, M and Forsyth, K and Porrachia, M and Burke, L and Morris, S and Rawlings, SA and Karris, M and Chaillon, A and Blumenthal, J},
title = {Brief Report: Genital Microbiome, Inflammation, and Tenofovir Levels in Transgender Men and Cisgender Women Taking Oral PrEP.},
journal = {Journal of acquired immune deficiency syndromes (1999)},
volume = {97},
number = {5},
pages = {477-481},
doi = {10.1097/QAI.0000000000003521},
pmid = {39792141},
issn = {1944-7884},
support = {P30 AI036214/NH/NIH HHS/United States ; AI158293/NH/NIH HHS/United States ; DA055491/NH/NIH HHS/United States ; KL2t001444/NH/NIH HHS/United States ; EI11-SD-005B/NH/NIH HHS/United States ; },
mesh = {Humans ; *Transgender Persons ; *Tenofovir/therapeutic use/administration &amp; dosage ; Female ; *Pre-Exposure Prophylaxis ; *HIV Infections/prevention &amp; control ; Adult ; *Microbiota/drug effects ; Male ; *Vagina/microbiology ; *Anti-HIV Agents/therapeutic use/administration &amp; dosage ; *Inflammation ; Young Adult ; Testosterone ; },
abstract = {BACKGROUND: Little is known about the efficacy of preexposure prophylaxis (PrEP) or what biologic factors may influence HIV transmission in transgender men (TGM). In this study, we sought to explore the effect of testosterone on the vaginal microbiome, cervicovaginal fluid (CVF) tenofovir concentrations, and levels of CVF inflammatory markers in TGM on PrEP.<br><br>METHODS: Cervicovaginal fluid was collected from 13 TGM (7 using testosterone) and 32 cisgender women (CGW) on PrEP. The vaginal microbiome, CVF tenofovir concentrations, and CVF inflammatory markers were determined and compared.<br><br>RESULTS: The proportion of CVF Lactobacillus was significantly higher in CGW than in TGM (78% vs 24%, P < 0.001). Among TGM, the proportion of CVF Lactobacillus was lower, though not statistically significant, in those taking testosterone than in those not taking testosterone (14% vs 35%, P-value = 0.3). Interestingly, mean CVF tenofovir concentrations were the lowest in TGM on testosterone at 884 ng/mL compared with 3150 ng/mL in TGM not on testosterone and 1932 ng/mL in CGW; however, this difference was not statistically significant. There was no statistically significant difference in any of the genital inflammatory markers between groups and no correlation between inflammation and tenofovir levels.<br><br>CONCLUSIONS: Our findings suggest a potential correlation between testosterone use, Lactobacillus dominance, and lower TFV concentrations in CVF, which may have implications on HIV acquisition from vaginal sex in TGMT. Future studies with larger sample sizes are needed to further investigate these relationships.},
}
@article {pmid39792104,
year = {2025},
author = {Pantlin, B},
title = {Benefits of a diverse gut microbiome in systemic anti-cancer therapy patients.},
journal = {British journal of nursing (Mark Allen Publishing)},
volume = {34},
number = {1},
pages = {8-12},
doi = {10.12968/bjon.2025.0156},
pmid = {39792104},
issn = {2052-2819},
}
@article {pmid39792005,
year = {2025},
author = {Yang, W and Li, T and An, S and Chen, R and Zhao, Y and Cui, J and Zhang, M and Lu, J and Tian, Y and Bao, L and Zhao, P},
title = {Ligilactobacillus salivarius LZZAY01 accelerated autophagy and apoptosis in colon cancer cells and improved gut microbiota in CAC mice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0186124},
doi = {10.1128/spectrum.01861-24},
pmid = {39792005},
issn = {2165-0497},
abstract = {Colorectal cancer (CRC) is one of the malignant tumors globally, with high morbidity and mortality rates. The mainstay treatment of CRC includes surgery, radiotherapy, and chemotherapy. However, these treatments are associated with a high recurrence rate, poor prognosis, and highly toxic side effects. The probiotics have the potential to prevent CRC, and they display a favorable safety performance. Probiotics could provide a potential strategy to prevent and treat CRC. The impact of LZZAY01 on cancer cell lines CT-26, HCT-116, and SW-620 was evaluated by conducting cytotoxicity and clonogenicity tests. A model of colitis-associated cancer (CAC) was established in C57BL/6j mice following induction with AOM/DSS. The levels of autophagy and apoptosis proteins, tight junction proteins, and inflammatory factors were detected by western blotting, immunofluorescence assay, and enzyme-linked immunosorbent assay. High-throughput sequencing of gut 16S rRNA was performed to analyze the abundance and diversity of the gut microbiome. LZZAY01, a new strain of Ligilactobacillus salivarius, was certified by an evolutionary tree and average nucleotide identity. LZZAY01 enhanced autophagy and apoptosis in CT-26, HCT-116, and SW-620 cell lines. It preserved the integrity of the intestinal barrier by regulating the tight junction protein ZO-1 and claudin-1. The tumor necrosis factor-α and interleukin-6 were reduced by LZZAY01. The abundance and diversity of the intestinal microbiota were enhanced, especially the beneficial bacterial species maintaining the balance of the intestinal flora such as Bifidobacterium and Lactobacillus. L. salivarius LZZAY01 improved CAC via suppressing the growth of colon cancer cells, promoting autophagy and apoptosis, enhancing intestinal tight junctions, reducing intestinal barrier degradation, modifying the gut microbiota abundance, and decreasing inflammatory reactions.IMPORTANCEAlthough similar probiotics have been shown to have anticancer potential in colorectal cancer (CRC), there is a paucity of research related to the preventive function of probiotics against CRC. And there are fewer studies about the mechanism of probiotics' preventive effects on CRC. The regulation of tumor cell proliferation and apoptosis by the active ingredients of probiotics may be one of the mechanisms of their prevention of CRC. In this study, we explored the effects of L. salivarius LZZAY01 on autophagy and apoptosis of colon cancer cells in vitro and in vivo and proposed a possible mechanism for the prevention of CRC by probiotics.},
}
@article {pmid39791908,
year = {2025},
author = {Johnke, J and Zimmermann, J and Stegemann, T and Langel, D and Franke, A and Thingholm, L and Schulenburg, H},
title = {Caenorhabditis nematodes influence microbiome and metabolome characteristics of their natural apple substrates over time.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0153324},
doi = {10.1128/msystems.01533-24},
pmid = {39791908},
issn = {2379-5077},
abstract = {The microbiomes of host organisms and their direct source environments are closely linked and key for shaping microbial community dynamics. The relationship between these linked dynamics is largely unexplored because source substrates are usually unavailable. To address this current knowledge gap, we employed bacteriovorous Caenorhabditis nematodes as a unique model system, for which source substrates like rotting apples can be easily collected. We compared single host microbiomes with their corresponding apple source substrates, as well as nematode-free substrates, over a 2-year sampling period in the botanical garden in Kiel, Germany. We found that single worms have unique microbiomes, which overlap most strongly with nematodes from the same source apple. A comparison to previous, related work revealed that variation in microbiome composition of natural Caenorhabditis isolates is significantly influenced by the substrate type, from which worms were obtained (e.g., fruits or compost). Our current sampling further showed that microbiome assembly is mostly driven by dispersal limitation. Importantly, two independent analysis approaches consistently suggest that worm microbiomes significantly influence characteristics of the apple microbiomes, possibly indicating niche construction by nematodes. Moreover, combining apple microbiome and metabolome data, we identified individual microbes and specific compounds indicative of fruit ripening that are significantly associated with nematode presence. In conclusion, our study elucidates the complex relationship between host microbiomes and their directly connected substrate microbiomes. Our analyses underscore the significant influence of nematode microbiomes on shaping the apple microbiome and, consequently, the fruit's metabolic capacity, thereby enhancing our general understanding of host-microbiome interactions in their natural habitat.IMPORTANCEAlmost all complex organisms are host to a microbial community, the microbiome. This microbiome can influence diverse host functions, such as food processing, protection against parasites, or development. The relationship between host and microbiome critically depends on the assembly of the microbial community, which may be shaped by microbes in the directly linked environment, the source microbiome. This assembly process is often not well understood because of the unavailability of source substrates. Here, we used Caenorhabditis nematodes as a model system that facilitates a direct comparison of host and source microbiomes. Based on a 2-year sampling period, we identified (i) a clear link between assembly dynamics of host and source microbiomes, (ii) a significant influence of nematode microbiomes on apple microbiomes, and (iii) specific microbes and compounds that are associated with the presence of nematodes in the sampled substrates. Overall, our study enhances our understanding of microbiome assembly dynamics and resulting functions.},
}
@article {pmid39791890,
year = {2025},
author = {Soborowski, AL and Hackley, RK and Hwang, S and Zhou, G and Dulmage, KA and Schönheit, P and Daniels, C and Bisson-Filho, AW and Marchfelder, A and Maupin-Furlow, JA and Allers, T and Schmid, AK},
title = {Genomic re-sequencing reveals mutational divergence across genetically engineered strains of model archaea.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0108424},
doi = {10.1128/msystems.01084-24},
pmid = {39791890},
issn = {2379-5077},
abstract = {UNLABELLED: Archaeal molecular biology has been a topic of intense research in recent decades as their role in global ecosystems, nutrient cycles, and eukaryotic evolution comes to light. The hypersaline-adapted archaeal species Halobacterium salinarum and Haloferax volcanii serve as important model organisms for understanding archaeal genomics, genetics, and biochemistry, in part because efficient tools enable genetic manipulation. As a result, the number of strains in circulation among the haloarchaeal research community has increased in recent decades. However, the degree of genetic divergence and effects on genetic integrity resulting from the creation and inter-lab transfer of novel lab stock strains remain unclear. To address this, we performed whole-genome re-sequencing on a cross-section of wild-type, parental, and knockout strains in both model species. Integrating these data with existing repositories of re-sequencing data, we identify mutations that have arisen in a collection of 60 strains, sampled from two species across eight different labs. Independent of sequencing, we construct strain lineages, identifying branch points and significant genetic events in strain history. Combining this with our sequencing data, we identify small clusters of mutations that definitively separate lab strains. Additionally, an analysis of gene knockout strains suggests that roughly one in three strains currently in use harbors second-site mutations of potential phenotypic impact. Overall, we find that divergence among lab strains is thus far minimal, though as the archaeal research community continues to grow, careful strain provenance and genomic re-sequencing are required to keep inter-lab divergence to a minimum, prevent the compounding of mutations into fully independent lineages, and maintain the current high degree of reproducible research between lab groups.<br><br>IMPORTANCE: Archaea are a domain of microbial life whose member species play a critical role in the global carbon cycle, climate regulation, the human microbiome, and persistence in extreme habitats. In particular, hypersaline-adapted archaea are important, genetically tractable model organisms for studying archaeal genetics, genomics, and biochemistry. As the archaeal research community grows, keeping track of the genetic integrity of strains of interest is necessary. In particular, routine genetic manipulations and the common practice of sharing strains between labs allow mutations to arise in lab stocks. If these mutations affect cellular processes, they may jeopardize the reproducibility of work between research groups and confound the results of future studies. In this work, we examine DNA sequences from 60 strains across two species of archaea. We identify shared and unique mutations occurring between and within strains. Independently, we trace the lineage of each strain, identifying which genetic manipulations lead to observed off-target mutations. While overall divergence across labs is minimal so far, our work highlights the need for labs to continue proper strain husbandry.},
}
@article {pmid39791884,
year = {2025},
author = {Sterrett, JD and Quinn, KD and Doenges, KA and Nusbacher, NM and Levens, CL and Armstrong, ML and Reisdorph, RM and Smith, H and Saba, LM and Kuhn, KA and Lozupone, CA and Reisdorph, NA},
title = {Appearance of green tea compounds in plasma following acute green tea consumption is modulated by the gut microbiome in mice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0179924},
doi = {10.1128/spectrum.01799-24},
pmid = {39791884},
issn = {2165-0497},
abstract = {UNLABELLED: Studies have suggested that phytochemicals in green tea have systemic anti-inflammatory and neuroprotective effects. However, the mechanisms behind these effects are poorly understood, possibly due to the differential metabolism of phytochemicals resulting from variations in gut microbiome composition. To unravel this complex relationship, our team utilized a novel combined microbiome analysis and metabolomics approach applied to low complexity microbiome (LCM) and human colonized (HU) gnotobiotic mice treated with an acute dose of powdered matcha green tea. A total of 20 LCM mice received 10 distinct human fecal slurries for an n = 2 mice per human gut microbiome; 9 LCM mice remained un-colonized with human slurries throughout the experiment. We performed untargeted metabolomics on green tea and plasma to identify green tea compounds that were found in the plasma of LCM and HU mice that had consumed green tea. 16S ribosomal RNA gene sequencing was performed on feces of all mice at study end to assess microbiome composition. We found multiple green tea compounds in plasma associated with microbiome presence and diversity (including acetylagmatine, lactiflorin, and aspartic acid negatively associated with diversity). Additionally, we detected strong associations between bioactive green tea compounds in plasma and specific gut bacteria, including associations between spiramycin and Gemmiger and between wildforlide and Anaerorhabdus. Notably, some of the physiologically relevant green tea compounds are likely derived from plant-associated microbes, highlighting the importance of considering foods and food products as meta-organisms. Overall, we describe a novel workflow for discovering relationships between individual food compounds and the composition of the gut microbiome.<br><br>IMPORTANCE: Foods contain thousands of unique and biologically important compounds beyond the macro- and micro-nutrients listed on nutrition facts labels. In mammals, many of these compounds are metabolized or co-metabolized by the community of microbes in the colon. These microbes may impact the thousands of biologically important compounds we consume; therefore, understanding microbial metabolism of food compounds will be important for understanding how foods impact health. We used metabolomics to track green tea compounds in plasma of mice with and without complex microbiomes. From this, we can start to recognize certain groups of green tea-derived compounds that are impacted by mammalian microbiomes. This research presents a novel technique for understanding microbial metabolism of food-derived compounds in the gut, which can be applied to other foods.},
}
@article {pmid39791681,
year = {2025},
author = {Quansah, M and David, MA and Martins, R and El-Omar, E and Aliberti, SM and Capunzo, M and Jensen, SO and Tayebi, M},
title = {The Beneficial Effects of Lactobacillus Strains on Gut Microbiome in Alzheimer's Disease: A Systematic Review.},
journal = {Healthcare (Basel, Switzerland)},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/healthcare13010074},
pmid = {39791681},
issn = {2227-9032},
support = {01//Western Sydney University/ ; },
abstract = {BACKGROUND/OBJECTIVES: Growing evidence suggests that the gut-brain axis influences brain function, particularly the role of intestinal microbiota in modulating cognitive processes. Probiotics may alter brain function and behavior by modulating gut microbiota, with implications for neurodegenerative diseases like Alzheimer's disease (AD). The purpose of this review is to systematically review the current literature exploring the effects of probiotic supplementation on gut microbiota and cognitive function in AD and mild cognitive impairment (MCI).<br><br>METHODS: A comprehensive literature search was conducted across PubMed/Medline, Embase, and Scopus to identify relevant randomized controlled trials (RCTs) from inception to 20 August 2024. The search focused on comparing outcomes between intervention and control/placebo groups. Data searches, article selection, data extraction, and risk of bias assessment were performed in accordance with Cochrane guidelines.<br><br>PROSPERO registration no: CRD42023446796.<br><br>RESULTS: Data from four RCTs involving 293 Individuals (AD and MCI patients) receiving mainly Lactobacillus and Bifidobacterium strains showed some beneficial effects on cognitive function, altered gut microbiota composition, and positively affected metabolic biomarkers. However, variability in microbiota assessment across studies limits the interpretation of results. The limited number and quality of the existing studies make it difficult to draw definitive conclusions from the data. Additional high-quality research is clearly needed.<br><br>CONCLUSIONS: Probiotics show promise as an adjunctive intervention for cognitive decline, but larger, long-term trials are needed to confirm their efficacy and clinical applicability in neurodegenerative diseases like AD.},
}
@article {pmid39791454,
year = {2025},
author = {Xiao, X and Li, K and Shi, Z and Song, Z},
title = {Tongue Coating Metabolites and Microbiome Associated With Intra-Oral Halitosis.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.15255},
pmid = {39791454},
issn = {1601-0825},
support = {20224Y0390//Project of Shanghai Municipal Health Commission/ ; SSH-2023-05//Shanghai Stomatological Hospital Foundation/ ; },
}
@article {pmid39791452,
year = {2025},
author = {Gu, Y and Liu, T and Al-Ansi, W and Qian, H and Fan, M and Li, Y and Wang, L},
title = {Functional microbiome assembly in food environments: addressing sustainable development challenges.},
journal = {Comprehensive reviews in food science and food safety},
volume = {24},
number = {1},
pages = {e70074},
doi = {10.1111/1541-4337.70074},
pmid = {39791452},
issn = {1541-4337},
support = {//Ministry of Science and Technology of the People's Republic of China/ ; //National Natural Science Foundation of China/ ; //Qinglan Project of Jiangsu Province of China/ ; //Earmarked Fund for China Agriculture Research System/ ; 2020QNRC001//the Young Elite Scientists Sponsorship Program by CAST/ ; },
mesh = {*Microbiota/physiology ; *Sustainable Development ; *Food Microbiology ; Bacteria ; },
abstract = {The global food system faces numerous challenges, creating an urgent need for sustainable reform. Functional microbiome assemblies offer transformative potential by endowing microbial foods with diverse, beneficial characteristics. These assemblies can dynamically influence specific food systems, positioning them as a promising approach for reshaping food production. However, the current applications and types of microbiome assemblies in foods remain limited, with a lack of effective screening and regulatory methods. This review introduces the functions and practical approaches for implementing microbiome assemblies in food systems alongside future directions for enhancing their applications. Several ecological studies evaluated how to regulate functional output and revealed that environmental conditions, which shape the niche for species survival, significantly influenced the functional output of microbiomes. Building on this theoretical foundation, this review presents a model for functional output comprising niche conditions, functional gene codes, and corresponding functional outputs. This model is illustrated with examples to explore sustainable applications and regulatory mechanisms for functional microbiome assemblies. By highlighting the roles of functional outputs in food systems and examining the potential for food environments to induce and modulate microbiome functions, this review provides a roadmap to address emerging challenges in food sustainability.},
}
@article {pmid39790219,
year = {2024},
author = {Sharma, NK and Sarode, SC and Sekar, G and Sonawane, K and Bomle, D},
title = {Challenges in Metabolite Biomarkers as Avenues of Diagnosis and Prognosis of Cancer.},
journal = {Journal of cancer prevention},
volume = {29},
number = {4},
pages = {105-112},
pmid = {39790219},
issn = {2288-3649},
abstract = {Given the evolutionary nature of tumor complexities and heterogeneity, the early diagnosis of cancer encounters various challenges. Complexities at the level of metabolite reprogramming are compelling in the background of invasiveness, metastasis, drug- and radiation-induced metabolic alterations, immunotherapy-influenced changes, and pro-tumor niche including microbiome. Therefore, it is crucial to examine both current and future obstacles associated with early cancer detection specifically in the context of tumor metabolite biomarkers at preclinical and clinical levels. In conclusion, the significance of tumor metabolite biomarkers must be aligned with a comprehensive approach to achbieve diagnosis and prognosis of cancer patients by securing solutions to formidable challenges.},
}
@article {pmid39789999,
year = {2025},
author = {Kong, W and Pan, Y and Wu, Y and Hu, Y and Jiang, Z and Tian, X and Bi, S and Wang, S and Feng, F and Jin, Y and Li, J and Li, H and Wang, Y and Liang, H and Tang, W and Liu, D},
title = {Microdose Cocktail Study Reveals the Activity and Key Influencing Factors of OATP1B, P-Gp, BCRP, and CYP3A in End-Stage Renal Disease Patients.},
journal = {Clinical pharmacology and therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1002/cpt.3546},
pmid = {39789999},
issn = {1532-6535},
abstract = {OATP1B, P-gp, BCRP, and CYP3A are the most contributing drug-metabolizing enzymes or transporters (DMETs) for commonly prescribed medication. Their activities may change in end-stage renal disease (ESRD) patients with large inter-individual variabilities (IIVs), leading to altered substrate drug exposure and ultimately elevated safety risk. However, the changing extent and indictive influencing factors are not quantified so far. Here, a microdose cocktail regimen containing five sensitive substrate drugs (pitavastatin, dabigatran etexilate, rosuvastatin, midazolam, and atorvastatin) for these DMETs was administrated to Chinese healthy volunteers and ESRD patients. Drug pharmacokinetics profiles were determined, together with physiological, pharmacogenetic, and gut microbiome signature. Population pharmacokinetic and machine learning model were established to identify key influencing factors and quantify their contribution to drug exposure change. The exposure of pitavastatin, dabigatran, rosuvastatin, and atorvastatin increased to 1.8-, 3.1-, 1.1-, and 1.3-fold, respectively, whereas midazolam exposure decreased by 72% in ESRD patients. Notably, in addition to disease state, the relative abundance of genus Veillonella and Clostridium_XIVb were firstly identified as significant influencing factors for PTV and RSV apparent clearance, respectively, suggesting their indicative role for OATP and BCRP activity evaluation. Moreover, several genera were found to strongly associate with drug clearance and reduce unexplained IIVs. Accordingly, it was estimated that OATP1B and intestine P-gp activity decreased by 35-75% and 29-44%, respectively, whereas BCRP and CYP3A4 activity may upregulate to some extent. Our study provides a quantitative and mechanistic understanding of individual DMET activity and could support precision medicine of substrate drugs in ESRD patients.},
}
@article {pmid39789866,
year = {2025},
author = {Mehvish, HB and Zhang, S and Liang, Y and Sun, D and Qiu, X and Qu, K and Qin, X and Li, J and Yan, F and Lang, C and Xu, L and Wang, G and Chen, J and He, B and Zhang, K and Wu, W},
title = {Enhanced Osteoporosis Treatment via Nano Drug Coating Encapsulating Lactobacillus rhamnosus GG.},
journal = {ACS applied materials &amp; interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.4c17985},
pmid = {39789866},
issn = {1944-8252},
abstract = {Osteoporosis is the most common systemic skeletal disorder, particularly associated with aging and postmenopausal women. With the growing knowledge about the gut-bone axis, the therapeutic strategies for osteoporosis have been shifted toward regulating gut microbiota to promote positive bone metabolism. AlthoughLactobacillus rhamnosus GG (LGG) is widely reported to positively regulate bone metabolism by restoring the dysbiotic microbiome, oral administration is associated with sensitivity to gastric fluid and low bioavailability. Other studies also demonstrated that bisphosphonates ameliorate osteoporosis by directly regulating bone metabolism, especially inhibiting osteoclast activity. However, the side effects caused by bisphosphonate treatment still represent a significant problem. In this study, we assembled alendronate, a clinically used bisphosphonate, with DSPE-phospholipid nanoencapsulation and LGG (ADB), to protect LGG from the acidic environment of the stomach, while simultaneously reducing the gastrointestinal side effects associated with the oral administration of alendronate. We further investigated the potential of these DSPE-phospholipid nanoencapsulated bacteria ADB to repair osteoporotic bone deterioration, and their ability to regulate gut microbiota in vivo, which is strongly associated with the intrinsic environment. Compared with the same dosage of LGG and alendronate alone, ADB positively regulated bone metabolism, and osteoporosis was significantly revised in ovariectomized mice models.},
}
@article {pmid39789616,
year = {2025},
author = {Casaro, S and Prim, JG and Gonzalez, TD and Cunha, F and Silva, ACM and Yu, H and Bisinotto, RS and Chebel, RC and Santos, JEP and Nelson, CD and Jeon, SJ and Bicalho, RC and Driver, JP and Galvão, KN},
title = {Multi-omics integration and immune profiling identify possible causal networks leading to uterine microbiome dysbiosis in dairy cows that develop metritis.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {4},
pmid = {39789616},
issn = {2524-4671},
support = {2019-67015-29836//U.S. Department of Agriculture/ ; 2019-67015-29836//U.S. Department of Agriculture/ ; 2019-67015-29836//U.S. Department of Agriculture/ ; 2019-67015-29836//U.S. Department of Agriculture/ ; 2019-67015-29836//U.S. Department of Agriculture/ ; 2019-67015-29836//U.S. Department of Agriculture/ ; 2019-67015-29836//U.S. Department of Agriculture/ ; 2019-67015-29836//U.S. Department of Agriculture/ ; },
abstract = {BACKGROUND: Cows that develop metritis experience dysbiosis of their uterine microbiome, where opportunistic pathogens overtake uterine commensals. An effective immune response is critical for maintaining uterine health. Nonetheless, periparturient cows experience immune dysregulation, which seems to be intensified by prepartum over-condition. Herein, Bayesian networks were applied to investigate the directional correlations between prepartum body weight (BW), BW loss, pre- and postpartum systemic immune profiling and plasma metabolome, and postpartum uterine metabolome and microbiome.<br><br>RESULTS: The Bayesian network analysis showed a positive directional correlation between prepartum BW, prepartum BW loss, and plasma fatty acids at parturition, suggesting that heavier cows were in lower energy balance than lighter cows. There was a positive directional correlation between prepartum BW, prepartum systemic leukocyte death, immune activation, systemic inflammation, and metabolomic changes associated with oxidative stress prepartum and at parturition. Immune activation and systemic inflammation were characterized by increased proportion of circulating polymorphonuclear cells (PMN) prepartum, B-cell activation at parturition, interleukin-8 prepartum and at parturition, and interleukin-1&#x3b2; at parturition. These immune changes together with plasma fatty acids at parturition had a positive directional correlation with PMN extravasation postpartum, which had a positive directional correlation with uterine metabolites associated with tissue damage. These results suggest that excessive PMN migration to the uterus leads to excessive endometrial damage. The aforementioned changes had a positive directional correlation with Fusobacterium, Porphyromonas, and Bacteroides in cows that developed metritis, suggesting that excessive tissue damage may disrupt physical barriers or increase substrate availability for bacterial growth.<br><br>CONCLUSIONS: This work provides robust mechanistic hypotheses for how prepartum BW may impact peripartum immune and metabolic profiles, which may lead to uterine opportunistic pathogens overgrowth and metritis development.},
}
@article {pmid39789543,
year = {2025},
author = {Lederer, AK and Görrissen, N and Nguyen, TT and Kreutz, C and Rasel, H and Bartsch, F and Lang, H and Endres, K},
title = {Exploring the effects of gut microbiota on cholangiocarcinoma progression by patient-derived organoids.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {34},
pmid = {39789543},
issn = {1479-5876},
mesh = {*Cholangiocarcinoma/microbiology/pathology ; Humans ; *Organoids/pathology/microbiology ; *Gastrointestinal Microbiome ; *Disease Progression ; *Bile Duct Neoplasms/pathology/microbiology ; Animals ; Models, Biological ; },
abstract = {BACKGROUND: Recent research indicates a role of gut microbiota in development and progression of life-threatening diseases such as cancer. Carcinomas of the biliary ducts, the so-called cholangiocarcinomas, are known for their aggressive tumor biology, implying poor prognosis of affected patients. An impact of the gut microbiota on cholangiocarcinoma development and progression is plausible due to the enterohepatic circulation and is therefore the subject of scientific debate, however evidence is still lacking. This review aimed to discuss the suitability of complex cell culture models to investigate the role of gut microbiota in cholangiocarcinoma progression.<br><br>MAIN BODY: Clinical research in this area is challenging due to poor comparability of patients and feasibility reasons, which is why translational models are needed to understand the basis of tumor progression in cholangiocarcinoma. A promising approach to investigate the influence of gut microbiota could be an organoid model. Organoids are 3D cell models cultivated in a modifiable and controlled condition, which can be grown from tumor tissue. 3D cell models are able to imitate physiological and pathological processes in the human body and thus contribute to a better understanding of health and disease.<br><br>CONCLUSION: The use of complex cell cultures such as organoids and organoid co-cultures might be powerful and valuable tools to study not only the growth behavior and growth of cholangiocarcinoma cells, but also the interaction with the tumor microenvironment and with components of the gut microbiota.},
}
@article {pmid39789296,
year = {2025},
author = {Seneff, S and Kyriakopoulos, AM},
title = {Taurine prevents mitochondrial dysfunction and protects mitochondria from reactive oxygen species and deuterium toxicity.},
journal = {Amino acids},
volume = {57},
number = {1},
pages = {6},
pmid = {39789296},
issn = {1438-2199},
support = {6950759//Quanta Computer, Inc./ ; },
mesh = {*Taurine/pharmacology/metabolism ; Humans ; *Mitochondria/metabolism/drug effects ; *Deuterium ; *Reactive Oxygen Species/metabolism ; Oxidative Stress/drug effects ; Animals ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Taurine, although not a coding amino acid, is the most common free amino acid in the body. Taurine has multiple and complex functions in protecting mitochondria against oxidative-nitrosative stress. In this comprehensive review paper, we introduce a novel potential role for taurine in protecting from deuterium (heavy hydrogen) toxicity. This can be of crucial impact to either normal or cancer cells that have highly different mitochondrial redox status. Deuterium is an isotope of hydrogen with a neutron as well as a proton, making it about twice as heavy as hydrogen. We first explain the important role that the gut microbiome and the gut sulfomucin barrier play in deuterium management. We describe the synergistic effects of taurine in the gut to protect against the deleterious accumulation of deuterium in the mitochondria, which disrupts ATP synthesis by ATPase pumps. Moreover, taurine's derivatives, N-chlorotaurine (NCT) and N-bromotaurine (NBrT), produced through spontaneous reaction of taurine with hypochlorite and hypobromite, have fascinating regulatory roles to protect from oxidative stress and beyond. We describe how taurine could potentially alleviate deuterium stress, primarily through metabolic collaboration among various gut microflora to produce deuterium depleted nutrients and deuterium depleted water, and in this way protect against leaky gut barrier, inflammatory bowel disease, and colon cancer.},
}
@article {pmid39789196,
year = {2025},
author = {Vaupel, A and Küsters, M and Toups, J and Herwig, N and Bösel, B and Beule, L},
title = {Trees shape the soil microbiome of a temperate agrosilvopastoral and syntropic agroforestry system.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1550},
pmid = {39789196},
issn = {2045-2322},
support = {28DE204D21//Bundesministerium f&#xfc;r Ern&#xe4;hrung und Landwirtschaft/ ; 28DE204D21//Bundesministerium f&#xfc;r Ern&#xe4;hrung und Landwirtschaft/ ; 28DE204D21//Bundesanstalt f&#xfc;r Landwirtschaft und Ern&#xe4;hrung/ ; 28DE204D21//Bundesanstalt f&#xfc;r Landwirtschaft und Ern&#xe4;hrung/ ; },
mesh = {*Soil Microbiology ; *Microbiota ; *Trees/microbiology ; *Forestry/methods ; Agriculture/methods ; Soil/chemistry ; Bacteria/classification/growth &amp; development ; Crops, Agricultural/microbiology/growth &amp; development ; Fungi ; Populus/microbiology/growth &amp; development ; },
abstract = {Agroforestry systems are multifunctional land-use systems that promote soil life. Despite their large potential spatio-temporal complexity, the majority of studies that investigated soil organisms in temperate cropland agroforestry systems focused on rather non-complex systems. Here, we investigated the topsoil and subsoil microbiome of two complex and innovative alley cropping systems: an agrosilvopastoral system combining poplar trees, crops, and livestock and a syntropic agroforestry system combining 35 tree and shrub species with forage crops. Increasing soil depth resulted in a decline of bacterial and fungal richness and a community shift towards oligotrophic taxa in both agroforestry systems, which we attribute to resource-deprived conditions in subsoil. At each soil depth, the microbiome of the tree rows was compositionally distinct from the crop rows. We detected a shift towards beneficial microorganisms as well as a decline in putative phytopathogens under the trees as compared to the crop rows. Finally, based on our results on community dissimilarity, we found that compared to an open cropland without trees, spatial heterogeneity introduced by the tree rows in the agrosilvopastoral system translated into a compositionally less homogeneous soil microbiome, highlighting the potential of agroforestry to counteract the homogenization of the soil microbiome through agriculture.},
}
@article {pmid39789171,
year = {2025},
author = {Barman, I and Seo, H and Kim, S and Rahim, MA and Yoon, Y and Hossain, MS and Shuvo, MSH and Song, HY},
title = {Isolation of New Strains of Lactic Acid Bacteria from the Vaginal Microbiome of Postmenopausal Women and their Probiotic Characteristics.},
journal = {Current microbiology},
volume = {82},
number = {2},
pages = {76},
pmid = {39789171},
issn = {1432-0991},
support = {20018499//Ministry of Trade, Industry and Energy/ ; RS-2023-00219563//Ministry of Science and ICT, South Korea/ ; Soon Chun Hyang University Research Fund//Soon Chun Hyang University/ ; },
mesh = {Female ; *Probiotics ; Humans ; *Vagina/microbiology ; *Lactobacillales/genetics/isolation &amp; purification/classification/metabolism ; *Postmenopause ; Bacterial Adhesion ; Microbial Sensitivity Tests ; Microbiota ; Anti-Bacterial Agents/pharmacology ; Cytokines/metabolism ; Macrophages/microbiology ; },
abstract = {Lactic acid bacteria (LAB), traditionally consumed as fermented foods, are now being applied to the medical field beyond health-functional food as probiotics. Therefore, it is necessary to continuously discover and evaluate new strains with suitable probiotic characteristics, mainly focusing on safety. In this study, we isolated eight new strains from postmenopausal vaginal fluid using culturomics approaches, an emerging area of interest. Data showed that most strains possessed significant cell surface hydrophobicity (≥ 76%), auto-aggregation capacity (17 to 61%), strong adhesion activity (8 to 34%), and excellent resistance to gastric acid, bile salt, and digestive enzyme, enhancing their survival in the gastrointestinal tract. Moreover, the strains exhibited functional characteristics, including substantial antibacterial activity with a minimal inhibitory concentration (MIC) ranging from 12.5 to 50%. They also harbored bacteriocins genes, produced short-chain fatty acids (acetate and propionate), exhibited significant phagocytic activity, possessed high antioxidative properties, rapidly depleted sodium nitrite, and exhibited proteolysis and β-glucosidase activity. In addition, heat-killed LAB strains significantly reduced the gene expressions of proinflammatory cytokines such as IL-β, IL-6, and iNOS in macrophages. Safety assessment revealed no cytotoxicity in macrophage cell lines. All strains tested negative for biogenic amine or H2O2 production, displayed no gelatinase or hemolytic activity, lacked virulence genes or detrimental enzymes, and displayed antibiotic susceptibility. In summary, these newly isolated strains demonstrate excellent probiotic functionality with a strong focus on safety, making them promising candidates for future drug development in the relevant fields.},
}
@article {pmid39789014,
year = {2025},
author = {Adelfio, M and Callen, GE and Diaz, AR and Paster, BJ and He, X and Hasturk, H and Ghezzi, CE},
title = {Underscoring long-term host-microbiome interactions in a physiologically relevant gingival tissue model.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {9},
pmid = {39789014},
issn = {2055-5008},
support = {R03DE030224//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; Ralph E. Powe Junior Faculty Enhancement Awards//Oak Ridge Associated Universities (ORAU)/ ; },
mesh = {Humans ; *Gingiva/microbiology ; *Microbiota ; *Host Microbial Interactions ; Bacteria/classification/genetics ; Mouth/microbiology ; Models, Biological ; },
abstract = {The human body houses many distinct and interconnecting microbial populations with long-lasting systemic effects, where the oral cavity serves as a pathogens' reservoir. The correlation of different disease states strongly supports the need to understand the interplay between the oral tissue niche and microbiome. Despite efforts, the recapitulation of gingival architecture and physiological characteristics of the periodontal niche has yet to be accomplished by traditional cultural strategies. Here, we are showing for the first time the investigation of host-microbiome interactions in healthy conditions within a human oral tissue model over seven days. Our results indicated long-term host and microbiome viability, host barrier integrity, phenotypic functional response, and preservation of healthy microbial populations and interbacterial dialogs. This in vitro platform can maintain tissue homeostasis at the interface of the periodontal niche, thus, offering opportunities to identify predictive disease biomarkers and to develop intervention strategies to promote oral and overall health.},
}
@article {pmid39789003,
year = {2025},
author = {Almási, &#xc9;DH and Eisenhard, L and Osbelt, L and Lesker, TR and Vetter, AC and Knischewski, N and Bielecka, AA and Gronow, A and Muthukumarasamy, U and Wende, M and Tawk, C and Neumann-Schaal, M and Brönstrup, M and Strowig, T},
title = {Klebsiella oxytoca facilitates microbiome recovery via antibiotic degradation and restores colonization resistance in a diet-dependent manner.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {551},
pmid = {39789003},
issn = {2041-1723},
support = {01KI1824//Joint Programming Initiative on Antimicrobial Resistance (Joint Programming Initiative for Antimicrobial Resistance)/ ; 01KI213//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 06.826//Deutsches Zentrum f&#xfc;r Infektionsforschung (German Center for Infection Research)/ ; 390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Klebsiella oxytoca/drug effects/metabolism ; Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; *Anti-Bacterial Agents/pharmacology ; *Ampicillin/pharmacology ; *Klebsiella pneumoniae/drug effects ; Mice ; *Klebsiella Infections/microbiology/drug therapy ; *Mice, Inbred C57BL ; Diet, Western/adverse effects ; Diet, High-Fat/adverse effects ; Male ; beta-Lactamases/metabolism ; Female ; },
abstract = {Competition among bacteria for carbohydrates is pivotal for colonization resistance (CR). However, the impact of Western-style diets on CR remains unclear. Here we show how the competition between Klebsiella oxytoca and Klebsiella pneumoniae is modulated by consuming one of three Western-style diets characterized by high-starch, high-sucrose, or high-fat/high-sucrose content. In vivo competition experiments in ampicillin-treated mice reveal that K. oxytoca promotes K. pneumoniae decolonization on all dietary backgrounds. However, mice on the high-fat/high-sucrose diet show reduced pathogen clearance. Microbiome analysis reveals that the combination of Western-style diets and ampicillin treatment synergize in microbiome impairment, particularly noticeable in the presence of high dietary fat content. The diet-independent degradation of ampicillin in the gut lumen by K. oxytoca beta-lactamases facilitates rapid commensal outgrowth, which is required for subsequent pathogen clearance. Our findings provide insights into how diet modulates functional microbiome recovery and K. oxytoca-mediated pathogen elimination from the gut.},
}
@article {pmid39788996,
year = {2025},
author = {Ercumen, A and Mertens, AN and Butzin-Dozier, Z and Jung, DK and Ali, S and Achando, BS and Rao, G and Hemlock, C and Pickering, AJ and Stewart, CP and Tan, ST and Grembi, JA and Benjamin-Chung, J and Wolfe, M and Ho, GG and Rahman, MZ and Arnold, CD and Dentz, HN and Njenga, SM and Meerkerk, T and Chen, B and Nadimpalli, M and Islam, MA and Hubbard, AE and Null, C and Unicomb, L and Rahman, M and Colford, JM and Luby, SP and Arnold, BF and Lin, A},
title = {Water, sanitation, handwashing, and nutritional interventions can reduce child antibiotic use: evidence from Bangladesh and Kenya.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {556},
pmid = {39788996},
issn = {2041-1723},
support = {OPPGD759//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; },
mesh = {Kenya/epidemiology ; Humans ; Bangladesh/epidemiology ; *Anti-Bacterial Agents/therapeutic use/administration &amp; dosage ; *Hand Disinfection ; *Sanitation ; Child, Preschool ; Infant ; Male ; Female ; },
abstract = {Antibiotics can trigger antimicrobial resistance and microbiome alterations. Reducing pathogen exposure and undernutrition can reduce infections and antibiotic use. We assess effects of water, sanitation, handwashing (WSH) and nutrition interventions on caregiver-reported antibiotic use in Bangladesh and Kenya, longitudinally measured at three timepoints among birth cohorts (ages 3-28 months) in a cluster-randomized trial. Over 50% of children used antibiotics at least once in the 90 days preceding data collection. In Bangladesh, the prevalence of antibiotic use was 10-14% lower in groups receiving WSH (prevalence ratio [PR] = 0.90 (0.82-0.99)), nutrition (PR = 0.86 (0.78-0.94)), and nutrition+WSH (PR = 0.86 (0.79-0.93)) interventions. The prevalence of using antibiotics multiple times was 26-35% lower in intervention arms. Reductions were largest when the birth cohort was younger. In Kenya, interventions did not affect antibiotic use. In this work, we show that improving WSH and nutrition can reduce antibiotic use. Studies should assess whether such reductions translate to reduced antimicrobial resistance.},
}
@article {pmid39788961,
year = {2025},
author = {Banerjee, G and Papri, SR and Huang, H and Satapathy, SK and Banerjee, P},
title = {Deep sequencing-derived Metagenome Assembled Genomes from the gut microbiome of liver transplant patients.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {39},
pmid = {39788961},
issn = {2052-4463},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Liver Transplantation ; *Metagenome ; High-Throughput Nucleotide Sequencing ; Akkermansia ; Fatty Liver/microbiology ; },
abstract = {Recurrence of metabolic dysfunction-associated steatotic liver disease (MASLD) after liver transplantation (LT) is a continuing concern. The role of gut microbiome dysbiosis in MASLD initiation and progression has been well established. However, there is a lack of comprehensive gut microbiome shotgun sequence data for patients experiencing MASLD recurrence after LT. In this data descriptor, we describe a dataset of deep metagenomic sequences of a well-defined LT recipient population. Community-based analysis revealed a high abundance of Akkermansia muciniphila, consistently observed in most patient samples with a low (0-2) MASLD Activity Score (NAS). We constructed 357 metagenome-assembled genomes (MAGs), including 220 high-quality MAGs (>90% completion). The abundance of different species of Bacteroides MAGs dominated in patient samples with NAS > 5 ("definite MASH"). In contrast, the MAGs of A. muciniphila, Akkermansia sp., and Blutia sp. dominated in samples from patients without MASH (NAS = 0-2). In addition, the phylogenetic analysis of A. muciniphila and Akkermansia sp. MAGs identified two new phylogroups of Akkermansia that are distinct from the previously reported three phylogroups.},
}
@article {pmid39788854,
year = {2025},
author = {Yu, YH and Crosbie, DB and Marín Arancibia, M},
title = {Pseudomonas in the spotlight: emerging roles in the nodule microbiome.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2024.12.002},
pmid = {39788854},
issn = {1878-4372},
abstract = {While rhizobia have long been recognised as the primary colonisers of legume nodules, microbiome studies have revealed the presence of other bacteria in these organs. This opinion delves into the factors shaping the nodule microbiome and explores the potential roles of non-rhizobial endophytes, focusing particularly on Pseudomonas as prominent players. We explore the mechanisms by which Pseudomonas colonise nodules, their interactions with rhizobia, and their remarkable potential to promote plant growth and protect against pathogens. Furthermore, we discuss the promising prospects of using Pseudomonas as inoculants alongside rhizobia to enhance crop growth and promote sustainable agricultural practices.},
}
@article {pmid39788824,
year = {2025},
author = {Sánchez-González, MC and Gallardo-Real, I and Gutiérrez-Sánchez, E and De-Hita-Cantalejo, C and Capote-Puente, R and Sánchez-González, JM},
title = {Diversity and composition of ocular microbiota in contact lens wearers: Efficacy of liposomal ozonated oil.},
journal = {Contact lens &amp; anterior eye : the journal of the British Contact Lens Association},
volume = {},
number = {},
pages = {102368},
doi = {10.1016/j.clae.2025.102368},
pmid = {39788824},
issn = {1476-5411},
abstract = {PURPOSE: To characterize the ocular surface microbiota in regular contact lens wearers with dry eyes and assess the effectiveness of reducing bacterial load using a liposomal ozonated oil solution.<br><br>METHODS: This prospective, longitudinal, controlled study randomized subjects into two groups. Group A (45 subjects) received hydroxypropylmethylcellulose (HPMC, Artific&#xae;), while Group B (41 subjects) received ozonated sunflower seed oil with soybean phospholipids (OSSO, Ozonest&#xae;). Microbial communities were analyzed via DNA metabarcoding of the 16S rRNA gene, and statistical analyses (alpha and beta diversity) were performed in R.<br><br>RESULTS: Both groups predominantly harbored Staphylococcus caprae, Streptococcus oralis, and Corynebacterium spp., with OSSO and HPMC users showing distinct bacterial profiles. Alpha diversity showed no significant differences, but beta diversity revealed differences in bacterial composition between the groups.<br><br>CONCLUSIONS: The results seem to indicate that the use of ozonized oil reduces the bacterial load compared to the solution used as a control.},
}
@article {pmid39788811,
year = {2025},
author = {Godoy-Vitorino, F},
title = {Solutions to expand microbiome sciences in the Caribbean Region: an insider's perspective.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.12.005},
pmid = {39788811},
issn = {1878-4380},
abstract = {The Caribbean harbors diverse genetic resources, yet microbiome research in the region remains poorly characterized. Addressing infrastructure and training challenges through collaborations and capacity building is vital. This article reflects on the obstacles facing microbiome research in the region and proposes solutions to ensure equitable participation in the global microbial research ecosystem.},
}
@article {pmid39788783,
year = {2025},
author = {Franz, K and Markó, L and Mähler, A and Chakaroun, R and Heinitz, S and Schlögl, H and Sacher, J and Steckhan, N and Dechend, R and Adams, N and Andersen, M and Glintborg, D and Viehweger, M and Bahr, LS and Forslund-Startceva, SK},
title = {Sex hormone-dependent host-microbiome interactions and cardiovascular risk (XCVD): design of a longitudinal multi-omics cohort study.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e087982},
doi = {10.1136/bmjopen-2024-087982},
pmid = {39788783},
issn = {2044-6055},
mesh = {Humans ; *Cardiovascular Diseases/microbiology/epidemiology ; Longitudinal Studies ; Male ; Female ; *Gonadal Steroid Hormones/metabolism/blood ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Transgender Persons ; Research Design ; Heart Disease Risk Factors ; Adult ; Sex Reassignment Procedures ; Multiomics ; },
abstract = {INTRODUCTION: Cardiovascular diseases (CVDs) present differently in women and men, influenced by host-microbiome interactions. The roles of sex hormones in CVD outcomes and gut microbiome in modifying these effects are poorly understood. The XCVD study examines gut microbiome mediation of sex hormone effects on CVD risk markers by observing transgender participants undergoing gender-affirming hormone therapy (GAHT), with findings expected to extrapolate to cisgender populations.<br><br>METHODS AND ANALYSES: This observational, longitudinal cohort study includes baseline, 1- and 2-year follow-ups with transgender participants beginning GAHT. It involves comprehensive phenotyping and microbiome genotyping, integrating computational analyses of high-dimensional data. Microbial diversity will be assessed using gut, skin, and oral samples via 16S rRNA and shotgun metagenomic sequencing of gut samples. Blood measurements will include sex hormones, CVD risk markers, cardiometabolic parameters, cytokines, and immune cell counts. Hair samples will be analysed for cortisol. Participants will complete online questionnaires on physical activity, mental health, stress, quality of life, fatigue, sleep, pain, and gender dysphoria, tracking medication use and diet to control for confounders. Statistical analyses will integrate phenomic, lifestyle, and multi-omic data to model health effects, testing gut microbiome mediation of CVD risk as the endocrine environment shifts between that typical for cisgender men to women and vice versa.<br><br>ETHICS AND DISSEMINATION: The study adheres to Good Clinical Practice and the Declaration of Helsinki. The protocol was approved by the Charit&#xe9; Ethical Committee (EA1/339/21). Signed informed consent will be obtained. Results will be published in peer-reviewed journals and conferences and shared as accessible summaries for participants, community groups, and the public, with participants able to view their data securely after public and patient involvement review for accessibility.<br><br>TRIAL REGISTRATION NUMBER: The XCVD study was registered on ClinicalTrials.gov (NCT05334888) as 'Sex-differential host-microbiome CVD risk - a longitudinal cohort approach (XCVD)" on 4 April 2022. Data set link can be found at https://classic.<br><br>CLINICALTRIALS: gov/ct2/show/NCT05334888.},
}
@article {pmid39788762,
year = {2025},
author = {Augustijn, QJJ and Grefhorst, A and de Groen, P and Wortelboer, K and Seegers, JFM and Gül, IS and Suenaert, P and Verheij, J and de Vos, WM and Herrema, H and Nieuwdorp, M and Holleboom, AG},
title = {Randomised double-blind placebo-controlled trial protocol to evaluate the therapeutic efficacy of lyophilised faecal microbiota capsules amended with next-generation beneficial bacteria in individuals with metabolic dysfunction-associated steatohepatitis.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e088290},
doi = {10.1136/bmjopen-2024-088290},
pmid = {39788762},
issn = {2044-6055},
mesh = {Humans ; Double-Blind Method ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Adult ; Male ; Randomized Controlled Trials as Topic ; Capsules ; Female ; Middle Aged ; Fatty Liver/therapy ; Feces/microbiology ; Freeze Drying ; },
abstract = {BACKGROUND: The spectrum of metabolic dysfunction-associated steatotic liver disease (MASLD) is highly prevalent, affecting 30% of the world's population, with a significant risk of hepatic and cardiometabolic complications. Different stages of MASLD are accompanied by distinct gut microbial profiles, and several microbial components have been implicated in MASLD pathophysiology. Indeed, earlier studies demonstrated that hepatic necroinflammation was reduced in individuals with MASLD after allogenic faecal microbiota transplantation (FMT) from healthy donors on a vegan diet. Here, we further investigate the therapeutic potential of gut microbiome modulation using a syntrophic combination of next-generation beneficial bacteria with FMT in individuals with advanced MASLD.<br><br>METHODS AND ANALYSIS: This trial is a randomised, double-blind, placebo-controlled study investigating the therapeutic potential of lyophilised faecal microbiota capsules (LFMCs) in individuals with metabolic dysfunction-associated steatohepatitis. In this study, 48 participants will be randomised 1:1 to receive either healthy vegan donor LFMCs or placebo for 24 weeks. In addition, all participants will be supplemented with a set of next-generation beneficial bacteria, including Anaerobutyricum soehngenii, pasteurised Akkermansia muciniphila and Bifidobacterium animalis subsp. lactis, as well as fructo-oligosaccharides. A liver biopsy will be performed at baseline and at the end of the trial. In addition, participants will be assessed through MRI, FibroScan, blood tests, faecal samples and continuous glucose monitoring. The first participant was enrolled on 25 April 2023.<br><br>ETHICS AND DISSEMINATION: Ethical approval was obtained from the Medical Ethics Committee of the University Medical Centre of Amsterdam. The results of this study will be disseminated through peer-reviewed journals.<br><br>TRIAL REGISTRATION NUMBER: The trial is registered on clinicaltrials.gov (NCT05821010).},
}
@article {pmid39788725,
year = {2025},
author = {Robinson, LR and McDevitt, CJ and Regan, MR and Quail, SL and Wadsworth, CB},
title = {In vitro evolution of ciprofloxacin resistance in Neisseria commensals and derived mutation population dynamics in natural Neisseria populations.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae107},
pmid = {39788725},
issn = {1574-6968},
abstract = {Commensal Neisseria are members of a healthy human oropharyngeal microbiome; however, they also serve as a reservoir of antimicrobial resistance for their pathogenic relatives. Despite their known importance as sources of novel genetic variation for pathogens, we still do not understand the full suite of resistance mutations commensal species can harbor. Here, we use in vitro selection to assess the mutations that emerge in response to ciprofloxacin selection in commensal Neisseria by passaging 4 replicates of 4 different species in the presence of a selective antibiotic gradient for 20 days; then categorized derived mutations with whole genome sequencing. 10/16 selected cells lines across the 4 species evolved ciprofloxacin resistance (≥ 1 ug/ml); with resistance-contributing mutations primarily emerging in DNA gyrase subunit A and B (gyrA and gyrB), topoisomerase IV subunits C and E (parC and parE), and the multiple transferable efflux pump repressor (mtrR). Of note, these derived mutations appeared in the same loci responsible for ciprofloxacin reduced susceptibility in the pathogenic Neisseria, suggesting conserved mechanisms of resistance across the genus. Additionally, we tested for zoliflodacin cross-resistance in evolved strain lines and found 6 lineages with elevated zoliflodacin minimum inhibitory concentrations. Finally, to interrogate the likelihood of experimentally derived mutations emerging and contributing to resistance in natural Neisseria, we used a population-based approach and identified GyrA 91I as a substitution circulating within commensal Neisseria populations and ParC 85C in a single gonococcal isolate. A small cluster of gonococcal isolates shared commensal alleles at parE, suggesting recent cross-species recombination events.},
}
@article {pmid39788433,
year = {2025},
author = {Abavisani, M and Faraji, S and Ebadpour, N and Karav, S and Sahebkar, A},
title = {Beyond the Hayflick Limit: How Microbes Influence Cellular Aging.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {102657},
doi = {10.1016/j.arr.2025.102657},
pmid = {39788433},
issn = {1872-9649},
abstract = {Cellular senescence, a complex biological process resulting in permanent cell-cycle arrest, is central to aging and age-related diseases. A key concept in understanding cellular senescence is the Hayflick Limit, which refers to the limited capacity of normal human cells to divide, after which they become senescent. Senescent cells (SC) accumulate with age, releasing pro-inflammatory and tissue-remodeling factors collectively known as the senescence-associated secretory phenotype (SASP). The causes of senescence are multifaceted, including telomere attrition, oxidative stress, and genotoxic damage, and they extend to influences from microbial sources. Research increasingly emphasizes the role of the microbiome, especially gut microbiota (GM), in modulating host senescence processes. Beneficial microbial metabolites, such as short-chain fatty acids (SCFAs), support host health by maintaining antioxidant defenses and reducing inflammation, potentially mitigating senescence onset. Conversely, pathogenic bacteria like Pseudomonas aeruginosa and Helicobacter pylori introduce factors that damage host DNA or increase ROS, accelerating senescence via pathways such as NF-κB and p53-p21. This review explores the impact of bacterial factors on cellular senescence, highlighting the role of specific bacterial toxins in promoting senescence. Additionally, it discusses how dysbiosis and the loss of beneficial microbial species further contribute to age-related cellular deterioration. Modulating the gut microbiome to delay cellular senescence opens a path toward targeted anti-aging strategies. This work underscores the need for deeper investigation into microbial influence on aging, supporting innovative interventions to manage and potentially reverse cellular senescence.},
}
@article {pmid39788425,
year = {2025},
author = {Menghani, SV},
title = {Carcinogenetic mechanisms employed by the oral microbiome: a narrative review.},
journal = {The American journal of the medical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.amjms.2025.01.001},
pmid = {39788425},
issn = {1538-2990},
abstract = {Cancers of the oral cavity, lip, salivary gland, and oropharynx cause substantial global disease burden. While tobacco-use and alcohol use are highly associated with oral cancers, the rising incidence of disease in patients who do not use tobacco or alcohol points to additional carcinogenic risk factors. Chronic inflammation, disruption of the oral microbiome, and dysbiosis are becoming more widely implicated in the pathogenesis of oral cancer. Several studies have identified specific bacterial species enriched in patients with oral cancer, including Porphyromonas gingivalis and Fusobacterium nucleatum. In this narrative review, we describe potential carcinogenic mechanisms exhibited by these species and other microbes in the development of oral cancer.},
}
@article {pmid39788355,
year = {2025},
author = {Elkins, M and Horrelt, M and Woods, B and Lawton, S and Ohsumi, TK and Fleischman, A and Taudte, V and Chou, J},
title = {Overfeeding and overweight rapidly reprogram inflammatory signaling.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {},
number = {},
pages = {110428},
doi = {10.1016/j.clim.2025.110428},
pmid = {39788355},
issn = {1521-7035},
abstract = {Epidemiologic studies have shown a continuous increase in mortality risk associated with overweight, thus highlighting the health risks beginning before the onset of obesity. However, early changes in inflammatory signaling induced by an obesogenic diet remain largely unknown since studies of obesity typically utilize models induced by months of continuous exposure to a high-fat diet. Here, we investigated how short-term overfeeding remodels inflammatory signaling. We developed and characterized a mouse model of overweight induced by seven days of the Western diet enriched in saturated fats and sucrose, compared to the standard, low-fat laboratory diet or a long-term Western diet for 22 weeks. The short-term Western diet caused a median weight gain of 6 %, while the long-term Western diet increased weight by 92 %. Circulating levels of cholesterol, triglycerides, insulin, and leptin were increased by both diets, but only the long-term Western diet caused transaminitis and significant hepatic steatosis. Both models reduced the alpha and beta diversity of the microbiome. Tryptophan metabolism was perturbed by both models; the long-term Western diet also affected histidine and vitamin B6 metabolism. The short-term and long-term Western diets increased expression of TLR4 on peritoneal immune cells and TLR4-driven plasma levels of proinflammatory cytokines comparably, showing one week of the Western diet was sufficient for inducing inflammation typical of chronic obesity. These findings highlight the importance of diet not only in preclinical studies, but also in the clinical care of individuals with inflammatory disorders.},
}
@article {pmid39788169,
year = {2025},
author = {Xu, B and Luo, Z and Niu, X and Li, Z and Lu, Y and Li, J},
title = {Fungi, immunosenescence and cancer.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2025.01.002},
pmid = {39788169},
issn = {1096-3650},
abstract = {Fungal microbes are a small but immunoreactive component of the human microbiome, which may influence cancer development, progression and therapeutic response. Immunosenescence is a process of immune dysfunction that occurs with aging, including lymphoid organ remodeling, contributing to alterations in the immune system in the elderly, which plays a critical role in many aspects of cancer. There is evidence for the interactions between fungi and immunosenescence in potentially regulating cancer progression and remodeling the tumor microenvironment (TME). In this review, we summarize potential roles of commensal and pathogenic fungi in modulating cancer-associated processes and provide more-detailed discussions on the mechanisms of which fungi affect tumor biology, including local and distant regulation of the TME, modulating antitumor immune responses and interactions with neighboring bacterial commensals. We also delineate the features of immunosenescence and its influence on cancer development and treatment, and highlight the interactions between fungi and immunosenescence in cancer. We discuss the prospects and challenges for harnessing fungi and immunosenescence in cancer diagnosis and/or treatment. Considering the limited understanding and techniques in conducting such research, we also provide our view on how to overcome challenges faced by the exploration of fungi, immunosenescence and their interactions on tumor biology.},
}
@article {pmid39788163,
year = {2025},
author = {Zeng, H and Safratowich, BD and Liu, Z and Bukowski, MR},
title = {Resistant starch inhibits high-fat diet-induced oncogenic responses in the colon of C57BL/6 mice.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {109838},
doi = {10.1016/j.jnutbio.2025.109838},
pmid = {39788163},
issn = {1873-4847},
abstract = {The beneficial effects of dietary fiber for colon health may be due to short chain fatty acids (SCFAs), such as butyrate, produced by colonic bacterial fermentation. In contrast, obesogenic diet induced obesity is linked to increased colon cancer incidence. We hypothesize that increasing fiber intake promotes healthy microbiome and reduces bacterial dysbiosis and oncogenic signaling in the colon of mice fed an obesogenic diet. Five-week-old male C57BL/6 mice were assigned to 5 dietary groups (n= 22/group) for 24 weeks:(1) AIN93G as a control diet (AIN); (2) a high fat diet (HFD, 45% energy fat); (3) HFD+5% resistant starch enriched dietary fiber (RSF) from maize; (4) HFD+10%RSF; or (5) HFD+20%RSF. Compared to the AIN group, mice receiving the HFD exhibited more than 15% increase in body mass and body fat composition irrespective of RSF dosage. However, the HFD+RSF groups exhibited an increase (> 300%) of fecal butyrate but a decrease (> 45%) of secondary bile acids in a RSF dose-dependent manner over the HFD group. Similarly, there were concomitant decreases (> 25%) in pro-inflammatory plasma cytokines (TNFα, IL-6 and MCP-1), β-catenin and Ki67 protein staining in the colon of the HFD+20%RSF group relative to the HFD group. Furthermore, the abundance of colonic Proteobacteria, signatures of dysbiosis, was decreased (> 63%) in a RSF dose-dependent manner compared to the HFD. Collectively, these data indicate that RSF not only increases butyrate but also reduces secondary bile acids, bacterial dysbiosis and β-catenin in the colon of mice fed a HFD.},
}
@article {pmid39788158,
year = {2025},
author = {Theodosiou, AA and Fady, PE and Bennett, N and Read, RC and Bogaert, D and Jones, CE},
title = {Microbiotoxicity: a call to arms for cross-sector protection of the human microbiome.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106408},
doi = {10.1016/j.jinf.2025.106408},
pmid = {39788158},
issn = {1532-2742},
}
@article {pmid39788096,
year = {2025},
author = {Wang, W and Pi, Z and Yu, Y and Zhang, F},
title = {The butterfly effect of the strain richness influences the efficacy of microbiota transplantation.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {1},
pages = {3-5},
doi = {10.1016/j.chom.2024.12.010},
pmid = {39788096},
issn = {1934-6069},
mesh = {*Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Humans ; Animals ; Feces/microbiology ; Bacteria/classification ; },
abstract = {Strain-level variation in the gut microbiome modulates its impact on host health. Recently in Nature, Chen-Liaw et al. propose that strain richness is a crucial element in the gut ecosystem, thus influencing efficacy of fecal microbiota transplantation, and provide a theoretical foundation for optimizing microbiota-based treatments and developing microbiota medicine.},
}
@article {pmid39788094,
year = {2025},
author = {Liu, AJ and Lynch, JB},
title = {Bugs take the sting out.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {1},
pages = {15-16},
doi = {10.1016/j.chom.2024.12.008},
pmid = {39788094},
issn = {1934-6069},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Neuralgia, Postherpetic/virology ; Brain-Gut Axis/physiology ; Herpesvirus 3, Human/physiology ; Butyrates/metabolism ; Animals ; },
abstract = {Jiang et al. investigate the role of the microbiota in postherpetic neuralgia (PHN), a chronic pain condition resulting from varicella-zoster virus reactivation. They identify microbiome alterations in PHN patients, linking microbes and pain sensitivity. The researchers identify butyrate-producing Roseburia intestinalis as a mediator of pain sensitivity along the "gut-brain axis."},
}
@article {pmid39788033,
year = {2025},
author = {Xu, R and Zhang, Y and Wu, T and Liu, H and Peng, J and Wang, Z and Ba, T and Zhang, B and Li, Z and Wei, Y},
title = {Traffic-related air pollution (TRAP) exposure, lung function, airway inflammation and expiratory microbiota: A randomized crossover study.},
journal = {Ecotoxicology and environmental safety},
volume = {289},
number = {},
pages = {117545},
doi = {10.1016/j.ecoenv.2024.117545},
pmid = {39788033},
issn = {1090-2414},
abstract = {Traffic-related air pollution (TRAP) has been linked with numerous respiratory diseases. Recently, lung microbiome is proposed to be characterized with development and progression of respiratory diseases. However, the underlying effects of TRAP exposure on lung microbiome are rarely explored. We conducted a randomized, crossover study among 35 healthy adults, who participated in 2-h exposure treatments in the road or park scenario alternately, to investigate the impact of short-term TRAP exposure on expiratory health. Particle matters (PMs), nitrogen dioxide (NO2), carbon monoxide (CO) and volatile organic compounds (VOCs), lung function, fractional exhaled nitric oxide (FeNO) and lung microbiota were measured. We applied linear mixed-effect models to explore the associations. TRAP including NO2 and CO in the road were about 1.5 times higher than that in the park except for PMs, and total VOCs also showed higher concentrations. We observed elevated difference in FeNO was associated with high TRAP exposure in the road session, but didn't find obvious changes in lung function. The abundance of Lentilactobacillus and Haepmophilus were distinct in the two groups, with significant correlations with changes to PEF and FeNO, respectively. Enrichment pathways related to transcription, amino acid and carbohydrate metabolism were altered following high TRAP exposure, suggesting TRAP contributed to the respiratory disease by changing metabolism of lung microbes. Our findings reveal VOCs in the road are another key air pollutant and provide novel mechanism for the respiratory effects of TRAP from the perspective of microbiome.},
}
@article {pmid39787933,
year = {2024},
author = {Gulizia, AM and Bell, SC and Kuek, F and Santana, MMF and Edmunds, RC and Yeoh, YK and Sato, Y and Haikola, P and van Herwerden, L and Motti, CA and Bourne, DG and Vamvounis, G},
title = {Biofilm development as a factor driving the degradation of plasticised marine microplastics.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {136975},
doi = {10.1016/j.jhazmat.2024.136975},
pmid = {39787933},
issn = {1873-3336},
abstract = {Biodegradation of microplastics facilitated by natural marine biofouling is a promising approach for ocean bioremediation. However, implementation requires a comprehensive understanding of how interactions between the marine microbiome and dominant microplastic debris types (e.g., polymer and additive combinations) can influence biofilm development and drive biodegradation. To investigate this, polystyrene (PS) and polyvinyl chloride (PVC) microplastics (< 200 µm in diameter) were prepared either without any additives (i.e., virgin) or containing 15 wt% of the plasticisers diethylhexyl phthalate (DEHP) or bisphenol A (BPA). Each polymer-plasticiser microplastic combination was exposed to environmentally relevant conditions in a simulated seawater mesocosm representative of tropical reef waters over a 21-day period to allow for natural biofilm development. Following this, microplastic degradation and the colonising bacterial biofilm was assessed as a function of time, polymer and plasticiser type using infrared, thermal, gel permeation and surface characterisation techniques, as well as 16S ribosomal RNA bacterial gene sequencing, respectively. Together, these analyses revealed time-, polymer- and plasticiser-dependent degradation, particularly of the PS-BPA microplastics. Degradation of the PS-BPA microplastics also coincided with changes in bacterial community composition and an increased total relative abundance of putative biodegradative bacteria. These findings indicate that the metabolic potential and biodegradative capability of the colonising marine biofilm can be significantly impacted by the chemical properties of the microplastic substrate, even within short timeframes.},
}
@article {pmid39787926,
year = {2025},
author = {Wang, M and Sun, X and Ye, D and Duan, Y and Li, D and Guo, Y and Wang, M and Huang, Y and Chen, F and Feng, H and Dong, X and Cheng, S and Yu, Y and Xu, S and Zhu, Z},
title = {Glycine betaine enhances heavy metal phytoremediation via rhizosphere modulation and nitrogen metabolism in king grass-Serratia marcescens strain S27 symbiosis.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137153},
doi = {10.1016/j.jhazmat.2025.137153},
pmid = {39787926},
issn = {1873-3336},
abstract = {Microbe-Assisted Phytoremediation (MAP) is an eco-friendly method for remediating soil contaminated with heavy metals such as cadmium (Cd) and chromium (Cr). This study demonstrates the potential of a king grass-Serratia marcescens strain S27 (KS) co-symbiotic system to enhance heavy metal remediation. The KS symbiosis increased the biomass of king grass by 48 % and enhanced the accumulation of Cd and Cr in the whole plant by 2.75-fold and 1.82-fold, respectively. Root exudates like γ-aminobutyric acid (GABA), glycine betaine (GB), and allantoin (Alla) were tested for enhancing the KS symbiotic, with 0.75 mM GB (GB3X-KS) showing the highest removal efficiencies at 15.1 % for Cd and 14.2 % for Cr. Correlation analysis indicated a link between this enhancement and increased soil nitrogen content. Mechanistic studies revealed GB treatment altered the rhizosphere microbial community, promoting denitrifying bacteria and upregulating nitrogen transformation genes (nrfA) by over 7-fold. GB also enhanced nitrogen assimilation enzymes and antioxidant defenses in king grass, facilitating Cd and Cr transport and sequestration. X-ray fluorescence imaging and two-dimensional correlation spectroscopy showed GB promoted Cd and Cr accumulation in the xylem and phloem of king grass, with phenols and alcohols as key functional groups. The study highlights the potential of the GB-KS symbiotic system for effective soil remediation.},
}
@article {pmid39787869,
year = {2025},
author = {Acharyya, S and Saha, S and Ghosh, A and Majumder, S and Bhattacharya, M},
title = {Mercury tolerance and bioremediation potential of mountain soil bacteria: Insights from Darjeeling, containing elevated levels of mercury.},
journal = {The Science of the total environment},
volume = {960},
number = {},
pages = {178351},
doi = {10.1016/j.scitotenv.2024.178351},
pmid = {39787869},
issn = {1879-1026},
abstract = {More and more research is now being focused on the mercury contamination of remote mountain environments. This study aimed to explore the mountain soil of Tiger Hill, Darjeeling, through the lens of its mercury tolerant bacterial microbiome to characterize regional mercury pollution and isolate strains with mercury bioremediation potential. The soil bacteria isolated from the region displayed an extreme tolerance to mercury at previously unseen levels of up to 7 mg/mL. The mercury removal capacity of the two best isolates, MTD11C and MTD11E, identified as strains of Brevundimonas naejangsanensis and Staphylococcus arlettae, exhibited a mercury removal capacity of 99.74 % and 99.56 %, respectively. As per our research, such extreme tolerance to mercury as demonstrated by the bacterial strains has not been reported thus far. The prevalence of such tolerance in the microbiota of a region may well be an indication of the degree of mercury pollution harbored by it. Their tolerance to other heavy metals and antibiotics, as well as active plant growth promotion traits, were also characterized in this study. The topsoil of this region was estimated to contain elevated levels of mercury at around 0.52-2.39 mg kg[-1]. Ecological risk assessment further showed the potential for harm to the environment posed by the level of mercury. Collected vegetation samples from tea plantations surrounding Tiger Hill displayed an accumulation of mercury in the leaves and roots of the tea plants as well, suggesting rampant mercury pollution that needs to be addressed.},
}
@article {pmid39787728,
year = {2025},
author = {Giri, S and Shi, H and Typas, A and Huang, KC},
title = {Harnessing gut microbial communities to unravel microbiome functions.},
journal = {Current opinion in microbiology},
volume = {83},
number = {},
pages = {102578},
doi = {10.1016/j.mib.2024.102578},
pmid = {39787728},
issn = {1879-0364},
abstract = {The gut microbiome impacts human health in direct and indirect ways. While many associations have been discovered between specific microbiome compositions and diseases, establishing causality, understanding the underlying mechanisms, and developing successful microbiome-based therapies require novel experimental approaches. In this opinion, we discuss how in vitro cultivation of diverse communities enables systematic investigation of the individual and collective functions of gut microbes. Up to now, the field has relied mostly on simple, bottom-up assembled synthetic communities or more complex, undefined stool-derived communities. Although powerful for dissecting interactions and mapping causal effects, these communities suffer either from ignoring the complexity, diversity, coevolution, and dynamics of natural communities or from lack of control of community composition. These limitations can be overcome in the future by establishing personalized culture collections from stool samples of different donors and assembling personalized communities to investigate native interactions and ecological relationships in a controlled manner.},
}
@article {pmid39787587,
year = {2025},
author = {Petit, P and Vuillerme, N},
title = {Leveraging Administrative Health Databases to Address Health Challenges in Farming Populations: Scoping Review and Bibliometric Analysis (1975-2024).},
journal = {JMIR public health and surveillance},
volume = {11},
number = {},
pages = {e62939},
doi = {10.2196/62939},
pmid = {39787587},
issn = {2369-2960},
mesh = {Humans ; *Bibliometrics ; *Databases, Factual ; Agriculture/statistics &amp; numerical data/methods ; Public Health/methods ; Farmers/statistics &amp; numerical data ; },
abstract = {BACKGROUND: Although agricultural health has gained importance, to date, much of the existing research relies on traditional epidemiological approaches that often face limitations related to sample size, geographic scope, temporal coverage, and the range of health events examined. To address these challenges, a complementary approach involves leveraging and reusing data beyond its original purpose. Administrative health databases (AHDs) are increasingly reused in population-based research and digital public health, especially for populations such as farmers, who face distinct environmental risks.<br><br>OBJECTIVE: We aimed to explore the reuse of AHDs in addressing health issues within farming populations by summarizing the current landscape of AHD-based research and identifying key areas of interest, research gaps, and unmet needs.<br><br>METHODS: We conducted a scoping review and bibliometric analysis using PubMed and Web of Science. Building upon previous reviews of AHD-based public health research, we conducted a comprehensive literature search using 72 terms related to the farming population and AHDs. To identify research hot spots, directions, and gaps, we used keyword frequency, co-occurrence, and thematic mapping. We also explored the bibliometric profile of the farming exposome by mapping keyword co-occurrences between environmental factors and health outcomes.<br><br>RESULTS: Between 1975 and April 2024, 296 publications across 118 journals, predominantly from high-income countries, were identified. Nearly one-third of these publications were associated with well-established cohorts, such as Agriculture and Cancer and Agricultural Health Study. The most frequently used AHDs included disease registers (158/296, 53.4%), electronic health records (124/296, 41.9%), insurance claims (106/296, 35.8%), population registers (95/296, 32.1%), and hospital discharge databases (41/296, 13.9%). Fifty (16.9%) of 296 studies involved >1 million participants. Although a broad range of exposure proxies were used, most studies (254/296, 85.8%) relied on broad proxies, which failed to capture the specifics of farming tasks. Research on the farming exposome remains underexplored, with a predominant focus on the specific external exposome, particularly pesticide exposure. A limited range of health events have been examined, primarily cancer, mortality, and injuries.<br><br>CONCLUSIONS: The increasing use of AHDs holds major potential to advance public health research within farming populations. However, substantial research gaps persist, particularly in low-income regions and among underrepresented farming subgroups, such as women, children, and contingent workers. Emerging issues, including exposure to per- and polyfluoroalkyl substances, biological agents, microbiome, microplastics, and climate change, warrant further research. Major gaps also persist in understanding various health conditions, including cardiovascular, reproductive, ocular, sleep-related, age-related, and autoimmune diseases. Addressing these overlooked areas is essential for comprehending the health risks faced by farming communities and guiding public health policies. Within this context, promoting AHD-based research, in conjunction with other digital data sources (eg, mobile health, social health data, and wearables) and artificial intelligence approaches, represents a promising avenue for future exploration.},
}
@article {pmid39787359,
year = {2024},
author = {Sadeghi, F and Sohrabi, A and Zagai, U and Andreasson, A and Vieth, M and Talley, NJ and Agréus, L and Ye, W},
title = {Oral microbiome dysbiosis is associated with precancerous lesions and disorders of upper gastrointestinal tract: A population-based study.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000003279},
pmid = {39787359},
issn = {1572-0241},
abstract = {BACKGROUND AND AIMS: Oral microbiota may contribute to the development of upper gastrointestinal (UGI) disorders. We aimed to study the association between the microbiome of saliva, subgingival and buccal mucosa, and UGI disorders, particularly precancerous lesions. We also aimed to determine which oral site might serve as the most effective biomarker for UGI disorders.<br><br>METHODS: In this population-based study, 388 adults underwent upper endoscopy with biopsies for histopathological analysis. UGI symptoms were assessed using a validated questionnaire and 16S rRNA gene sequencing characterized the microbiota in 380 saliva, 200 subgingival and 267 buccal mucosa samples collected during endoscopy.<br><br>RESULTS: Dysbiosis of the salivary microbiota was observed in subjects with gastroesophageal reflux symptoms (GERS) alone, as well as in those with combined conditions such as GERS and esophagitis, or esophagitis and Barrett's esophagus. Significant microbial alterations were also found in individuals with stomach disorders including H. pylori infection, chemical reactive gastritis, atrophic gastritis, and intestinal metaplasia. However, microbiota dissimilarity in subgingival and buccal mucosa samples, was associated primarily with Barrett's esophagus or gastric atrophy. Among several identified genera, Prevotella, and Fusabacterium in saliva were associated with atrophic gastritis and intestinal metaplasia. In subgingival samples, the link between Fretibacterium in Barrett's esophagus, and Fusabacterium in gastric atrophy and intestinal metaplasia are also notable.<br><br>CONCLUSION: Dysbiosis of the saliva microbiota is linked to various UGI disorders. However, microbiota dysbiosis in subgingival and buccal mucosa sites are specifically associated with the pre-malignant conditions Barrett's esophagus and gastric atrophy. The oral microbiome, particularly in the subgingival location, might act as biomarkers for UGI cancers.},
}
@article {pmid39787157,
year = {2025},
author = {Li, C and Chen, X and Yao, J and Zha, W and Li, M and Shen, J and Jiang, H and Tian, P},
title = {Curcumin modulated gut microbiota and alleviated renal fibrosis in 5/6 nephrectomy-induced chronic kidney disease rats.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0314029},
pmid = {39787157},
issn = {1932-6203},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Renal Insufficiency, Chronic/microbiology/drug therapy/pathology/metabolism ; Rats ; *Curcumin/pharmacology/therapeutic use ; *Nephrectomy ; *Fibrosis ; Male ; *Rats, Sprague-Dawley ; Kidney/pathology/drug effects/metabolism ; Disease Models, Animal ; Dysbiosis/microbiology/drug therapy ; },
abstract = {Increasing evidence suggests that dysbiosis of gut microbiota exacerbates chronic kidney disease (CKD) progression. Curcumin (CUR) has been reported to alleviate renal fibrosis in animal models of CKD. However, the relationship between CUR and gut microbiome in CKD remains unclear. This study aims to investigate the potential anti-renal fibrosis effects of CUR from the gut microbiota perspective. A 5/6 nephrectomy (5/6Nx) rat model was used to explore the therapeutic effect of CUR on renal fibrosis. Tight junction protein expression levels were measured to assess intestinal barrier function. 16S rRNA sequencing was employed to evaluate changes in gut microbiota composition, and metabolomics was utilized to detect alterations in plasma metabolites. The administration of CUR significantly ameliorated renal fibrosis and inhibited inflammation in 5/6Nx rats. Additionally, CUR markedly improved the expression of tight junction proteins and local colon inflammation. CUR also positively reconstructed gut microbiota, significantly increasing the abundance of beneficial bacteria, such as Lachnospiraceae_NK4A136_group, Eubacterium_siraeum_group, and Muribaculaceae was significantly increased. Metabolomics revealed that CUR reduced uremic retention solutes and elevated Vitamin D and short-chain fatty acids (SCFAs). Spearman correlation analysis indicated that gut genera enriched by CUR were positively correlated with Vitamin D and SCFA and negatively correlated with chronic renal injury biomarkers. Mechanistically, we found inhibition of the LPS/TLR4/NF-κB and TGF-β1/Smads pathway in CUR-treated rats. Our study indicates that CUR has the potential to modulate gut microbiota composition, and that this modulation may contribute to the anti-fibrosis effects of CUR.},
}
@article {pmid39786379,
year = {2024},
author = {Yang, Q and Zhu, Y and Jian, X and Qiu, Y and Zhu, Y and Zhao, L and He, Y and An, G and Qiu, L and Guo, J and He, N and Abudumijiti, H and Hu, C and Chen, X and Huang, S and Feng, X and Li, X and Liu, J and Xu, Y and Zhou, W},
title = {Targeting Enterobacter cloacae attenuates osteolysis by reducing ammonium in multiple myeloma.},
journal = {Blood},
volume = {},
number = {},
pages = {},
doi = {10.1182/blood.2024025694},
pmid = {39786379},
issn = {1528-0020},
abstract = {Multiple myeloma (MM)-induced bone disease affects not only patients' quality of life but also their overall survival. Our previous work demonstrated that the gut microbiome plays a crucial role in MM progression and drug resistance. However, the role of altered gut microbiota in MM bone disease remains unclear. In this study, we show that intestinal E. cloacae is significantly enriched in MM patients with osteolysis. Through fecal microbial transplantation and single bacterial colonization experiments in a 5TGM1 MM mouse model, we found that intestinal colonization of E. cloacae promotes osteolysis by increasing circulating ammonium levels. Elevated ammonium promotes osteoclastogenesis by increasing Trap protein levels in osteoclast precursors and by acetylating and stabilizing CCL3 protein in MM cells. Inhibition of ammonium synthesis, using E. cloacae with a deleted dcd gene, along with probiotic supplementation, alleviated osteolysis in MM. Overall, our work suggests that E. cloacae promotes osteolysis in MM by synthesizing ammonium. This establishes a novel mechanism and potential intervention strategy for managing MM with osteolysis.},
}
@article {pmid39782002,
year = {2025},
author = {Pan, M and Qian, C and Huo, S and Wu, Y and Zhao, X and Ying, Y and Wang, B and Yang, H and Yeerken, A and Wang, T and Fu, M and Wang, L and Wei, Y and Zhao, Y and Shao, C and Wang, H and Zhao, C},
title = {Gut-derived lactic acid enhances tryptophan to 5-hydroxytryptamine in regulation of anxiety via Akkermansia muciniphila.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2447834},
doi = {10.1080/19490976.2024.2447834},
pmid = {39782002},
issn = {1949-0984},
mesh = {*Tryptophan/metabolism ; *Gastrointestinal Microbiome ; *Serotonin/metabolism ; Animals ; *Lactic Acid/metabolism ; *Akkermansia/metabolism ; Humans ; Mice ; *Anxiety/metabolism/microbiology ; Male ; Young Adult ; Feces/microbiology ; Kynurenine/metabolism ; Tryptophan Hydroxylase/metabolism ; Adult ; Female ; Mice, Inbred C57BL ; },
abstract = {The gut microbiota plays a pivotal role in anxiety regulation through pathways involving neurotransmitter production, immune signaling, and metabolic interactions. Among these, gut-derived serotonin (5-hydroxytryptamine, 5-HT), synthesized from tryptophan metabolism, has been identified as a key mediator. However, it remains unclear whether specific microbial factors regulate tryptophan metabolism to influence 5-HT production and anxiety regulation. In this study, we analyzed 110 athletes undergoing closed training and found that fecal lactate levels were significantly associated with anxiety indicators. We observed a significant negative correlation between Akkermansia abundance and anxiety levels in athletes. Co-supplementation with lactate and Akkermansia muciniphila (A. muciniphila) modulated tryptophan metabolism by increasing key enzyme TPH1 and reducing IDO1, thus shifting metabolism from kynurenine (Kyn) to 5-HT. In addition, lactate enhanced the propionate production capacity of A. muciniphila, potentially contributing to anxiety reduction in mice. Taken together, these findings suggest that enteric lactate and A. muciniphila collaboratively restore the imbalance in tryptophan metabolism, leading to increased 5-HT activity and alleviating anxiety phenotypes. This study highlights the intricate interplay between gut metabolites and anxiety regulation, offering potential avenues for microbiota-targeted therapeutic strategies for anxiety.},
}
@article {pmid39781720,
year = {2025},
author = {Vakadaris, G and Korovesis, T and Balomenakis, C and Papazoglou, AS and Papadakos, SP and Karniadakis, I and Moysidis, DV and Arvanitakis, K and Germanidis, G and Brilakis, ES and Milkas, A},
title = {Prognostic Value of Serum TMAO Measurement in Patients with STEMI: A Systematic Literature Review.},
journal = {Current vascular pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115701611318147241118082012},
pmid = {39781720},
issn = {1875-6212},
abstract = {BACKGROUND: Gut microbiota-derived metabolite Trimethylamine-N-oxide (TMAO) is increasingly recognized as a potential novel prognostic biomarker for cardiovascular disease. Our research work aimed to investigate the potential utility of TMAO measurement in patients with STelevation Myocardial Infarction (STEMI).<br><br>METHODS: We performed a systematic literature search in PubMed from inception to the 1st of February 2024 to identify all studies examining the association between plasma TMAO levels and disease complexity or clinical outcomes in STEMI patients.<br><br>RESULTS: A total of eight prospective cohort studies were included, encompassing a total of 2,378 STEMI patients. Three of the studies provided only in-hospital evidence (i.e., increased odds for more severe coronary artery disease, plaque rupture, and plaque healing in patients with increased TMAO levels). Four studies examined the long-term prognostic value of TMAO after 10-12 months of follow-up post-STEMI (i.e., increased risk of adverse cardiovascular events in patients with increased TMAO levels), while one study provided data for both in-hospital and mid-term prognosis, indicating that 4-months after STEMI patients with greater TMAO elevation had larger infarct size.<br><br>CONCLUSION: Higher TMAO levels were associated with a greater prevalence of high-risk coronary plaque characteristics and worse in-hospital and follow-up outcomes in STEMI patients. Further study is needed on whether modulating the diet-dependent TMAO levels could improve clinical outcomes in these patients.<br><br>REGISTRATION NUMBER: [(OSF): https://doi.org/10.17605/OSF.IO/WNG8V].},
}
@article {pmid39781670,
year = {2025},
author = {Daiy, K and Wiley, K and Allen, J and Bailey, MT and Dettmer, AM},
title = {Associations among rearing environment and the infant gut microbiome with early-life neurodevelopment and cognitive development in a nonhuman primate model (Macaca mulatta).},
journal = {Journal of developmental origins of health and disease},
volume = {16},
number = {},
pages = {e1},
doi = {10.1017/S2040174424000400},
pmid = {39781670},
issn = {2040-1752},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Macaca mulatta/microbiology ; *Cognition/physiology ; Female ; Male ; Animals, Newborn/microbiology ; },
abstract = {Early gut microbiome development may impact brain and behavioral development. Using a nonhuman primate model (Macaca mulatta), we investigated the association between social environments and the gut microbiome on infant neurodevelopment and cognitive function. Infant rhesus monkeys (n = 33) were either mother-peer-reared (MPR) or nursery-reared (NR). Neurodevelopmental outcomes, namely emotional responsivity, visual orientation, and motor maturity, were assessed with the Primate Neonatal Neurobehavioral Assessment (PNNA) at 14-30 days. Cognitive development was assessed through tasks evaluating infant reward association, cognitive flexibility, and impulsivity at 6-8 months. The fecal microbiome was quantified from rectal swabs via 16S rRNA sequencing. Factor analysis was used to identify "co-abundance factors" describing patterns of microbial composition. We used multiple linear regressions with AIC Model Selection and differential abundance analysis (MaAsLin2) to evaluate relationships between co-abundance factors, microbiome diversity, and neuro-/cognitive development outcomes. At 30 days of age, a gut microbiome co-abundance factor, or pattern, with high Prevotella and Lactobacillus (β = -0.88, p = 0.04, AIC Weight = 68%) and gut microbiome alpha diversity as measured by Shannon diversity (β = -1.33, p = 0.02, AIC Weight = 80%) were both negatively associated with infant emotional responsivity. At 30 days of age, being NR was also associated with lower emotional responsivity (Factor 1 model: β = -3.13, p < 0.01; Shannon diversity model: β = -3.77, p < 0.01). The infant gut microbiome, along with early-rearing environments, may shape domains of neuro-/cognitive development related to temperament.},
}
@article {pmid39781526,
year = {2025},
author = {Zhang, L and Dong, Q and Wang, Y and Li, X and Li, C and Li, F and Zhang, J},
title = {Global trends and risk factors in gastric cancer: a comprehensive analysis of the Global Burden of Disease Study 2021 and multi-omics data.},
journal = {International journal of medical sciences},
volume = {22},
number = {2},
pages = {341-356},
pmid = {39781526},
issn = {1449-1907},
mesh = {Humans ; *Stomach Neoplasms/epidemiology/microbiology/genetics ; *Global Burden of Disease ; Risk Factors ; Mendelian Randomization Analysis ; Male ; Female ; Disability-Adjusted Life Years ; Quantitative Trait Loci ; Machine Learning ; Global Health/statistics &amp; numerical data ; Middle Aged ; Multiomics ; },
abstract = {Background: Gastric cancer (GC) remains a significant global health challenge. This study aimed to comprehensively analyze GC epidemiology and risk factors to inform prevention and intervention strategies. Methods: We analyzed the Global Burden of Disease Study 2021 data, conducted 16 different machine learning (ML) models of NHANES data, performed Mendelian randomization (MR) studies on disease phenotypes, dietary preferences, microbiome, blood-based markers, and integrated differential gene expression and expression quantitative trait loci (eQTL) data from multiple cohorts to identify factors associated with GC risk. Results: Global age-standardized disability-adjusted life year rates (ASDR) for GC declined from 886.24 to 358.42 per 100,000 population between 1990 and 2030, with significant regional disparities. Despite this decline, total disability-adjusted life years show a concerning upward trend from 2015, rising from approximately 22.9 million to a projected 24.3 million by 2030. The slope index of inequality shifted from 87 in 1990 to -184 in 2021, indicating a reversal in GC burden distribution, with higher ASDR now associated with lower socio-demographic index countries. The ML models analysis identified higher levels of clinical characteristics such as phosphorus, calcium, eosinophils percent, and triglycerides, as well as lower levels of iron and monocyte percent, may be associated with an increased risk of GC. MR analyses revealed causal associations between GC risk and disease phenotypes such as Helicobacter pylori infection, chronic gastritis, obesity, depression, and dietary preferences such as dairy and processed meats. Gut microbiome analysis showed associations with microbiome such as Phascolarctobacterium and Ruminococcaceae species. Blood-based markers analysis identified protective and risk effects for cortisol, glutamate, nicotinamide, Natural Killer %lymphocyte, CD4-CD8- T cell Absolute Count, Phosphatidylcholine (16:0_18:1), and Interleukin-1-alpha. Integrated genomic analysis identified 10 genes significantly associated with GC risk, with strong evidence for colocalization in genes such as CCR6 and PILRB. Conclusions: This systematic analysis reveals complex global trends in GC burden and identifies novel clinical, disease phenotypes, dietary preferences, microbial, blood-based, and genetic risk factors. These findings provide potential targets for improved risk stratification, prevention, and intervention strategies to reduce the global burden of GC.},
}
@article {pmid39781515,
year = {2025},
author = {Khanduja, A and Mohanty, D},
title = {SProtFP: a machine learning-based method for functional classification of small ORFs in prokaryotes.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {1},
pages = {lqae186},
pmid = {39781515},
issn = {2631-9268},
mesh = {*Machine Learning ; *Open Reading Frames/genetics ; Neural Networks, Computer ; Humans ; Bacterial Proteins/genetics/metabolism/chemistry ; Bacteria/genetics/metabolism/classification ; Gastrointestinal Microbiome/genetics ; Antimicrobial Peptides/genetics/chemistry/metabolism ; Molecular Sequence Annotation/methods ; Computational Biology/methods ; },
abstract = {Small proteins (≤100 amino acids) play important roles across all life forms, ranging from unicellular bacteria to higher organisms. In this study, we have developed SProtFP which is a machine learning-based method for functional annotation of prokaryotic small proteins into selected functional categories. SProtFP uses independent artificial neural networks (ANNs) trained using a combination of physicochemical descriptors for classifying small proteins into antitoxin type 2, bacteriocin, DNA-binding, metal-binding, ribosomal protein, RNA-binding, type 1 toxin and type 2 toxin proteins. We have also trained a model for identification of small open reading frame (smORF)-encoded antimicrobial peptides (AMPs). Comprehensive benchmarking of SProtFP revealed an average area under the receiver operator curve (ROC-AUC) of 0.92 during 10-fold cross-validation and an ROC-AUC of 0.94 and 0.93 on held-out balanced and imbalanced test sets. Utilizing our method to annotate bacterial isolates from the human gut microbiome, we could identify thousands of remote homologs of known small protein families and assign putative functions to uncharacterized proteins. This highlights the utility of SProtFP for large-scale functional annotation of microbiome datasets, especially in cases where sequence homology is low. SProtFP is freely available at http://www.nii.ac.in/sprotfp.html and can be combined with genome annotation tools such as ProsmORF-pred to uncover the functional repertoire of novel small proteins in bacteria.},
}
@article {pmid39781512,
year = {2025},
author = {Sato, N and Katayama, K and Miyaoka, D and Uematsu, M and Saito, A and Fujimoto, K and Uematsu, S and Imoto, S},
title = {stana: an R package for metagenotyping analysis and interactive application based on clinical data.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {1},
pages = {lqae191},
pmid = {39781512},
issn = {2631-9268},
mesh = {Humans ; *Software ; *Gastrointestinal Microbiome/genetics ; Crohn Disease/genetics/microbiology ; Metagenomics/methods ; Parkinson Disease/genetics ; Kidney Failure, Chronic/genetics ; Metagenome/genetics ; },
abstract = {Metagenotyping of metagenomic data has recently attracted increasing attention as it resolves intraspecies diversity by identifying single nucleotide variants. Furthermore, gene copy number analysis within species provides a deeper understanding of metabolic functions in microbial communities. However, a platform for examining metagenotyping results based on relevant grouping data is lacking. Here, we have developed the R package, stana, for the processing and analysis of metagenotyping results. The package consists of modules for preprocessing, statistical analysis, functional analysis and visualization. An interactive analysis environment for exploring the metagenotyping results was also developed and publicly released with over 1000 publicly available metagenome samples related to human diseases. Three examples exploring the relationship between the metagenotypes of the gut microbiome and human diseases are presented-end-stage renal disease, Crohn's disease and Parkinson's disease. The results suggest that stana facilitated the confirmation of the original study's findings and the generation of a new hypothesis. The GitHub repository for the package is available at https://github.com/noriakis/stana.},
}
@article {pmid39781508,
year = {2024},
author = {Park, SS and Park, SH and Jeong, HT and Shin, MS and Kim, MK and Kim, BK and Yoon, HS and Kim, SH and Kim, TW},
title = {The effect of treadmill exercise on memory function and gut microbiota composition in old rats.},
journal = {Journal of exercise rehabilitation},
volume = {20},
number = {6},
pages = {205-212},
pmid = {39781508},
issn = {2288-176X},
abstract = {Aging is associated with declines in memory function and significant change in gut microbiota. In this study, we investigated how exercise affects age-related memory decline and inflammation, and gut microbiota diversity. Bl6 mice were divided into control, control and exercise, old, and old and exercise groups. Treadmill exercise was performed once a day, 5 days a week for 8 consecutive weeks. Short-term memory was assessed using step-through test and spatial learning memory was assessed using Morris water maze task. Enzyme-linked immunosorbent assay was performed for the proinflammatory cytokines, tumor necrosis factor (TNF)-α and interleukin (IL)-6, in the hippocampus. Western blot analysis was conducted for the neurotrophic factors, brain-derived neurotrophic factor (BDNF) and tyrosine kinase B (TrkB), in the hippocampus. In addition, fecal samples were collected for sequencing and metagenomic analysis. Old rats showed decline in short-term memory and spatial learning memory. Increment of TNF-α and IL-6 concentration with decrement of BDNF and TrkB expression were observed in the old rats. Decreased diversity of gut microbiota composition and decreased beneficial gut microbiota were found in the old rats. However, treadmill exercise improved short-term memory, decreased TNF-α and IL-6 concentration, and increased BDNF and TrkB expression in the old rats. Treadmill exercise also increased the diversity of gut microbiota composition and affected the increase of beneficial gut microbiota in the old rats. In conclusion, treadmill exercise reduced age-related inflammatory markers and effectively improved memory decline while enhancing the diversity and abundance of beneficial gut microbiota.},
}
@article {pmid39781133,
year = {2024},
author = {Tahara, H and Sanda, M and Itsumi, M and Fukamachi, H and Nishi, H and Iwasa, F and Kuwata, H and Baba, K},
title = {Efficacy of Cetylpyridinium Chloride Mouthwash on Denture Plaque Reduction and Microbiome Alteration in a Randomized Crossover Trial.},
journal = {Cureus},
volume = {16},
number = {12},
pages = {e75357},
pmid = {39781133},
issn = {2168-8184},
abstract = {Purpose This study aimed to evaluate the effectiveness of cetylpyridinium chloride (CPC) mouthwash in reducing denture plaque and its impact on the microbial composition of denture plaque. Materials and methods A randomized, placebo-controlled crossover trial included 29 participants with maxillary complete dentures. Participants used either CPC or a placebo mouthwash for one week each in a crossover design. The denture plaque area was quantified using image analysis, and microbiome composition was analyzed via 16S rRNA gene sequencing. Results The use of CPC mouthwash significantly reduced the denture plaque area compared to placebo (p<0.025). Microbiome analysis revealed a significant decrease in the relative abundance of the genus Actinomyces (p=0.025) and a significant increase in the genus Haemophilus (p<0.001) after CPC use. While alpha diversity showed no significant changes, beta diversity analysis indicated a significant shift in microbial composition (p=0.002). Conclusion CPC mouthwash effectively reduces denture plaque accumulation and modifies its microbial composition. These findings highlight the potential of CPC mouthwash as an effective tool in denture hygiene management, which may help lower the risk of denture-related oral and systemic infections.},
}
@article {pmid39780983,
year = {2025},
author = {Wang, ZT and Tan, WT and Huang, JL and Zhang, PF and Li, Q and Wang, MM and Meng, MM and Su, H and Guo, CM and Liu, H},
title = {Correlation Between Gastroesophageal Reflux Disease and Small Intestinal Bacterial Overgrowth: Analysis of Intestinal Microbiome and Metabolic Characteristics.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {33-51},
pmid = {39780983},
issn = {1178-7031},
abstract = {BACKGROUND: Our study examines the relationship between gastroesophageal reflux disease (GERD) and small intestinal bacterial overgrowth (SIBO), focusing on the potential impact of acid-suppressive drugs. We also explore changes in gut microbiota and metabolism in patients with both conditions.<br><br>METHODS: This study included patients from the Department of Gastroenterology, Beijing Shijitan Hospital, between February 2021 and November 2023. All patients underwent assessments including questionnaires, hydrogen and methane breath tests, and gastroscopy. GERD was diagnosed using the GERD-Q scale and gastroscopy, while SIBO was diagnosed via breath tests. We analyzed the correlation between GERD and SIBO, identified risk factors for SIBO, and examined the gut microbiota using 16S rRNA sequencing to explore the relationship between GERD and SIBO.<br><br>RESULTS: The retrospective study included 394 patients.148 with GERD and 287 with positive SIBO results. Among these, 270&#xa0;had a positive methane (CH4) breath test and 97&#xa0;had a positive hydrogen (H2) breath test. GERD was more common in patients with positive SIBO (P = 0.007), and the link between CH4 breath tests and GERD was stronger than that with H2 breath tests (P = 0.020). Logistic regression showed GERD is an independent risk factor for SIBO. Short-term, low-dose acid-suppressive drugs did not affect SIBO development. 16S rRNA sequencing of fecal microbiota from 24 patients showed dominant microbiota in SIBO-positive GERD patients included bacteroides uniformis and bacteroides stercoris. Patients with both GERD and SIBO had differential metabolites, mainly associated with ATP-Binding Cassette transporters (ABC transporters).<br><br>CONCLUSION: GERD is strongly linked to SIBO, especially in patients with a positive CH4 breath test. The gut microbiota in GERD and SIBO patients differs from healthy individuals, with bacteroides uniformis as a key marker. Metabolic changes are mainly related to ABC transporter metabolites.},
}
@article {pmid39780216,
year = {2025},
author = {Sundararajan, P and Ghosh, S and Kelbessa, BG and Whisson, SC and Dubey, M and Chawade, A and Vetukuri, RR},
title = {The impact of spray-induced gene silencing on cereal phyllosphere microbiota.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {1},
pmid = {39780216},
issn = {2524-6372},
abstract = {BACKGROUND: Fusarium head blight (FHB) is a major disease affecting cereal crops including wheat, barley, rye, oats and maize. Its predominant causal agent is the ascomycete fungus Fusarium graminearum, which infects the spikes and thereby reduces grain yield and quality. The frequency and severity of FHB epidemics has increased in recent years, threatening global food security. Spray-induced gene silencing (SIGS) is an alternative technique for tackling this devastating disease through foliar spraying with exogenous double-stranded RNA (dsRNA) to silence specific pathogen genes via RNA interference. This has the advantage of avoiding transgenic approaches, but several aspects of the technology require further development to make it a viable field-level management tool. One such existing knowledge gap is how dsRNA spraying affects the microbiota of the host plants.<br><br>RESULTS: We found that the diversity, structure and composition of the bacterial microbiota are subject to changes depending on dsRNA targeted and host studied, while the fungal microbiota in the phyllosphere remained relatively unchanged upon spraying with dsRNA. Analyses of fungal co-occurrence patterns also showed that F. graminearum established itself among the fungal communities through negative interactions with neighbouring fungi. Through these analyses, we have also found bacterial and fungal genera ubiquitous in the phyllosphere, irrespective of dsRNA treatment. These results suggest that although rarer and less abundant microbial species change upon dsRNA spray, the ubiquitous bacterial and fungal components of the phyllosphere in wheat and barley remain unchanged.<br><br>CONCLUSION: We show for the first time the effects of exogenous dsRNA spraying on bacterial and fungal communities in the wheat and barley phyllospheres using a high-throughput amplicon sequencing approach. The results obtained further validate the safety and target-specificity of SIGS and emphasize its potential as an environmentally friendly option for managing Fusarium head blight in wheat and barley.},
}
@article {pmid39780051,
year = {2025},
author = {Thibaut, MM and Roumain, M and Piron, E and Gillard, J and Loriot, A and Neyrinck, AM and Rodriguez, J and Massart, I and Thissen, JP and Huot, JR and Pin, F and Bonetto, A and Delzenne, NM and Muccioli, GG and Bindels, LB},
title = {The microbiota-derived bile acid taurodeoxycholic acid improves hepatic cholesterol levels in mice with cancer cachexia.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2449586},
doi = {10.1080/19490976.2025.2449586},
pmid = {39780051},
issn = {1949-0984},
mesh = {Animals ; *Cachexia/metabolism/drug therapy/microbiology/etiology ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Bile Acids and Salts/metabolism ; *Cholesterol/metabolism ; *Liver/metabolism/drug effects ; Humans ; Male ; Dysbiosis/microbiology/drug therapy ; Neoplasms/complications/metabolism/microbiology ; Disease Models, Animal ; Bacteria/classification/isolation &amp; purification/metabolism/genetics ; },
abstract = {Alterations in bile acid profile and pathways contribute to hepatic inflammation in cancer cachexia, a syndrome worsening the prognosis of cancer patients. As the gut microbiota impinges on host metabolism through bile acids, the current study aimed to explore the functional contribution of gut microbial dysbiosis to bile acid dysmetabolism and associated disorders in cancer cachexia. Using three mouse models of cancer cachexia (the C26, MC38 and HCT116 models), we evidenced a reduction in the hepatic levels of several secondary bile acids, mainly taurodeoxycholic (TDCA). This reduction in hepatic TDCA occurred before the appearance of cachexia. Longitudinal analysis of the gut microbiota pinpointed an ASV, identified as Xylanibacter rodentium, as a bacterium potentially involved in the reduced production of TDCA. Coherently, stable isotope-based experiments highlighted a robust decrease in the microbial 7α-dehydroxylation (7α-DH) activity with no changes in the bile salt hydrolase (BSH) activity in cachectic mice. This approach also highlighted a reduced microbial 7α-hydroxysteroid dehydrogenase (7α-HSDH) and 12α-hydroxysteroid dehydrogenase (12α-HSDH) activities in these mice. The contribution of the lower production of TDCA to cancer cachexia was explored in vitro and in vivo. In vitro, TDCA prevented myotube atrophy, whereas in vivo hepatic whole transcriptome analysis revealed that TDCA administration to cachectic mice improved the unfolded protein response and cholesterol homeostasis pathways. Coherently, TDCA administration reversed hepatic cholesterol accumulation in these mice. Altogether, this work highlights the contribution of the gut microbiota to bile acid dysmetabolism and the therapeutic interest of the secondary bile acid TDCA for hepatic cholesterol homeostasis in the context of cancer cachexia. Such discovery may prove instrumental in the understanding of other metabolic diseases characterized by microbial dysbiosis. More broadly, our work demonstrates the interest and relevance of microbial activity measurements using stable isotopes, an approach currently underused in the microbiome field.},
}
@article {pmid39779898,
year = {2025},
author = {Klinhom, S and Kunasol, C and Sriwichaiin, S and Kerdphoo, S and Chattipakorn, N and Chattipakorn, SC and Thitaram, C},
title = {Characteristics of gut microbiota profiles in Asian elephants (Elephas maximus) with gastrointestinal disorders.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1327},
pmid = {39779898},
issn = {2045-2322},
support = {59/2565//CMU Presidential Scholarship/ ; N42A670594//Research Chair Grant, the National Research Council of Thailand/ ; N42A660301//Distinguished Research Professor Grant, the National Research Council of Thailand/ ; RSA6280095//Thailand Research Fund/ ; },
mesh = {Animals ; *Elephants/microbiology ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Diseases/microbiology/veterinary ; *Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Thailand ; Female ; Diarrhea/microbiology/veterinary ; Male ; High-Throughput Nucleotide Sequencing ; Dysbiosis/microbiology/veterinary ; },
abstract = {Colic and diarrhea are common gastrointestinal (GI) disorders in captive Asian elephants, which can severely impact health and lead to mortality. Gut dysbiosis, indicated by alterations in gut microbiome composition, can be observed in individuals with GI disorders. However, changes in gut microbial profiles of elephants with GI disorders have never been investigated. Thus, this study aimed to elucidate the profiles of gut microbiota in captive elephants with different GI symptoms. Fecal samples were collected from eighteen elephants in Chiang Mai, Thailand, including seven healthy individuals, seven with impaction colic, and four with diarrhea. The samples were subjected to DNA extraction and amplification targeting the V3-V4 region of 16S rRNA gene for next-generation sequencing analysis. Elephants with GI symptoms exhibited a decreased microbial stability, as characterized by a significant reduction in microbiota diversity within individual guts and notable differences in microbial community composition when compared with healthy elephants. These changes included a decrease in the relative abundance of specific bacterial taxa, in elephants with GI symptoms such as a reduction in genera Rubrobacter, Rokubacteria, UBA1819, Nitrospira, and MND1. Conversely, an increase in genera Lysinibacillus, Bacteroidetes_BD2-2, and the family Marinifilaceae was observed when, compared with the healthy group. Variations in taxa of gut microbiota among elephants with GI disorders indicated diverse microbial characteristics associated with different GI symptoms. This study suggests that exploring gut microbiota dynamics in elephant health and GI disorders can lead to a better understanding of food and water management for maintaining a healthy gut and ensuring the longevity of the elephants.},
}
@article {pmid39779879,
year = {2025},
author = {Pribyl, AL and Hugenholtz, P and Cooper, MA},
title = {A decade of advances in human gut microbiome-derived biotherapeutics.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39779879},
issn = {2058-5276},
abstract = {Microbiome science has evolved rapidly in the past decade, with high-profile publications suggesting that the gut microbiome is a causal determinant of human health. This has led to the emergence of microbiome-focused biotechnology companies and pharmaceutical company investment in the research and development of gut-derived therapeutics. Despite the early promise of this field, the first generation of microbiome-derived therapeutics (faecal microbiota products) have only recently been approved for clinical use. Next-generation therapies based on readily culturable and as-yet-unculturable colonic bacterial species (with the latter estimated to comprise 63% of all detected species) have not yet progressed to pivotal phase 3 trials. This reflects the many challenges involved in developing a new class of drugs in an evolving field. Here we discuss the evolution of the live biotherapeutics field over the past decade, from the development of first-generation products to the emergence of rationally designed second- and third-generation live biotherapeutics. Finally, we present our outlook for the future of this field.},
}
@article {pmid39779855,
year = {2025},
author = {Handa, S and Biswas, T and Chakraborty, J and Ghosh, G and Paul, BG and Ghosh, P},
title = {RNA control of reverse transcription in a diversity-generating retroelement.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39779855},
issn = {1476-4687},
abstract = {Diversity-generating retroelements (DGRs) create massive protein sequence variation (up to 10[30])[1] in ecologically diverse microorganisms. A recent survey identified around 31,000 DGRs from more than 1,500 bacterial and archaeal genera, constituting more than 90 environment types[2]. DGRs are especially enriched in the human gut microbiome[2,3] and nano-sized microorganisms that seem to comprise most microbial life and maintain DGRs despite reduced genomes[4,5]. DGRs are also implicated in the emergence of multicellularity[6,7]. Variation occurs during reverse transcription of a protein-encoding RNA template coupled to misincorporation at adenosines. In the prototypical Bordetella bacteriophage DGR, the template must be surrounded by upstream and downstream RNA segments for complementary DNA synthesis to be carried out by a complex of the DGR reverse transcriptase bRT and associated protein Avd. The function of the surrounding RNA was unknown. Here we show through cryogenic electron microscopy that this RNA envelops bRT and lies over the barrel-shaped Avd, forming an intimate ribonucleoprotein. An abundance of essential interactions in the ribonucleoprotein precisely position an RNA homoduplex in the bRT active site for initiation of reverse transcription. Our results explain how the surrounding RNA primes complementary DNA synthesis, promotes processivity, terminates polymerization and strictly limits mutagenesis to specific proteins through mechanisms that are probably conserved in DGRs belonging to distant taxa.},
}
@article {pmid39779812,
year = {2025},
author = {Marongiu, L and Brzozowska, E and Brykała, J and Burkard, M and Schmidt, H and Szermer-Olearnik, B and Venturelli, S},
title = {The non-nutritive sweetener rebaudioside a enhances phage infectivity.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1337},
pmid = {39779812},
issn = {2045-2322},
mesh = {*Bacteriophages/physiology ; *Diterpenes, Kaurane/pharmacology/metabolism ; Non-Nutritive Sweeteners/pharmacology ; Molecular Docking Simulation ; Viral Proteins/metabolism ; Klebsiella pneumoniae/drug effects/pathogenicity/virology ; Protein Binding ; },
abstract = {Non-nutritive sweeteners (NNS) are widely employed in foodstuffs. However, it has become increasingly evident that their consumption is associated with bacterial dysbiosis, which, in turn, is linked to several health conditions, including a higher risk of type 2 diabetes and cancer. Among the NNS, stevia, whose main component is rebaudioside A (rebA), is gaining popularity in the organic food market segment. While the effect of NNS on bacteria has been established, the impact of these sweeteners on bacterial viruses (phages) has been neglected, even though phages are crucial elements in maintaining microbial eubiosis. The present study sought to provide a proof-of-concept of the impact of NNS on phage infectivity by assessing the binding of rebA to phage proteins involved in the infection process of enteropathogenic bacteria, namely the fiber protein gp17 of Yersinia enterocolitica phage φYeO3-12 and the tubular baseplate protein gp31 of Klebsiella pneumoniae phage 32. We employed docking analysis and a panel of in vitro confirmatory tests (microscale thermophoresis, RedStarch™ depolymerization, adsorption, and lysis rates). Docking analysis indicated that NNS can bind to both fiber and baseplate proteins. Confirmatory assays demonstrated that rebA can bind gp31 and that such binding increased the protein's enzymatic activity. Moreover, the binding of rebA to gp17 resulted in a decrease in the adsorption rate of the recombinant protein to its host but increased the Yersinia bacteriolysis caused by the whole phage compared to unexposed controls. These results support the hypothesis that NNS can impair phage infectivity, albeit the resulting effect on the microbiome remains to be elucidated.},
}
@article {pmid39779737,
year = {2025},
author = {Corcione, S and Ferrocino, I and Lupia, T and Busca, A and Bianco, G and Dellacasa, C and Giaccone, L and Brunello, L and Butera, S and Costa, C and Bruno, B and De Rosa, FG},
title = {Influence of ESBL colonization status on gut microbiota composition during allogenic hematopoietic stem cell transplantation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1275},
pmid = {39779737},
issn = {2045-2322},
support = {Project no. PE00000007, INF-ACT//EU funding within the MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Male ; Female ; Middle Aged ; Adult ; Prospective Studies ; Pilot Projects ; *beta-Lactamases/metabolism ; *Transplantation, Homologous/adverse effects ; Aged ; Feces/microbiology ; Italy ; Anti-Bacterial Agents/therapeutic use/pharmacology ; },
abstract = {After allogeneic HSCT (allo-HSCT), the diversity of the intestinal microbiota significantly decreases. The changes can be rapid and are thought to be caused by chemotherapy, antibiotics, or intestinal inflammation. Most patients are exposed to prophylactic and therapeutic antibiotics during neutropenia and several patients are colonized by ESBL bacteria. We investigated the changes in gut microbiota composition in allo-HSCT, aiming at investigating if the acquisition of ESBL colonization may affect gut microbiome diversity during allo-HSCT. This was a single-center prospective pilot study. All patients consecutively admitted to the Haematological Unit of the City of Health and Science, Molinette Hospital in Turin, Italy, and undergoing allo-HSCT between August 2017 to August 2020 were enrolled in the study. Microbiome analysis on fecal samples were collected every 7 days from hospital admission to discharge and until 1 year after HSCT. 48 patients were enrolled in the study. At baseline 14 patients (29.16%) were colonized by MDR bacteria, mostly extended-spectrum beta-lactamase (ESBL)-producing gram negatives (N = 11; 78.57%). During allo-HSCT, one patient had a positive rectal swab for a carbapenemase-producing Klebsiella pneumoniae and eight patients lost the colonization during the hospital stay. Microbiota composition was compared between patients colonized by ESBL at baseline and non-colonized patients. Patients colonized by ESBL had a greater abundances of Bifidobacterium, Blautia, Clostridium, Coprococcus, L-Ruminococcus Mogibacteriaceae, Peptostreptococceae and Oscillospira, while non-colonized ESBL patients had a greater abundance of Actinomycetales, Staphylococcus and Sutterella. Moreover, microbiota composition of colonized by ESBL that retained colonization after HSCT showed an increased in abundances of Akkermansia, Dialister, Erysipelotrichaceae and Methanobrevibacter when compared with patients that become negative at rectal swabs. From a clinical perspective, the evolution of this prospective pilot study will be to investigate markers of gut barrier functions, SCFA productions and to correlate the predictivity of these parameters with risk of invasive infections and clinical outcomes in allo-HSCT population.},
}
@article {pmid39779730,
year = {2025},
author = {Guan, W and Zhou, T and Jiao, J and Xiao, L and Wang, Z and Liu, S and Yan, F and Zhao, F and Wang, X},
title = {Signature of pre-pregnancy microbiome in infertile women undergoing frozen embryo transfer with gestational diabetes mellitus.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {6},
pmid = {39779730},
issn = {2055-5008},
mesh = {Humans ; Female ; Pregnancy ; *Diabetes, Gestational/microbiology ; Adult ; *Embryo Transfer/methods ; *Infertility, Female/microbiology/etiology/therapy ; *Gastrointestinal Microbiome ; Bacteria/classification/isolation &amp; purification/genetics ; Case-Control Studies ; },
abstract = {This study aims to evaluate differences in gut microbiota structures between infertile women undergoing frozen embryo transfer (FET) with gestational diabetes mellitus (GDM) and healthy controls (HCs), and to identify potential markers. We comprehensively enrolled 193 infertile women undergoing FET (discovery cohort: 38 HCs and 31 GDM; validation cohort: 85 HCs and 39 GDM). Gut microbial profiles of the discovery cohort were investigated during the pre-pregnancy (Pre), first trimester (T1), and second trimester (T2). The microbial community in the HCs group remained relatively stable throughout the pregnancy, while the microbial structure alteration occurred in the GDM group during T2. A model based on ten bacteria and ten metabolites simultaneously was used to predict the risk of GDM developing in the pre-pregnancy state with the ROC value of 0.712. Algorithms on the basis of marker species and biochemical parameters can be used as effective tools for GDM risk evaluation before pregnancy.},
}
@article {pmid39779716,
year = {2025},
author = {Gałęcka, I and Rychlik, A and Całka, J},
title = {Influence of selected dosages of plastic microparticles on the porcine fecal microbiome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1269},
pmid = {39779716},
issn = {2045-2322},
support = {2020/37/N/NZ7/01383//Narodowe Centrum Nauki/ ; The Regional Initiative of Excellence Program//Minister of Science Poland/ ; },
mesh = {Animals ; Swine ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; Female ; Plastics ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Studies conducted so far have shown that nano- and microplastic may disturb the intestinal microenvironment by interacting with the intestinal epithelium and the gut microbiota. Depending on the research model used, the effect on the microbiome is different-an increase or decrease in selected taxa resulting in the development of dysbiosis. Dysbiosis may be associated with intestinal inflammation, development of mental disorders or diabetes. The aim of the study was to analyze the intestinal microbiome in 15 gilts divided into 3 research groups (n = 5; control group, receiving micropartices at a dose 0.1 g/day (LD) and 1 g/day (HD)). Feaces were collected before and after 28 days of exposure to PET microplastics. The analysis of the intestinal microbiome was performed using next-generation sequencing. Alpha and beta diversity indices were compared, showing, that repetition affected only the abundance indices in the control and LD groups, but not in the HD group. The relationships between the number of reads at the phylum, genus and species level and the microplastic dose were calculated using statistical methods (r-Pearson correlation, generalized regression model, analysis of variance). The statistical analysis revealed, that populations of Family XIII AD3011 group, Coprococcus, V9D2013 group, UCG-010 and Sphaerochaeta increased with increasing MP-PET dose. The above-mentioned taxa are mainly responsible for the production of short-chain fatty acids (SCFA). It may be assumed, that SCFA are one of the mechanisms involved in the response to oral exposure to MP-PET.},
}
@article {pmid39779588,
year = {2025},
author = {Chen, LJ and Plantinga, AM and Burr, R and Cain, K and Barney, P and Savidge, T and Shulman, RJ and Heitkemper, M and Kamp, K},
title = {Exploration of Cytokines and Microbiome Among Males and Females with Diarrhea-Predominant Irritable Bowel Syndrome.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {39779588},
issn = {1573-2568},
support = {R01NR014479/NR/NINR NIH HHS/United States ; K23NR020044/NR/NINR NIH HHS/United States ; },
abstract = {BACKGROUND: Whether pathophysiological factors differ between males and females with irritable bowel syndrome-diarrhea (IBS-D) remains to be tested. To better understand potential sex differences, males with IBS-D were compared to naturally cycling females and to females with IBS-D taking hormonal contraception on plasma levels of cytokines and gut microbiome characteristics.<br><br>METHODS: Males and females with Rome III IBS-D completed questionnaires and kept a daily symptom diary for 28&#xa0;days. Blood and stool samples were collected between days 3 and 8 of the daily diary (estrogen-dominant days in naturally cycling females). Blood samples were analyzed for lipopolysaccharide (LPS)-stimulated and unstimulated cytokine levels. Stool samples were analyzed for microbiota signatures using 16S rRNA sequencing.<br><br>RESULTS: Forty-seven participants with IBS-D (13 males, 22 naturally cycling females, 12 females with hormonal contraception use) ages 18 to 50&#xa0;years were studied. Males had similar unstimulated IL10, IL12P40, IL12P70, IL1&#x3b2;, IL8, and TNF&#x3b1; plasma cytokine levels compared to naturally cycling females, but higher levels compared with females using hormonal contraception. LPS-stimulated IL12P70 levels were lower in both groups of females vs. males. Alpha- and beta-diversity did not differ although differences in genus-level bacteria were found.<br><br>CONCLUSION: Cytokine levels differed between males and females using hormonal contraceptives but not between males and normally cycling females. It is important to consider that naturally cycling females may have a different cytokine and microbiome profile than females using hormonal contraceptives. Whether this portends a sex difference in potential etiologic factors remains to be determined.},
}
@article {pmid39779558,
year = {2025},
author = {Mofrad, MD and Ahn, S and Chun, OK},
title = {The Interplay of Diet, Genome, Metabolome, and Gut Microbiome in Cardiovascular Disease: A Narrative Review.},
journal = {Current medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0109298673342364241119114722},
pmid = {39779558},
issn = {1875-533X},
abstract = {INTRODUCTION/OBJECTIVE: The responsiveness to dietary interventions is influenced by complex, multifactorial interactions among genetics, diet, lifestyle, gut microbiome, environmental factors, and clinical characteristics, such as the metabolic phenotype. Detailed metabolic and microbial phenotyping using large human datasets is essential for better understanding the link between diet, the gut microbiome, and host metabolism in cardiovascular diseases (CVD). This review provides an overview of the interplay between diet, genome, metabolome, and gut microbiome in CVD.<br><br>METHODS: A literature review was conducted using PubMed and Scopus databases to identify pertinent cohort studies published between January 2022 and May 2024. This review focused on English articles that assessed the interplay of diet, genome, metabolome, and gut microbiome in relation to CVD in humans.<br><br>RESULTS: This narrative review explored the role of single-omics technologies-genomics, metabolomics, and the gut microbiome-and multi-omics approaches to understand the molecular basis of the relationship between diet and CVD. Omics technologies enabled the identification of new genes, metabolites, and molecular mechanisms related to the association of diet and CVD. The integration of multiple omics approaches allows for more detailed phenotyping, offering a broader perspective on how dietary factors influence CVD.<br><br>CONCLUSION: Omics approaches hold great potential for deciphering the intricate crosstalk between diet, genome, gut microbiome, and metabolome, as well as their roles in CVD. Although large-scale studies integrating multiple omics in CVD research are still limited, notable progress has been made in uncovering molecular mechanisms. These findings could guide the development of targeted dietary strategies and guidelines to prevent CVD.},
}
@article {pmid39779320,
year = {2025},
author = {Brettell, LE and Hoque, AF and Joseph, TS and Dhokiya, V and Hornett, EA and Hughes, GL and Heinz, E},
title = {Mosquitoes Reared in Nearby Insectaries at the Same Institution Have Significantly Divergent Microbiomes.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70027},
pmid = {39779320},
issn = {1462-2920},
support = {//Liverpool School of Tropical Medicine Director's Catalyst Fund/ ; BB/T001240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/V011278/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/V011278/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/W018446/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X018024/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 20197//UK Research and Innovation/ ; 85336//UK Research and Innovation/ ; R21AI138074/NH/NIH HHS/United States ; RSWF\R1\180013//Royal Society/ ; V043811/1//Engineering and Physical Sciences Research Council/ ; INV-048598//Bill and Melinda Gates Foundation/ ; NIHR2000907//National Institute for Health and Care Research/ ; MR/N013514/1/MRC_/Medical Research Council/United Kingdom ; 217303/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Microbiota ; *Aedes/microbiology/growth &amp; development ; *Larva/microbiology ; Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; Female ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The microbiome influences critical aspects of mosquito biology and variations in microbial composition can impact the outcomes of laboratory studies. To investigate how biotic and abiotic conditions in an insectary affect the composition of the mosquito microbiome, a single cohort of Aedes aegypti eggs was divided into three batches and transferred to three different climate-controlled insectaries within the Liverpool School of Tropical Medicine. The bacterial microbiome composition was compared as mosquitoes developed, the microbiome of the mosquitoes' food sources was characterised, environmental conditions over time in each insectary were measured, and mosquito development and survival were recorded. While developmental success was similar across all three insectaries, differences in microbiome composition were observed between mosquitoes from each insectary. Environmental conditions and bacterial input via food sources varied between insectaries, potentially contributing to the observed differences in microbiome composition. At both adult and larval stages, specific members of the mosquito microbiome were associated with particular insectaries; the insectary with less stable and cooler conditions resulted in a slower pupation rate and higher diversity of the larval microbiome. These findings underscore that even minor inconsistencies in rearing conditions can affect the composition of the mosquito microbiome, which may influence experimental outcomes.},
}
@article {pmid39779304,
year = {2025},
author = {Diakaki, M and Jimenez, BA and de Lange, E and Butterbach, P and van der Heijden, L and Köhl, J and de Boer, W and Postma, J},
title = {Spinach Seed Microbiome Characteristics Linked to Suppressiveness Against Globisporangium ultimum Damping-Off.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf004},
pmid = {39779304},
issn = {1574-6941},
abstract = {Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesised that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (ITS1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process in turn could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.},
}
@article {pmid39779288,
year = {2025},
author = {Bermúdez-Sánchez, S and Bahl, MI and Hansen, EB and Licht, TR and Laursen, MF},
title = {Oral amoxicillin treatment disrupts the gut microbiome and metabolome without interfering with luminal redox potential in the intestine of Wistar Han rats.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf003},
pmid = {39779288},
issn = {1574-6941},
abstract = {Oral antibiotic treatment is well known to be one of the main factors affecting gut microbiota composition by altering bacterial diversity. It decreases the abundance of butyrate-producing bacteria such as Lachnospiraceae and Ruminococcaceae, while increasing abundance of Enterobacteriaceae. The recovery time of commensal bacteria post-antibiotic treatment varies among individuals, and often, complete recovery is not achieved. Recently, gut microbiota disruption has been associated with increased gut oxygen levels and higher redox potential in faecal samples. Given that redox balance is crucial for microbial metabolism and gut health, influencing fermentation processes and maintaining anaerobic conditions, we investigated the impact of oral amoxicillin treatment on the redox potential in the caecum. We used 24 Wistar Han male rats and measured caecal redox potential in situ with a probe, before and after 7 days of amoxicillin treatment, as well as after 7 days of recovery. Additionally, we analysed caecal weight, pH, antioxidant capacity, caecal microbiota, metabolome, and colonic tissue expression of relevant genes involved in the redox potential state. Our findings show that oral amoxicillin treatment significantly reduced archaeal load, and decreased the bacterial alpha diversity and affected bacterial composition of the caecal microbiome. The caecal metabolome was also significantly affected, exemplified by reduced amounts of short chain fatty acids during amoxicillin treatment. While the caecal metabolome fully recovered seven days post amoxicillin treatment, the microbiome did not fully recover within this time frame. However, amoxicillin did not lead to an increase in luminal redox potential in the cecum during or post amoxicillin treatment. Limited differences were observed for colonic expression of genes involved in intestinal barrier function and generation of reactive oxygen species, except for the catalase gene, which was significantly upregulated post-amoxicillin treatment. Our results suggest that while oral amoxicillin disrupts the gut microbiome and metabolome, it does not directly interfere with gut luminal redox state.},
}
@article {pmid39779069,
year = {2025},
author = {Sirko, J and Bor, B and He, X},
title = {Microbial dark matter and the future of dentistry.},
journal = {Journal of the American Dental Association (1939)},
volume = {156},
number = {1},
pages = {81-84},
doi = {10.1016/j.adaj.2024.11.003},
pmid = {39779069},
issn = {1943-4723},
}
@article {pmid39778887,
year = {2025},
author = {Pérez-Accino, J and Salavati, M and Glendinning, L and Salavati Schmitz, S},
title = {Effect of a single rectal fecal microbiota transplantation on clinical severity and fecal microbial communities in dogs with chronic inflammatory enteropathy.},
journal = {Journal of veterinary internal medicine},
volume = {39},
number = {1},
pages = {e17264},
pmid = {39778887},
issn = {1939-1676},
support = {//Fiona and Ian Russel Fund/ ; },
mesh = {Animals ; Dogs ; *Dog Diseases/therapy/microbiology ; *Fecal Microbiota Transplantation/veterinary ; *Feces/microbiology ; Male ; Female ; Inflammatory Bowel Diseases/veterinary/therapy/microbiology ; RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome ; Chronic Disease ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) has been advocated as a treatment for chronic enteropathy (CE) in dogs. However, so far only short-term clinical effects have been reported whereas the effect on the microbiota remains unexplored.<br><br>HYPOTHESIS/OBJECTIVES: Assess if a single FMT enema can lead to clinical improvement in dogs with CE when accompanied by presumed favorable microbiota changes. The effect of glycerol as a cryopreservative when storing FMT preparations also was assessed.<br><br>ANIMALS: Seven dogs with CE that received FMTs from 2 healthy donor dogs.<br><br>MATERIALS AND METHODS: Six dogs received a single FMT, 1 dog received 3 consecutive FMTs. Canine chronic enteropathy clinical activity index (CCECAI) and fecal samples were obtained before (Day 0), and 7, 30 and 90&#x2009;days after FMT. Samples were stored with and without 10% glycerol. Sequencing of microbiota (16S rRNA, Illumina) was performed and compared by accepted analysis pipelines.<br><br>RESULTS: Median CCECAI before FMT was 8 (range, 5-14), decreased to a median of 3 (range, 1-12) within 1&#x2009;week and a median of 1 (range, 0-12) by Day 30 (P&#x2009;<&#x2009;.01), with an average duration of response of approximately 10&#x2009;weeks. Significant variation in the donors' microbiota composition was observed across different donations. Recipient microbiota composition or diversity did not change over time. Glycerol addition was associated with a difference in microbiota composition (P&#x2009;&#x2264;&#x2009;.001).<br><br>A single FMT can be considered&#xa0;an appropriate treatment in dogs with CE, but consistent microbiota changes were not observed.},
}
@article {pmid39778678,
year = {2025},
author = {Hong, YJ and Cai, Y and Antoniewicz, MR},
title = {Cross-feeding of amino acid pathway intermediates is common in co-cultures of auxotrophic Escherichia coli.},
journal = {Metabolic engineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymben.2025.01.003},
pmid = {39778678},
issn = {1096-7184},
abstract = {Amino acid auxotrophy refers to an organism's inability to synthesize one or more amino acids that are required for cell growth. In microbiome research, co-cultures of amino acid auxotrophs are often used to investigate metabolite cross-feeding interactions and model community dynamics. Thus far, it has been implicitly assumed that amino acids are mainly cross-fed between these auxotrophs. However, this assumption has not been fully verified. For example, it could be that intermediates of amino acid biosynthesis pathways are exchanged instead, or in addition to amino acids. If true, this would significantly increase the complexity of metabolic interactions that needs to be considered. Here, we show that metabolic pathway intermediates are indeed exchanged in many co-cultures of amino acid auxotrophs. To demonstrate this, we selected 25 E. coli single gene knockouts that are auxotrophic for five different amino acids: arginine, histidine, isoleucine, proline, and tryptophan. In co-culture experiments, we paired strains that shared the same amino acid auxotrophy and monitored cell growth. We observed growth in 23 out of 55 strain pairings, indicating that pathway intermediates were exchanged between the strains. To provide further support for cross-feeding of pathway intermediates, auxotrophic E. coli strains were cultured in media supplemented with commercially available metabolic pathway intermediates at different concentrations. Supplementing media with these metabolites recovered cell growth as was predicted from the co-culture experiments. Most of these metabolites supported high growth rates, even when present at low concentrations (10 μM), suggesting the presence of high affinity transporters for these metabolites. In total, we identified eight metabolic pathway intermediates that were likely exchanged between the auxotrophic E. coli strains and verified six of these, including histidinol, N-acetyl-L-ornithine, L-ornithine, L-citrulline, keto-isoleucine and anthranilate. Taken together, this work demonstrates that exchange of metabolic pathway intermediates is more common than has been assumed so far. In future, these exchanges must be explicitly considered when constructing models of metabolite cross-feeding interactions in microbial communities and when interpreting results from microbiome studies involving auxotrophic strains.},
}
@article {pmid39778648,
year = {2025},
author = {Bellanco, A and Requena, T and Martínez-Cuesta, MC},
title = {POLYSORBATE 80 AND CARBOXYMETHYLCELLULOSE: A DIFFERENT IMPACT ON EPITHELIAL INTEGRITY WHEN INTERACTING WITH THE MICROBIOME.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {115236},
doi = {10.1016/j.fct.2025.115236},
pmid = {39778648},
issn = {1873-6351},
abstract = {The consumption of dietary emulsifiers, including polysorbate 80 (P80) and sodium carboxymethylcellulose (CMC), has raised safety concerns due to its interaction with the intestinal microbiome. This study demonstrated that increasing concentrations of P80 and CMC added to a dynamic four-stage gut microbiota model (BFBL gut simulator) altered the microbiome composition and impacted epithelial integrity in a dose-dependent manner. 16S rDNA amplicon-based metagenomics analysis revealed that these emulsifiers increased microbial groups with proinflammatory capacities while decreasing microbial taxa known to enhance barrier function. Increasing doses of P80 significantly decreased Bacteroides dorei and Akkermansia, taxa associated with anti-inflammatory potential, while increasing doses of CMC were linked to a higher abundance of Ruminococcus torques and Hungatella, which negatively impact barrier function. Both emulsifiers displayed a different impact on epithelial integrity when interacting with the microbiome. On one hand, supernatants from the BFBL simulator fed with P80 disrupted epithelial integrity to a lesser extent than the additive alone. On the other hand, both the microbiota and the supernatants from the BFBL simulator fed with CMC diminished the epithelial integrity, though the additive itself did not. These findings highlight the need to incorporate the gut microbiome in the risk assessment of these additives.},
}
@article {pmid39778631,
year = {2025},
author = {Harriman, D and Ng, A and Bronowski, M and Kazakov, H and Nguan, C and Dang, T and Sherwood, K and Miller, A and Lange, D},
title = {Characterizing the urobiome and associated metabolic profiles during acute rejection in renal transplant patients: A pilot study.},
journal = {Transplant immunology},
volume = {},
number = {},
pages = {102170},
doi = {10.1016/j.trim.2024.102170},
pmid = {39778631},
issn = {1878-5492},
abstract = {Characteristic alterations in the urinary microbiome, or urobiome, are associated with renal transplant pathology. To date, there has been no direct study of the urobiome during acute allograft rejection. The goal of this study was to determine if unique urobiome alterations are present during acute rejection in renal transplant recipients. We performed shotgun metagenomic sequencing of 32 mid-stream urine samples obtained from 15 transplant recipients pre-transplant, 1- and 3-months post-transplant, and at time of rejection discovered with for-cause biopsy. Within individuals, there was a 40-60 % difference in urobiome composition from pre-to-post-transplant in both rejectors and non-rejectors. The taxa Ureaplasma was enriched in rejectors compared to non-rejectors. However, a greater number of microbial genes were enriched in non-rejectors compared to rejectors, except for genes associated with tetracycline resistance, the lysophosphatidic acid synthesis pathway, and tryptophanyl-tRNA synthetase. Together, our findings suggest that the urobiome is significantly altered post-transplant with certain taxa and/or microbial genes potentially associated with acute allograft rejection/inflammation.},
}
@article {pmid39778526,
year = {2025},
author = {Kim, JH and Min, JH and Jo, YW and Kwon, JW and Her, Y},
title = {Association between acid-suppressive drugs and risk of psoriasis: retrospective study using Korean National Health Insurance Service-National Sample Cohort.},
journal = {The Korean journal of internal medicine},
volume = {40},
number = {1},
pages = {57-64},
doi = {10.3904/kjim.2024.096},
pmid = {39778526},
issn = {2005-6648},
support = {//Institute of Medical Sciences, Kangwon National University/ ; //National Research Foundation of Korea/ ; },
mesh = {Humans ; *Psoriasis/epidemiology/chemically induced ; Male ; Female ; *Proton Pump Inhibitors/adverse effects ; Republic of Korea/epidemiology ; Retrospective Studies ; Middle Aged ; Adult ; *Histamine H2 Antagonists/adverse effects ; Risk Factors ; Risk Assessment ; Aged ; Time Factors ; Young Adult ; Databases, Factual ; National Health Programs ; Gastric Acid/metabolism ; },
abstract = {BACKGROUND/AIMS: Psoriasis is a common inflammatory skin disorder following non-specific triggers. Involvement of immune system is widely accepted for pathogenesis studies have demonstrated importance of gut microbiota in pathogenesis of inflammatory skin diseases. Proton pump inhibitor (PPI) and histamine-2 receptor antagonist (H2RA) are acid-suppressive drugs widely used for acid related gastrointestinal diseases, and prolonged use has been associated with altered gut microbiota. This study aimed to investigate association between psoriasis and acid suppressing drugs in Korean population.<br><br>METHODS: This study was conducted with 3,662 patients diagnosed with psoriasis between 2002 and 2013 in NHIS-NSC. A total of 14,648 controls were matched at 1:4 based on sex, age, and gastrointestinal disease. ORs were estimated to determine the association between acid suppressing drug use and psoriasis.<br><br>RESULTS: Our study found a statistically significant association between the prolonged use of acid-suppressive drugs and the development of psoriasis in the Korean population. Specifically, patients with gastrointestinal diseases who used histamine-2 receptor antagonists (H2RA) or proton pump inhibitors (PPI) for extended periods exhibited a higher risk of developing psoriasis. The adjusted odds ratio for psoriasis was 1.89 (95% CI, 1.66-2.17) with long-term use, indicating a clear dose-response relationship.<br><br>CONCLUSION: Results from our study indicate that prolonged use of H2RA or PPI is associated with the risk of psoriasis among patients with gastrointestinal diseases in Korean population. The risk was increased in dose-response trend after adjusting for confounding variables. Clinicians should be aware of risks associated with prolonged use of acid suppressing drugs.},
}
@article {pmid39777720,
year = {2025},
author = {Shahin, NN and Ahmed-Farid, OA and Sakr, EAE and Kamel, EA and Mohamed, MM},
title = {Oral Supplements of Combined Lactobacillus plantarum and Asparagus officinalis Modulate Gut Microbiota and Alleviate High-Fat Diet-Induced Cognitive Deficits and Neurodegeneration in Rats.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {39777720},
issn = {1867-1314},
abstract = {High-fat diet (HFD) consumption disrupts the gut microbiome, instigating metabolic disturbance, brain pathology, and cognitive decline via the gut-brain axis. Probiotic and prebiotic supplementation have been found to improve gut microbiome health, suggesting they could be effective in managing neurodegenerative disorders. This study explored the potential benefits of the probiotic strain Lactobacillus plantarum 20174 (L. plantarum), prebiotic Asparagus officinalis (A. officinalis) extract, or their synbiotic combination against HFD-induced cognitive dysfunction and neurodegeneration in rats. Male Sprague-Dawley rats were fed either a normal diet or an HFD for 24 weeks. Starting from week 13, rats on either diet were divided into vehicle-, prebiotic-, probiotic-, and synbiotic-treated subgroups. Rats received their assigned intervention for 12 more weeks. Prebiotic, probiotic, or synbiotic treatment reverted HFD-instigated alterations in hippocampal amyloid beta, p-tau, α-synuclein, and BDNF levels, leading to restored cognitive function. The tested therapies also improved the HFD-disrupted lipid profile. Interestingly, probiotic and synbiotic therapies attenuated oxidative stress and inflammation, reinstated neurotransmitter balance, and mitigated the energy deficit in HFD-fed rats. Furthermore, L. plantarum and Asparagus administration modulated gut microbiota composition by raising Lactobacillus species and reducing Coliform and Staphylococci bacteria as well as fungi populations. These findings suggest that the oral consumption of A. officinalis prebiotics and/or L. plantarum probiotics alleviates HFD-induced cognitive deficit and neurodegeneration through modulation of the gut-brain axis with superior restorative effects being achieved by synbiotic treatment.},
}
@article {pmid39777551,
year = {2025},
author = {Nigro, A and Osman, A and Suryadevara, P and Cices, A},
title = {Vitiligo and the microbiome of the gut and skin: a systematic review.},
journal = {Archives of dermatological research},
volume = {317},
number = {1},
pages = {201},
pmid = {39777551},
issn = {1432-069X},
mesh = {*Vitiligo/microbiology ; Humans ; *Skin/microbiology/pathology ; *Gastrointestinal Microbiome/immunology ; *Dysbiosis/microbiology/immunology ; Microbiota/immunology ; },
abstract = {Vitiligo is a chronic autoimmune skin condition characterized by depigmentation due to the destruction of melanocytes. Recent research has identified potential links between vitiligo and alterations in both the gut and skin microbiomes. This systematic review aims to explore these microbiome changes and their potential role in the onset and progression of vitiligo. A comprehensive search of the PubMed, Medline (OVID), and Web of Science databases was conducted to identify studies examining the gut and/or skin microbiota in vitiligo patients. A total of six studies were included in the qualitative analysis. Data extracted included study type, patient demographics, microbiome sampling methods, bacterial diversity, and bacterial ratios. The studies were assessed using the Methodological Index for Non-Randomized Studies (MINORS) scale. The results revealed inconsistent findings regarding microbial diversity in vitiligo patients. Some studies observed decreased α-diversity in the gut microbiome, while others found an increase, particularly in patients with longer disease duration. An increased Firmicutes-to-Bacteroidetes ratio (higher levels of Firmicutes bacteria compared to Bacteroidetes) was noted in several studies, suggesting a dysbiotic gut microbiome. In the skin microbiome, similar trends of dysbiosis were observed, with alterations in bacterial diversity between lesional and non-lesional skin. The findings indicate that gut and skin microbiome changes may play a role in the pathogenesis of vitiligo. However, the data remain inconclusive due to variability in methodologies and sample sizes. Further research is needed to elucidate the clinical relevance of microbiome alterations in vitiligo, with a focus on controlling external factors such as diet and lifestyle.},
}
@article {pmid39777550,
year = {2025},
author = {Byers, AK and Wakelin, SA and Condron, L and Black, A},
title = {Land Use Change Disrupts the Network Complexity and Stability of Soil Microbial Carbon Cycling Genes Across an Agricultural Mosaic Landscape.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {167},
pmid = {39777550},
issn = {1432-184X},
mesh = {*Soil Microbiology ; *Carbon Cycle ; New Zealand ; *Agriculture ; *Soil/chemistry ; *Microbiota ; *Bacteria/genetics/classification/metabolism ; Carbon/metabolism ; Gene Regulatory Networks ; Forests ; Ecosystem ; },
abstract = {To understand the effects of agricultural land use change and management on soil carbon (C) cycling, it is crucial to examine how these changes can influence microbial soil C cycling. Network analysis can offer insights into the structure, complexity, and stability of the soil microbiome in response to environmental disturbances, including land use change. Using SparCC-based co-occurrence networks, we studied how land use change impacts the connectivity, complexity, and stability of microbial C-cycling gene networks across an agricultural mosaic landscape in Canterbury, New Zealand. The most densely connected networks were found in land uses that were under the most intensive agricultural management, or under naturally regenerating vegetation. The microbial C-cycling gene networks from both land uses presented high network connectivity, low modularity, and a low proportion of negative gene interactions. In contrast, microbial C-cycling genes from native forests, which had the most stable and undisturbed plant cover, had the lowest network connectivity, highest modularity, and a greater proportion of negative gene interactions. Although the differences in total soil C content between land uses were small, the large effects of land use on the network structure of microbial C-cycling genes may have important implications for long-term microbial soil C cycling. Furthermore, this research highlights the value of using microbial network analysis to study the metabolic gene interactions shaping the functional structure of soil microbial communities in a manner not typically captured by more traditional forms of microbial diversity analysis.},
}
@article {pmid39777420,
year = {2025},
author = {Ebrahim, M and Manji, K},
title = {Role of infant and early-childhood nutrition on gut inflammation, stunting, growth, and development in the African context: A narrative review.},
journal = {Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/ncp.11270},
pmid = {39777420},
issn = {1941-2452},
abstract = {This article synthesizes the existing research evidence from Tanzania, a low- to middle-income country, highlighting the persistent issue of growth stunting. Stunting begins early in life, potentially even in utero. It is becoming increasingly clear that infant and childhood environmental enteric dysfunction plays a significant role in perpetuating the observed stunting. The repercussions of this condition include poor growth and detrimental effects on neurodevelopment, preventing affected children from reaching their full potential. The economic implications of this are substantial. The manuscript outlines the trajectory from low birth weight and suboptimal lactation to altered weaning practices and changes in the gut microbiome. It also presents current perspectives on how to mitigate these adverse effects, with a focus on early interventions in lactation and feeding during the crucial first 1000 days of life.},
}
@article {pmid39777147,
year = {2024},
author = {Wang, Q and Liu, M and Liu, T and Li, L and Wang, C and Wang, X and Rong, S and Zhou, X},
title = {Alterations in the gut microbiome and metabolism with doxorubicin-induced heart failure severity.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1348403},
pmid = {39777147},
issn = {1664-302X},
abstract = {OBJECTIVE: This study aimed to explore the changes in gut microbiota and its metabolites in different pathophysiological stages of doxorubicin (DOX)-induced heart failure (DIHF) and the relationship between gut microbiota and metabolites in various degrees of DIHF.<br><br>MATERIALS AND METHODS: C57BL/6&#x202f;J mice were injected intraperitoneally with 5&#x202f;mg/kg of DOX once a week for 5&#x202f;consecutive weeks. At different times after injection, the cardiac function and histopathological analysis was conducted, the serum levels of creatine kinase (CK), CK-MB, lactic dehydrogenase, and cardiac troponin T were determined. 16S rRNA gene sequencing of feces and the nontargeted metabolomics analysis of serum were performed. Multi-omics analyses were used to explore the correlation between gut microbiota and serum metabolites.<br><br>RESULTS: The results showed that DOX caused cardiac contractile dysfunction and left ventricular (LV) dilation. The levels of myocardial enzymes significantly increase in 3 and 5&#x202f;weeks after DOX injection. DOX-treated mice showed significant differences in the composition and abundance of gut microorganisms, and the levels of serum metabolites at different times of treatment. Multi-omics analyses showed that intestinal bacteria were significantly correlated with the differential metabolites. Some bacteria and metabolites can be used as biomarkers of DIHF (AUC&#x202f;>&#x202f;0.8). KEGG analyses showed the involvement of different metabolic pathways in various degrees of DIHF.<br><br>CONCLUSION: Marked differences were found in the composition and abundance of gut microorganisms, the levels of serum metabolites and metabolic pathways in different degrees of DIHF. The intestinal bacteria were significantly correlated with differential metabolites in different degrees of DIHF. The gut microbiota may serve as new targets for the treatment of DIHF.},
}
@article {pmid39777145,
year = {2024},
author = {Wepking, C and Lucas, JM and Boulos, VS and Strickland, MS},
title = {Antibiotic legacies shape the temperature response of soil microbial communities.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1476016},
pmid = {39777145},
issn = {1664-302X},
abstract = {Soil microbial communities are vulnerable to anthropogenic disturbances such as climate change and land management decisions, thus altering microbially-mediated ecosystem functions. Increasingly, multiple stressors are considered in investigations of ecological response to disturbances. Typically, these investigations involve concurrent stressors. Less studied is how historical stressors shape the response of microbial communities to contemporary stressors. Here we investigate how historical exposure to antibiotics drives soil microbial response to subsequent temperature change. Specifically, grassland plots were treated with 32-months of manure additions from cows either administered an antibiotic or control manure from cows not treated with an antibiotic. In-situ antibiotic exposure initially increased soil respiration however this effect diminished over time. Following the 32-month field portion, a subsequent incubation experiment showed that historical antibiotic exposure caused an acclimation-like response to increasing temperature (i.e., lower microbial biomass at higher temperatures; lower respiration and mass-specific respiration at intermediate temperatures). This response was likely driven by a differential response in the microbial community of antibiotic exposed soils, or due to indirect interactions between manure and soil microbial communities, or a combination of these factors. Microbial communities exposed to antibiotics tended to be dominated by slower-growing, oligotrophic taxa at higher temperatures. Therefore, historical exposure to one stressor is likely to influence the microbial community to subsequent stressors. To predict the response of soils to future stress, particularly increasing soil temperatures, historical context is necessary.},
}
@article {pmid39776918,
year = {2024},
author = {Chrisman, LP and Pang, Y and Hooper, MJ and Rajeev-Kumar, G and Nguyen, WQ and Green, SJ and Seed, PC and Liang, H and Mittal, BB and Hasan, Y and Guitart, J and Weichselbaum, RR and Burns, MB and Zhou, XA},
title = {Ionizing radiation improves skin bacterial dysbiosis in cutaneous T-cell lymphoma.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1520214},
pmid = {39776918},
issn = {1664-3224},
mesh = {Humans ; *Lymphoma, T-Cell, Cutaneous/microbiology/radiotherapy ; *Dysbiosis/microbiology ; *Skin/microbiology/radiation effects ; Male ; Female ; Middle Aged ; *Microbiota/radiation effects ; *Radiation, Ionizing ; Aged ; Skin Neoplasms/microbiology/etiology/radiotherapy ; Bacteria/classification/radiation effects/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Adult ; },
abstract = {INTRODUCTION: Cutaneous T-cell lymphoma (CTCL) is closely associated with the host microbiome. While recent evidence suggests that shifts in specific bacterial taxa are associated with response to UV-B, a form of non-ionizing radiation, the impact of ionizing radiation (IR) has not been investigated.<br><br>METHODS: 16S rRNA and tuf gene amplicon sequencing were performed on DNA extracted from swabs of lesional/non-lesional skin of 12 CTCL patients before/after TSEBT or local IR and from 25 matched healthy controls (HC). Microbial diversity and taxonomic profiles were analyzed.<br><br>RESULTS: Radiation exposure increased CTCL skin &#x3b1;-diversity to levels approximating HC. TSEBT appeared to carry the greatest effect compared to local IR. Both &#x3b1; and &#x3b2;-diversity differed significantly post versus pre-IR for TSEBT, but not for local IR. IR was associated with decreases in known pathogenic bacteria such as Streptococcus and S. aureus and increases in healthy commensal bacteria such as Anaerococcus, Bifidobacterium and commensal staphylococci including S. pettenkoferi. Substantially more taxa shifts were seen with TSEBT versus local IR.<br><br>DISCUSSION: IR not only eliminates CTCL lesions via induction of apoptosis, but also facilitates skin barrier restoration and recolonization of bacterial taxa associated with a healthy skin microbiome. Local IR does not have as strong an effect on the skin microbiome as TSEBT. As skin microbiota act as immunomodulators with local and potentially systemic influence, TSEBT may also improve CTCL lesions via global effects on the skin microbiome. Future larger-scale studies are required to fully elucidate the relationship between cutaneous microbes and IR treatment in CTCL.},
}
@article {pmid39776539,
year = {2024},
author = {Chandel, N and Maile, A and Shrivastava, S and Verma, AK and Thakur, V},
title = {Establishment and perturbation of human gut microbiome: common trends and variations between Indian and global populations.},
journal = {Gut microbiome (Cambridge, England)},
volume = {5},
number = {},
pages = {e8},
pmid = {39776539},
issn = {2632-2897},
abstract = {Human gut microbial species are crucial for dietary metabolism and biosynthesis of micronutrients. Digested products are utilised by the host as well as several gut bacterial species. These species are influenced by various factors such as diet, age, geographical location, and ethnicity. India is home to the largest human population in the world. It is spread across diverse ecological and geographical locations. With variable dietary habits and lifestyles, Indians have unique gut microbial composition. This review captures contrasting and common trends of gut bacterial community establishment in infants (born through different modes of delivery), and how that bacterial community manifests itself along infancy, through old age between Indian and global populations. Because dysbiosis of the gut community structure is associated with various diseases, this review also highlights the common and unique bacterial species associated with various communicable as well as noncommunicable diseases such as diarrhoea, amoebiasis, malnutrition, type 2 diabetes, obesity, colorectal cancer, inflammatory bowel disease, and gut inflammation and damage to the brain in the global and Indian population.},
}
@article {pmid39776521,
year = {2024},
author = {Suther, C and Alba, B and Yurkevicius, BR and Radcliffe, PN and Fagnant, HS and Castellani, J and Karl, JP},
title = {Effects of short-term, high-dose cocoa-derived flavanol supplementation on gut microbiota composition: secondary findings from a randomized, double-blind, placebo-controlled crossover study.},
journal = {Journal of nutritional science},
volume = {13},
number = {},
pages = {e22},
pmid = {39776521},
issn = {2048-6790},
mesh = {Humans ; Double-Blind Method ; *Cross-Over Studies ; *Gastrointestinal Microbiome/drug effects ; Adult ; Male ; Female ; *Dietary Supplements ; *Feces/microbiology ; *Cacao ; *Bifidobacterium ; *Lactobacillus ; *Prebiotics ; Young Adult ; RNA, Ribosomal, 16S ; Flavonols/pharmacology ; },
abstract = {Cocoa-derived flavanols (CDF) may act as prebiotics. However, evidence is inconsistent, and the duration and dose of CDF intake needed to elicit any prebiotic effect are undefined. This randomized, double-blind, crossover study determined the effects of short-term, high-dose dietary supplementation with CDF versus matched placebo on gut microbiota composition in 8 healthy adults. A single faecal sample was collected 8 d after supplementation with 900 mg/d CDF or placebo. Gut microbiota composition and Bifidobacterium spp. and Lactobacillus spp. abundance were measured as secondary outcomes by 16S ribosomal ribonucleic acid (rRNA) amplicon sequencing and quantitative polymerase chain reaction, respectively. No between-treatment differences in the relative or absolute abundance of Bifidobacterium spp. (Cohen's d = 0.89, P = 0.22) or Lactobacillus spp. (Cohen's d = 0.42, P = 0.65) were detected. Shannon diversity (Cohen's d = 0.38, P = 0.04) and overall community richness (Cohen's d = 0.34, P = 0.06) were lower following CDF supplementation versus placebo, but no between-treatment differences in β-diversity or taxa relative abundances were observed. Findings are not consistent with a clear prebiotic effect of this short-term, high-dose CDF supplementation strategy relative to placebo.},
}
@article {pmid39776440,
year = {2024},
author = {Fang, L and Ning, J},
title = {Recent advances in gut microbiota and thyroid disease: pathogenesis and therapeutics in autoimmune, neoplastic, and nodular conditions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1465928},
pmid = {39776440},
issn = {2235-2988},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Probiotics/therapeutic use ; *Thyroid Diseases/therapy/microbiology ; *Fecal Microbiota Transplantation ; Animals ; Bacteria/classification/metabolism ; Neoplasms/therapy/microbiology ; Dysbiosis/therapy/microbiology ; },
abstract = {This review synthesizes key findings from the past five years of experimental literature, elucidating the gut microbiome's significant influence on the pathogenesis of thyroid diseases. A pronounced shift in the gut microbiota composition has been consistently observed, with a significant reduction in bacteria such as Bifidobacterium, Bacillaceae, Megamonas, and Clostridium, and a notable increase in bacteria, including Bacteroides, Proteobacteria, Actinobacteria, Desulfobacterota, and Klebsiella. These alterations are implicated in the development and progression of thyroid diseases by impacting metabolic pathways including bile acid and cytokine production, including a decrease in short-chain fatty acids (SCFAs) that are crucial for immune regulation and thyroid hormone homeostasis. The review also highlights the therapeutic implications of probiotics in managing thyroid conditions. Evidence suggests that probiotic adjunct therapy can modulate the gut microbiota, leading to improvements in thyroid function and patient outcomes. The use of specific probiotic strains, such as Lactiplantibacillus plantarum 299v and Bifidobacterium longum, has demonstrated potential in enhancing the effects of traditional treatments and possibly restoring a balanced gut microbiota. Notably, fecal microbiota transplantation (FMT) has emerged as a promising intervention in Graves' Disease (GD), demonstrating the potential to recalibrate the gut microbiota, thereby influencing neurotransmitters and trace elements via the gut-brain and gut-thyroid axes. The integration of microbiome-based therapies with traditional treatments is anticipated to usher in a new era of personalized thyroid disease management, offering a more nuanced approach to patient care. By integrating this body of work, the review offers an innovative perspective on the gut microbiome's broad impact on thyroid diseases and the therapeutic applications of probiotics.},
}
@article {pmid39776217,
year = {2025},
author = {Yang, HH and Simpson, CA and Srivastava, M and Bera, A and Cappelletti, M and Suh, JD and Wang, M and Beswick, DM and Maxim, T and Basak, SK and Srivatsan, ES and Fischer, JL and Jacobs, JP and Lee, JT},
title = {Biodiversity of the Bacterial and Fungal Microbiome and Associated Inflammatory Cytokine Profile in Chronic Rhinosinusitis.},
journal = {International forum of allergy &amp; rhinology},
volume = {},
number = {},
pages = {},
doi = {10.1002/alr.23519},
pmid = {39776217},
issn = {2042-6984},
abstract = {BACKGROUND: Dysbiosis of the bacterial and fungal microbiome has been increasingly implicated in the pathogenesis of chronic rhinosinusitis (CRS). This study explores the relationship between microbiome and mycobiome biodiversity and type 2 (T2) versus non-type 2 (NT2) inflammation.<br><br>METHODS: Mucosal tissues from the ethmoid sinus were collected during endoscopic sinus (CRS) and skull base (controls) surgery between January 2020 and July 2021. Specimens underwent 16S rRNA (bacterial) and internal transcribed spacer (fungal) gene sequencing, along with cytokine analysis using the Luminex assay. Based on cytokine (IL-4, IL-5, IL-13) concentrations and the presence of eosinophils, CRS cases were classified into T2 or NT2 inflammatory profiles. The relationships between CRS endotype and the biodiversity of the microbiome and mycobiome were assessed.<br><br>RESULTS: Specimens from 92 patients (30 control, 31 CRSwNP, 31 CRSsNP) were included in the analyses. Among 62 CRS cases, 20 exhibited T2 inflammation and 42 exhibited NT2 inflammation. Compared with control specimens, NT2 specimens exhibited significantly lower amplicon sequence variants (mean difference -149, 95% CI [-261, -37], p&#xa0;=&#xa0;0.007), Shannon index (-0.48 [-0.79, -0.16], p&#xa0;=&#xa0;0.002), and Simpson index (-0.003 [-0.005, -0.001], p&#xa0;=&#xa0;0.002) for bacterial alpha diversity. However, no significant differences in bacterial alpha diversity were observed between T2 specimens and controls, or between T2 and NT2 specimens. Fungal biodiversity did not differ significantly across endotype and control groups.<br><br>CONCLUSION: Dysbiosis of the sinus bacterial microbiome is more strongly associated with a NT2-mediated inflammatory profile than with a T2-mediated inflammatory profile.},
}
@article {pmid39775524,
year = {2025},
author = {Mancin, L and Burke, LM and Rollo, I},
title = {Fibre: The Forgotten Carbohydrate in Sports Nutrition Recommendations.},
journal = {Sports medicine (Auckland, N.Z.)},
volume = {},
number = {},
pages = {},
pmid = {39775524},
issn = {1179-2035},
abstract = {Although dietary guidelines concerning carbohydrate intake for athletes are well established, these do not include recommendations for daily fibre intake. However, there are many scenarios in sports nutrition in which common practice involves the manipulation of fibre intake to address gastrointestinal comfort around exercise, or acute or chronic goals around the management of body mass or composition. The effect of fibre intake in overall health is also important, particularly in combination with other dietary considerations such as the elevated protein requirements in this population. An athlete's habitual intake of dietary fibre should be assessed. If less than 20 g a day, athletes may consider dietary interventions to gradually increase intake. It is proposed that a ramp phase is adopted to gradually increase fibre ingestion to ~ 30 g of fibre a day (which includes ~ 2 g of beta-glucan) over a duration of 6 weeks. The outcomes of achieving a daily fibre intake are to help preserve athlete gut microbiome diversity and stability, intestinal barrier function as well as the downstream effects of short-chain fatty acids produced following the fermentation of microbiome accessible carbohydrates. Nevertheless, there are scenarios in which daily manipulation of fibre intake, either to reduce or increase intake, may be valuable in assisting the athlete to maintain gastrointestinal comfort during exercise or to contribute to body mass/composition goals. Although further research is required, the aim of this current opinion paper is to ensure that fibre is not forgotten as a nutrient in the athlete's diet.},
}
@article {pmid39775305,
year = {2025},
author = {Xu, Y and Wang, Z and Li, C and Tian, S and Du, W},
title = {Droplet microfluidics: unveiling the hidden complexity of the human microbiome.},
journal = {Lab on a chip},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4lc00877d},
pmid = {39775305},
issn = {1473-0189},
abstract = {The human body harbors diverse microbial communities essential for maintaining health and influencing disease processes. Droplet microfluidics, a precise and high-throughput platform for manipulating microscale droplets, has become vital in advancing microbiome research. This review introduces the foundational principles of droplet microfluidics, its operational capabilities, and wide-ranging applications. We emphasize its role in enhancing single-cell sequencing technologies, particularly genome and RNA sequencing, transforming our understanding of microbial diversity, gene expression, and community dynamics. We explore its critical function in isolating and cultivating traditionally unculturable microbes and investigating microbial activity and interactions, facilitating deeper insight into community behavior and metabolic functions. Lastly, we highlight its broader applications in microbial analysis and its potential to revolutionize human health research by driving innovations in diagnostics, therapeutic development, and personalized medicine. This review provides a comprehensive overview of droplet microfluidics' impact on microbiome research, underscoring its potential to transform our understanding of microbial dynamics and their relevance to health and disease.},
}
@article {pmid39775194,
year = {2025},
author = {Huang, A and Yeum, D and Sewaybricker, LE and Aleksic, S and Thomas, M and Melhorn, SJ and Earley, YF and Schur, EA},
title = {Update on Hypothalamic Inflammation and Gliosis: Expanding Evidence of Relevance Beyond Obesity.},
journal = {Current obesity reports},
volume = {14},
number = {1},
pages = {6},
pmid = {39775194},
issn = {2162-4968},
support = {P30DK035816//University of Washington Nutrition Obesity Research Center/ ; P30DK035816//University of Washington Nutrition Obesity Research Center/ ; P30DK035816//University of Washington Nutrition Obesity Research Center/ ; AHA#929228//American Heart Association/ ; 1K76AG083274//National Institute on Aging and American Federation for Aging Research/ ; R01HL122770/NH/NIH HHS/United States ; R01DK089036, R01DK117623, R01DK098466, R01DK134417, R01DK133356, K24HL144917, R01DK136602/NH/NIH HHS/United States ; },
mesh = {Humans ; *Gliosis ; *Obesity/complications ; *Hypothalamus ; Female ; Pregnancy ; Gastrointestinal Microbiome ; Inflammation ; Male ; Magnetic Resonance Imaging ; Prenatal Exposure Delayed Effects ; Polycystic Ovary Syndrome/complications ; Adult ; Hypogonadism ; Animals ; Child ; Hypothalamic Diseases/complications ; Obesity, Maternal/complications ; },
abstract = {PURPOSE OF REVIEW: To evaluate the role of hypothalamic inflammation and gliosis in human obesity pathogenesis and other disease processes influenced by obesity.<br><br>RECENT FINDINGS: Recent studies using established and novel magnetic resonance imaging (MRI) techniques to assess alterations in hypothalamic microarchitecture in humans support the presence of hypothalamic inflammation and gliosis in adults and children with obesity. Studies also identify prenatal exposure to maternal obesity or diabetes as a risk factor for hypothalamic inflammation and gliosis and increased obesity risk in offspring. Hypothalamic inflammation and gliosis have been further implicated in reproductive dysfunction (specifically polycystic ovarian syndrome and male hypogonadism), cardiovascular disease namely hypertension, and alterations in the gut microbiome, and may also accelerate neurocognitive aging. The most recent translational studies support the link between hypothalamic inflammation and gliosis and obesity pathogenesis in humans and expand our understanding of its influence on broader aspects of human health.},
}
@article {pmid39775133,
year = {2025},
author = {Zhang, Y and Chen, H and Shi, Y and Jiang, L and Hong, S},
title = {Genetic association between human skin microbiota with vaginitis: a two-sample Mendelian randomization study.},
journal = {Archives of dermatological research},
volume = {317},
number = {1},
pages = {191},
pmid = {39775133},
issn = {1432-069X},
mesh = {Humans ; Female ; *Microbiota/genetics ; *Mendelian Randomization Analysis ; *Skin/microbiology/pathology ; *Genome-Wide Association Study ; *Vaginitis/microbiology/diagnosis/epidemiology ; Genetic Predisposition to Disease ; },
abstract = {The human skin microbiome is closely associated with various diseases. We aimed to find the causal association of the human skin microbiome with vaginitis. A two-way two-sample Mendelian randomization study used summary statistics of the human skin microbiota from the largest genome-wide association study meta-analysis. Pooled statistics for vaginitis disease were obtained from the FinnGen consortium R10 release. Inverse variance weighted, MR-Egger, weighted median, weighted model, MR-PRESSO, and STEIGER methods were used to test for causal associations between different parts of the human skin microbiota and vaginitis disease in either dry or moist environments. IVW estimates suggest that phylococcus hominischaracterizes a protective effect against vaginitis lesions at the Antecubitalfossa wet site. Staphylococcus in the dry state at the Dorsalforearm site also demonstrated a protective effect against vaginitis lesions. Micrococcus showed a trend of up-regulation of vaginitis risk under IVW method estimation. In contrast, Anaerococcus and Veillonella were associated with a low risk of vaginitis as estimated by the IVW method: ASV061 and ASV065. In the Class, IVW estimation showed that Bacilli at Antecubitalfossa site had an increased risk effect on vaginitis in the moist skin condition. Similarly in Genus, Staphylococcus at Antecubitalfossa sites had an increased risk effect against vaginitis in the moist skin condition. Based on the results of the inverse MR analysis, no significant causal effect of vaginitis on the human skin microbiota was found. This two-sample bidirectional Mendelian randomization study found a causal relationship between seven human skin microbiota and vaginitis, further enriching our understanding of the value of skin flora in reproductive diseases such as vaginitis.},
}
@article {pmid39774821,
year = {2025},
author = {},
title = {Dietary exclusion of major food groups shapes the gut microbiome and may influence health.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39774821},
issn = {2058-5276},
}
@article {pmid39774633,
year = {2025},
author = {Burke, RM and Ramani, S and Lynch, J and Cooper, LV and Cho, H and Bandyopadhyay, AS and Kirkwood, CD and Steele, AD and Kang, G},
title = {Geographic disparities impacting oral vaccine performance: Observations and future directions.},
journal = {Clinical and experimental immunology},
volume = {},
number = {},
pages = {},
doi = {10.1093/cei/uxae124},
pmid = {39774633},
issn = {1365-2249},
abstract = {Oral vaccines have several advantages compared with parenteral administration: they can be relatively cheap to produce in high quantities, easier to administer, and induce intestinal mucosal immunity that can protect against infection. These characteristics have led to successful use of oral vaccines against rotavirus, polio, and cholera. Unfortunately, oral vaccines for all three diseases have demonstrated lower performance in the highest-burden settings where they are most needed. Rotavirus vaccines are estimated to have >85% effectiveness against hospitalization in children <12 months in countries with low child mortality, but only ~65% effectiveness in countries with high child mortality. Similarly, oral polio vaccines have lower immunogenicity in developing country settings compared with high-resource settings. Data are more limited for oral cholera vaccines, but suggest lower titers among children compared with adults, and, for some vaccines, lower efficacy in endemic settings compared with non-endemic settings. These disparities are likely multifactorial, and available evidence suggests a role for maternal factors (e.g., transplacental antibodies, breastmilk), host factors (e.g., genetic polymorphisms-with the best evidence for rotavirus-or previous infection), and environmental factors (e.g., gut microbiome, coinfections). Overall, these data highlight the rather ambiguous and often contradictory nature of evidence on factors affecting oral vaccine response, cautioning against broad extrapolation of outcomes based on one population or one vaccine type. Meaningful impact on performance of oral vaccines will likely only be possible with a suite of interventions, given the complex and multifactorial nature of the problem and the degree to which contributing factors are intertwined.},
}
@article {pmid39774594,
year = {2025},
author = {Ali, S and Peña, AN and Lafazanos, YS and Ehrenpreis, ED},
title = {What Gastroenterologists Should Know About Microplastics and Nanoplastics.},
journal = {Journal of clinical gastroenterology},
volume = {59},
number = {2},
pages = {105-109},
doi = {10.1097/MCG.0000000000002085},
pmid = {39774594},
issn = {1539-2031},
mesh = {*Microplastics/toxicity ; Humans ; *Gastrointestinal Microbiome ; Animals ; Nanoparticles/adverse effects ; Gastrointestinal Tract/drug effects/metabolism ; Gastroenterologists ; Environmental Exposure/adverse effects ; Inflammatory Bowel Diseases ; },
abstract = {Global production and widespread use of plastics are increasing dramatically. With current limited recycling and recovery options, microplastics and nanoplastics (MNPs) persist in the natural environment. Due to their ubiquity, human exposure to MNPs is inevitable. In addition to their inherent toxic effects, MNPs can adsorb harmful contaminants and act as vectors for microorganisms, compounding toxicological effects. After entering the body, bioaccumulation occurs in several tissues and organs, including the liver and the gastrointestinal (GI) tract. Proposed clinical effects of MNP absorption include endocrine disruption, alteration of the GI microbiome, and promotion of chronic inflammatory conditions. MNPs can also influence energy metabolism, activate inflammatory pathways, and increase oxidative stress leading to apoptosis. The GI tract is a major site of bioaccumulation for the MNPs in animals and humans. In this editorial, the current understanding of how MNPs are processed is discussed. Discussion on MNP effects on internal microflora, and their proposed role in developing inflammatory bowel diseases, MNP toxicokinetics, and their significance in health and disease are also reviewed. There is a need to understand the impact of MNP exposure on gut health and gut microbiota and identify current research gaps.},
}
@article {pmid39774426,
year = {2024},
author = {Segura, D and Sharma, D and Espin-Garcia, O},
title = {Comparing subsampling strategies for metagenomic analysis in microbial studies using amplicon sequence variants versus operational taxonomic units.},
journal = {PloS one},
volume = {19},
number = {12},
pages = {e0315720},
pmid = {39774426},
issn = {1932-6203},
mesh = {Humans ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome/genetics ; Microbiota/genetics ; Infant ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification ; Metagenome/genetics ; },
abstract = {The microbiome is increasingly regarded as a key component of human health, and analysis of microbiome data can aid in the development of precision medicine. Due to the high cost of shotgun metagenomic sequencing (SM-seq), microbiome analyses can be done cost-effectively in two phases: Phase 1-sequencing of 16S ribosomal RNA, and Phase 2-SM-seq of an informative subsample. Existing research suggests strategies to select the subsample based on biological diversity and dissimilarity metrics calculated using operational taxonomic units (OTUs). However, the microbiome field has progressed towards amplicon sequencing variants (ASVs), as they provide more precise microbe identification and sample diversity information. The aim of this work is to compare the subsampling strategies for two-phase metagenomic studies when using ASVs instead of OTUs, and to propose data driven strategies for subsample selection through dimension reduction techniques. We used 199 samples of infant-gut microbiome data from the DIABIMMUNE project to generate ASVs and OTUs, then generated subsamples based on five existing biologically driven subsampling methods and two data driven methods. Linear discriminant analysis Effect Size (LEfSe) was used to assess differential representation of taxa between the subsamples and the overall sample. The use of ASVs showed a 50-93% agreement in the subsample selection with the use of OTUs for the subsampling methods evaluated, and showed a similar bacterial representation across all methods. Although sampling using ASVs and OTUs typically lead to similar results for each subsample, ASVs had more clades that differed in expression levels between allergic and non-allergic individuals across all sample sizes compared to OTUs, and led to more biomarkers discovered at Phase 2-SM-seq level.},
}
@article {pmid39774258,
year = {2024},
author = {Raehtz, KD and Pandrea, I and Apetrei, C},
title = {It's all in the gut: the central role of the gut and microbiome in preventing disease progression in simian immunodeficiency viruses infected African nonhuman primates.},
journal = {Current opinion in HIV and AIDS},
volume = {},
number = {},
pages = {},
doi = {10.1097/COH.0000000000000911},
pmid = {39774258},
issn = {1746-6318},
abstract = {PURPOSE OF REVIEW: Typically, both HIV-infected humans and simian immunodeficiency virus (SIV)-infected Asian nonhuman primates (NHPs) eventually progress to AIDS, while African NHPs that are natural hosts of SIV do not, in spite of life-long, high levels of viral replication. Lack of disease progression in African NHPs is not due to some adaptation by the virus, but rather to host adaptations to the virus. Central to these adaptations is maintenance of the gut integrity during acute viral replication and inflammation, which allows natural hosts to avoid the chronic inflammation characteristic to pathogenic HIV/SIV infection.<br><br>RECENT FINDINGS: It has been recently shown that natural hosts of SIVs, such as the African green monkey (AGM), avoid damage to the mucosal epithelium through wound healing mechanisms, possibly with the contribution of a unique anti-inflammatory microbiome. Furthermore, these mechanisms are independent of viral replication, and CD4+ T-cell activation or depletion.<br><br>SUMMARY: Future SIV research on natural hosts should focus on further elucidating the anti-inflammatory state of their gut, and the role of microbiome/dysbiosis in the pathogenesis of SIV infection, with the goal of development new regiments or treatments to reduce or even halt the vicious cycle of gut damage and inflammation triggered by pathogenic HIV/SIV infection.},
}
@article {pmid39773995,
year = {2024},
author = {Mullish, BH and Innes, AJ and Roberts, LA and Anim-Burton, S and Webber, L and Johnson, NA and Ghani, R and Farshi, P and Khan, AB and Kinsella, F and Kottaridis, P and Krishnamurthy, P and Nicholson, E and Palanicawandar, R and Wheeler, G and Davies, F and Marchesi, JR and Pavlů, J},
title = {Intestinal Microbiota Transplant Prior to Allogeneic Stem Cell Transplant (MAST) trial: study protocol for a multicentre, double-blinded, placebo-controlled, phase IIa trial.},
journal = {BMJ open},
volume = {14},
number = {12},
pages = {e093120},
doi = {10.1136/bmjopen-2024-093120},
pmid = {39773995},
issn = {2044-6055},
mesh = {Adult ; Female ; Humans ; Male ; Clinical Trials, Phase II as Topic ; Double-Blind Method ; Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Hematologic Neoplasms/therapy ; *Hematopoietic Stem Cell Transplantation ; Multicenter Studies as Topic ; Randomized Controlled Trials as Topic ; Transplantation Conditioning/methods ; *Transplantation, Homologous ; },
abstract = {INTRODUCTION: Lower diversity of the gut microbiome prior to allogeneic haematopoietic cell transplantation (HCT) correlates with reduced survival after the intervention. Most patients undergoing HCT for a haematological malignancy have previously received intensive chemotherapy, resulting in prolonged neutropenic episodes requiring broad-spectrum antibiotics; use of these has been linked to reduced microbiome diversity. Intestinal microbiota transplant (IMT) is a novel treatment approach that restores this diversity. We hypothesised that IMT performed prior to initiation of HCT conditioning restores microbiome diversity during the early stages of HCT, leading to decreased frequency of complications and improved outcomes of HCT.<br><br>METHODS AND ANALYSIS: 50 adult patients receiving allogeneic HCT will be recruited into this phase IIa trial and randomised 1:1 to receive capsulised IMT or matched placebo shortly prior to initiation of HCT conditioning and followed for up to 12 months. The primary outcome will be to assess the increase in alpha diversity between pre-IMT and that measured at ~42 days after IMT administration (day +28 of HCT), comparing the difference between patients receiving IMT compared with placebo. Secondary outcomes will include tolerability, the dynamics of gut microbiome diversity metrics and taxonomy over all time points assessed, as well as clinical outcomes (including burden of invasive infections, days of fever, admission to intensive care, development of graft-vs-host disease and mortality).<br><br>ETHICS AND DISSEMINATION: This study was approved by a UK Research Ethics Committee (REC reference: 23/NE/0105). Dissemination of results will be in concert with patient and public involvement group input and is expected to be primarily via abstract presentation at conferences and manuscripts in peer-reviewed journals.<br><br>TRIAL REGISTRATION NUMBERS: NCT6355583; EudraCT: 2022-003617-10.},
}
@article {pmid39773949,
year = {2025},
author = {Portlock, T and Shama, T and Kakon, SH and Hartjen, B and Pook, C and Wilson, BC and Bhuttor, A and Ho, D and Shennon, I and Engelstad, AM and Di Lorenzo, R and Greaves, G and Rahman, N and Kelsey, C and Gluckman, PD and O'Sullivan, JM and Haque, R and Forrester, T and Nelson, CA},
title = {Interconnected pathways link faecal microbiota plasma lipids and brain activity to childhood malnutrition related cognition.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {473},
pmid = {39773949},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Brain/metabolism ; *Feces/microbiology ; Male ; Female ; *Cognition/physiology ; Bangladesh ; Lipids/blood ; Electroencephalography ; Child Nutrition Disorders/microbiology ; Bacteroides fragilis/physiology/isolation &amp; purification ; },
abstract = {Malnutrition affects over 30 million children annually and has profound immediate and enduring repercussions. Survivors often suffer lasting neurocognitive consequences that impact academic performance and socioeconomic outcomes. Mechanistic understanding of the emergence of these consequences is poorly understood. Using multi-system SHAP interpreted random forest models and network analysis, we show that Moderate Acute Malnutrition (MAM) associates with enrichment of faecal Rothia mucilaginosa, Streptococcus salivarius and depletion of Bacteroides fragilis in a cohort of one-year-old children in Dhaka, Bangladesh. These microbiome changes form interconnected pathways that involve reduced plasma odd-chain fatty acid levels, decreased gamma and beta electroencephalogram power in temporal and frontal brain regions, and reduced vocalization. These findings support the hypothesis that prolonged colonization by oral commensal species delay gut microbiome and brain development. While causal links require empirical validation, this study provides insights to improve interventions targeting MAM-associated neurodevelopmental deficits.},
}
@article {pmid39773907,
year = {2024},
author = {Català-Moll, F and Paredes, R},
title = {The rectal microbiome: understanding its role in HIV transmission.},
journal = {Current opinion in HIV and AIDS},
volume = {},
number = {},
pages = {},
doi = {10.1097/COH.0000000000000906},
pmid = {39773907},
issn = {1746-6318},
abstract = {PURPOSE OF THE REVIEW: Condomless receptive anal intercourse stands out as the sexual practice with highest risk of HIV-1 infection. Recent studies have suggested that the gut microbiome influences susceptibility to HIV transmission. This review explores recent research on host risk factors, the rectal microbiome composition, local inflammation, and bacteria-derived mediators that may affect HIV transmission.<br><br>RECENT FINDINGS: Constitutive host factors such as rectal mucosal structure and immune cell populations in the rectum contribute to increased susceptibility. Changes in the composition of the rectal microbiota, influenced by sexual practices and HIV infection modulate immune activation and inflammation, impacting HIV susceptibility. Bacteria-derived mediators may further influence immune responses and HIV replication in the rectal mucosa.<br><br>SUMMARY: Understanding the role of the rectal microbiome in HIV transmission has important clinical implications. Targeted interventions that modulate the microbiome may reduce susceptibility to HIV transmission by regulating immune responses and inflammation. Further research into the host-microbiome interactions could lead to novel preventive and therapeutic strategies to mitigate HIV transmission.},
}
@article {pmid39773704,
year = {2025},
author = {Gong, SG and Switzer, J and Nainar, SMH and Lévesque, CM},
title = {Microbiome in Early Childhood Caries: Caries Severity-Dependent Insights.},
journal = {Caries research},
volume = {},
number = {},
pages = {1-17},
doi = {10.1159/000543421},
pmid = {39773704},
issn = {1421-976X},
abstract = {INTRODUCTION: Children with early childhood caries (ECC) show different caries severities and susceptibility in different tooth types and location in the oral cavity. The study aimed to investigate differences in the oral microbiome in ECC subjects stratified according to the severity of caries and between more and less caries prone teeth within the same subjects.<br><br>METHODS: Supragingival plaque from the upper and lower anterior regions in the oral cavity of subjects were collected in 3 groups of increasing caries severity, G1 - Molar (M) caries only; G2 - Molar and Upper Anterior (UA) caries; and G3 - M + UA + lower anterior (LA) caries were obtained followed by microbiome analysis.<br><br>RESULTS: Alpha-diversity analyses showed inter- but no intra-individual statistically significant differences between the UA and LA (p-value &#x2c2; 0.001, LA&#x2c3;UA), and a significant difference between the microbiome of the three caries groups (p-value &#x2c2; 0.001). There were significant beta-diversity differences between G1 and G2 (p < 0.05) and in the composition and diversity among the three groups (p-value &#x2c2; 0.001). Actinomyces, Saccharibacteria_genera_inserta_sedis and Eikenella had increased differential abundance in G1 vs G3 and Fusobacterium was less abundant in G2 compared to the other groups.<br><br>CONCLUSIONS: There were clear distinct differences in tooth-site specific and caries-severity microbiome diversity patterns and bacterial abundance profiles in S-ECC children.},
}
@article {pmid39773069,
year = {2025},
author = {Beckers, KF and Schulz, CJ and Flanagan, JP and Blair, RV and Liu, CC and Childers, GW and Sones, JL},
title = {Pregnancy specific shifts in the maternal microbiome and metabolome in the BPH5 mouse model of superimposed preeclampsia.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00106.2024},
pmid = {39773069},
issn = {1531-2267},
support = {P20GM135002//HHS | National Institutes of Health (NIH)/ ; R01HL165467//HHS | National Institutes of Health (NIH)/ ; },
abstract = {Preeclampsia (PE) is a life-threatening hypertensive disorder of pregnancy with an incidence rate of up to 8% worldwide. However, the complete pathogenesis is still unknown. Obesity increases the risk of developing PE three-fold. To better understand the relationship of maternal risk factors, the BPH/5 mouse was described as a model of superimposed PE. Previous research demonstrated that adult BPH/5 female mice have an adverse cardiometabolic phenotype characterized by hypertension, obesity with increased white adipose tissue and dyslipidemia, exaggerated by pregnancy. We hypothesize that BPH/5 mice have gut dysbiosis characterized by changes in alpha and beta diversity of bacterial community structure as well as perturbed short chain fatty acids (SCFA) compared to controls in pregnancy. Fecal samples were used for Illumina sequencing of 16S v4 rRNA amplicons. Microbial community composition of the pregnant BPH/5 compared to C57 controls was different using PERMANOVA with Bray-Curtis dissimilarity. Alpha diversity was increased in pregnant BPH/5 dams compared to controls. Alistipes and Helicobacter were increased while Bacteroides, Lactobacillus, Parasulterrella, and Parabacteroides were decreased compared to controls. Fecal SCFAs were not different between groups, but BPH/5 serum acetic and butyric acid were decreased while isobutyric and isovaleric acid were increased specifically in pregnancy. BPH/5 pregnant colons had decreased expression of free fatty acid receptor, GPR41. In conclusion, the BPH/5 maternal fecal microbiome demonstrates microbial dysbiosis characterized by community structure and diversity changes before and after the onset of pregnancy. Gut dysbiosis may be a key mechanism linking SCFA signaling and obesity to the BPH/5 PE-like phenotype.},
}
@article {pmid39772953,
year = {2025},
author = {Teigen, LM and Hoeg, A and Zehra, H and Shah, P and Johnson, R and Hutchison, K and Kocher, M and Lin, AW and Johnson, AJ and Vaughn, BP},
title = {Nutritional optimization of fecal microbiota transplantation in humans: a scoping review.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2446378},
doi = {10.1080/19490976.2024.2446378},
pmid = {39772953},
issn = {1949-0984},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; *Diet ; Clostridium Infections/therapy/microbiology ; Feces/microbiology ; Dietary Supplements ; },
abstract = {Diet constitutes a major source of nutrient flow to the gut microbes. As such, it can be used to help shape the gut microbiome. Fecal microbiota transplantation (FMT) is an increasingly promising therapy in disease states beyond recurrent Clostridioides difficile infection, but diet is largely overlooked for its potential to help optimize this therapy. Therefore, the aim of this scoping review is to present the literature landscape that captures pre- and post-FMT dietary intake in humans, identify research gaps, and provide recommendations for future research. A comprehensive search strategy was developed and searches were run in five databases. Studies were included if they discussed adults who underwent FMT for any recognized treatment indication and had dietary intake as a study objective, this search encompassed studies with interventions that included foods and dietary supplements. The initial screening identified a total of 7721 articles, of which 18 met the inclusion criteria for this review. Studies were heterogeneous, but taken together, they introduce a framework that defines important nutritional considerations for both donors and FMT recipients in the period around FMT dosing. This framework is summarized with this review and highlights the opportunities available to develop FMT-based precision nutrition strategies to optimize its clinical efficacy.},
}
@article {pmid39772876,
year = {2025},
author = {Nazipi Bushi, S and Lund, MB and Sandfeld, T and Nørskov, SS and Fruergaard, S and Glasius, M and Bilde, T and Schramm, A},
title = {A modified iChip for in situ cultivation of bacteria in arid environments.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0132524},
doi = {10.1128/aem.01325-24},
pmid = {39772876},
issn = {1098-5336},
abstract = {Antimicrobial resistance is an ever-increasing problem for human health, and with only a few novel antimicrobials discovered in recent decades, an extraordinary effort is needed to circumvent this crisis. A promising source of new microbial-derived antimicrobial compounds resides in the large fraction of microbes that are not readily cultured by standard cultivation. It has previously been shown that nests of the social spider Stegodyphus dumicola contain a diverse bacterial community, where only a small fraction of the microbes could be recovered by standard cultivation. To improve the recovery of the bacterial diversity cultured from nests, we modified the previously described isolation chip (iChip) to fit the natural arid environment of S. dumicola nests. Here we provide a comprehensive analysis of the modified iChip's performance. We found that the modified iChip improved the overall culturability, performed equally or better at recovering the bacterial diversity from individual nests, and improved the recovery of rare isolates compared to standard cultivation. Furthermore, we show that the modified iChip can be used in the field. In addition, we observed that the nests contain volatile organic compounds (VOCs) that could serve as substrate for the selective enrichment of rare and iChip-specific isolates. Our modified iChip can be applied for in situ cultivation in a broad range of arid habitats that can be exploited for future drug discovery.IMPORTANCEThe demand for novel antimicrobial compounds is an ever-increasing problem due to the rapid spread of antibiotic-resistant microbes. Therefore, exploring new habitats for microbial-derived antimicrobial compounds is crucial. The nest microbiome of Stegodyphus dumicola remains largely unexplored and could potentially serve as a new source of antimicrobial compounds. To access the nest's microbial diversity, we designed a modified iChip for in situ cultivation inside spider nests and tested its applications in both field and laboratory settings. Our study shows that the iChip's ability to recover in situ abundant genera was comparable or superior to standard cultivation, while the recovery of rare (low-abundant genera) was higher. We argue that these low-abundant and iChip-specific isolates are enriched from naturally occurring nest volatile organic compounds (VOCs) during iChip incubation.},
}
@article {pmid39772703,
year = {2025},
author = {Meiners, F and Kreikemeyer, B and Newels, P and Zude, I and Walter, M and Hartmann, A and Palmer, D and Fuellen, G and Barrantes, I},
title = {Strawberry dietary intervention influences diversity and increases abundances of SCFA-producing bacteria in healthy elderly people.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0191324},
doi = {10.1128/spectrum.01913-24},
pmid = {39772703},
issn = {2165-0497},
abstract = {The gut microbiome is amenable to dietary interventions, and polyphenol-rich diets have been shown to enhance abundances of bacteria associated with short-chain fatty acid (SCFA) production. We examined the effects of a strawberry-based intervention on the gut microbiome of 69 healthy elderly German adults. Participants in five groups consumed varying amounts of strawberries, freeze-dried strawberries, and capers in olive oil over 10 weeks as part of a randomized controlled trial. 16S rRNA sequencing was used to analyze differences in microbial composition, diversity, phenotypes, differential abundance, and functional pathways. The intervention group featuring the highest amounts of fresh and freeze-dried strawberries without capers in olive oil (group 4) showed changes in gut microbial diversity and differential abundance that could be linked to improved health. Beta diversity, based on weighted UniFrac distances, increased significantly (P = 0.0035), potentially pathogenic bacteria decreased (P = 0.04), and abundances of SCFA-producing genera Faecalibacterium and Prevotella increased significantly. Other findings included a significant reduction of CAG-352, Preveotellaceae_NK3B31-group, and Eubacterium coprostanoligenes (group 2), and a trend of lowered Firmicutes-to-Bacteroidetes ratio (P = 0.067) and a reduction in Ruminococcaceae (group 3). Our findings suggest that a dietary intervention based on strawberries can positively alter the gut microbiota of healthy elderly people as seen in an enrichment of SCFA-producing genera, increased diversity, and a reduction in potentially pathogenic bacteria.IMPORTANCEAging is often associated with changes in the gut microbiome, including a decline in beneficial bacteria and an increase in potentially pathogenic species. Addressing these changes through lifestyle interventions is of significant interest. Our study demonstrates that a 10-week dietary intervention with strawberries can beneficially modulate gut microbial composition and diversity in healthy elderly individuals. Notably, the group consuming the highest amount of strawberries (without capers in olive oil) initially had higher abundances of potentially pathogenic bacteria. Here, the intervention led to increased abundances of the beneficial genera Faecalibacterium and Prevotella, which are linked to health benefits including reduced inflammation and improved lipid metabolism. These findings suggest that strawberry consumption can positively influence gut microbial composition, thereby contributing to overall health and disease prevention in older adults.},
}
@article {pmid39772525,
year = {2025},
author = {Yum, SJ and Yu, SY and Kim, SM and Jeong, HG},
title = {Antibiotic Resistance Genes and Microbiota in Brassica oleracea var. acephala Cultivated in South Korea: Potential for Resistance Transmission.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c11161},
pmid = {39772525},
issn = {1520-5118},
abstract = {Antimicrobial resistance (AMR) poses a critical global public health challenge. This study investigates the microbiome of Brassica oleracea var. acephala (kale) to evaluate the role of food production systems, particularly plant-derived foods, in AMR dissemination. Using 16S rRNA gene sequencing and metagenomic shotgun sequencing, we analyzed microbial diversity and antimicrobial resistance genes (ARGs) in kale samples. Results showed significant regional differences in microbiota composition and ARG distribution, with traditional fertilizer use linked to higher ARG prevalence in coliform bacteria compared to farms using other fertilization methods. Additionally, we confirmed ARG transfer potential by Klebsiella pneumoniae within coliform populations. Storage conditions notably affected microbial dynamics, with higher temperatures promoting K. pneumoniae growth in washed samples. These findings revealed the importance of AMR research in plant-derived foods and highlight the need for improved agricultural practices to mitigate the risks associated with high ARG abundance in coliform bacteria.},
}
@article {pmid39772304,
year = {2024},
author = {Xia, D and Xu, L and Cheng, X and Li, C and Chen, S and Zhang, Y},
title = {Causal association between gut microbiome and polycystic ovary syndrome: A bidirectional Mendelian randomization study.},
journal = {African journal of reproductive health},
volume = {28},
number = {12},
pages = {127-138},
doi = {10.29063/ajrh2024/v28i12.14},
pmid = {39772304},
issn = {1118-4841},
mesh = {*Polycystic Ovary Syndrome/microbiology ; Humans ; Female ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome ; },
abstract = {Through implementing a bidirectional Mendelian randomization (MR) study, the causal effects between gut microbiome and polycystic ovary syndrome (PCOS) were analyzed. Summary statistics for PCOS were acquired from the FinnGen consortium R8 release data, which included 27,943 cases and 162,936 controls. The inverse-variance weighting (IVW) method was adopted for analysis. Additionally, the causality involving exposure plus the outcome was evaluated by means of MR-Egger, weighted median, simple mode methods, as well as weighted mode. The IVW estimate showed that the genera Streptococcus plus Enterorhabdus served as protectors of PCOS. By contrast, the phylum Tenericutes, genera Anaerofilum, Coprococcus 2, Lachnospiraceae ND3007 group and Ruminiclostridium 5 were identified as risk elements of PCOS. Based on reverse MR analyses from PCOS on the intestinal microbiome based on the IVW method, the phyla Tenericutes, Actinobacteria, class Actinobacteria, genera Ruminococcaceae UCG004 and Christensenellaceae R 7group exhibited a down-regulation effect after PCOS onset. The genera Bacteroides, Barnesiella, Erysipelotrichaceae UCG003, Ruminococcus gnavus group, and Veillonella were up-regulated. No horizontal pleiotropy or significant IV heterogeneity was observed. We conclude that there is a causality relationship between gut microbiome and PCOS, where some bacterial taxa can be used as biomarkers to promote targeted diagnosis and therapy for PCOS.},
}
@article {pmid39772200,
year = {2024},
author = {Maswanganye, CK and Mkhize, PP and Matume, ND},
title = {Mapping the HPV Landscape in South African Women: A Systematic Review and Meta-Analysis of Viral Genotypes, Microbiota, and Immune Signals.},
journal = {Viruses},
volume = {16},
number = {12},
pages = {},
pmid = {39772200},
issn = {1999-4915},
support = {TTK230430100291//National Research Foundation/ ; 24/81//Poliomyelitis Research Foundation/ ; },
mesh = {Humans ; Female ; *Papillomavirus Infections/virology/epidemiology ; South Africa/epidemiology ; *Papillomaviridae/genetics/classification ; *Genotype ; *Microbiota ; Prevalence ; Vagina/microbiology/virology ; Cervix Uteri/virology/microbiology ; Cytokines/metabolism ; Adult ; Uterine Cervical Neoplasms/virology/microbiology ; },
abstract = {This systematic review and meta-analysis evaluate human papillomavirus (HPV) prevalence, genotype distribution, and associations with cervicovaginal microbiota and cytokine profiles among South African women, where cervical cancer ranks as the second most common cancer. PubMed, SCOPUS, and Web of Science were searched for studies on HPV infection up to 21 September 2024. The pooled prevalence was estimated using a random-effects model, with subgroup analyses by province, sample type, and HIV status. Publication bias was evaluated using funnel plots and Egger's test. Of the 19,765 studies screened, 120 met the inclusion criteria, comprising 83,266 participants. Results indicate a high HPV burden, with a pooled prevalence of 58% (95% CI: 52-64%), varying regionally from 53% (95% CI: 41-65%) to 64% (95% CI: 55-73%), with some regions under-researched. Cervical samples had the highest HPV prevalence (60% (95% CI: 54-66%)), while non-genital samples were less studied. High-risk (HR) HPV types, notably HPV 16 (7.5%), HPV 35 (4.1%), and HPV 18 (3.9%), were prominent, with HPV 35 emphasizing the need for expanded vaccine coverage. HIV-positive women had a higher pooled HPV prevalence (63% (95% CI: 55-71%)). Funnel plot analysis and Egger's test suggested a potential publication bias (p = 0.047). HPV-positive women exhibited lower Lactobacillus levels and an increase in Bacterial Vaginosis (BV)-associated species like Gardnerella, potentially supporting HPV persistence. Cytokine analysis showed elevated MIP-1α and MIP-1β in HPV infections, though cytokine profiles may depend on HPV genotypes. These findings underscore the need for research on HPV-microbiome-immune interactions and call for comprehensive HPV-prevention strategies, including vaccines targeting regional HPV types and tailored interventions for HIV-positive populations.},
}
@article {pmid39772099,
year = {2024},
author = {Meyer, T and Stockfleth, E},
title = {Treatment and Prevention of HPV-Associated Skin Tumors by HPV Vaccination.},
journal = {Vaccines},
volume = {12},
number = {12},
pages = {},
pmid = {39772099},
issn = {2076-393X},
abstract = {HPV-associated dermatological diseases include benign lesions like cutaneous warts and external genital warts. In addition, HPV infection is associated with the development of epithelial skin cancers, in particular cutaneous squamous cell carcinoma (cSCC). In contrast to anogenital and oropharyngeal cancers caused by mucosal HPV types of genus alpha papillomavirus, cSCC-associated HPV types belong to the genus beta papillomavirus. Currently available HPV vaccines that target mucosal HPV types associated with anogenital cancer and genital warts are type-specific and provide no cross-protection against beta HPV. When implementing vaccination to beta HPV to prevent skin tumors, it must be considered that acquisition of these HPV types occurs early in childhood and that the risk for cSCC increases with growing age and decreasing immune surveillance. Thus, individuals considered for beta HPV vaccination usually have pre-existing infection and are largely immunocompromised. On the other hand, worldwide increasing incidence rates of epithelial skin cancer reflect an urgent need for skin cancer prevention measures. Based on the pathogenic involvement of beta HPV, vaccination may represent a promising prevention strategy. Indeed, various procedures of prophylactic and therapeutic vaccination have been developed, and some of them have shown efficiency in animal models. Thus far, however, none of these vaccine candidates has been approved for application in humans.},
}
@article {pmid39771516,
year = {2024},
author = {Chesney, E and Mazibuko, N and Oliver, D and Minichino, A and Lamper, AD and Chester, L and Reilly, TJ and Lloyd, M and Kråkström, M and Dickens, AM and Orešič, M and Lynch, E and Stoloff, G and Mehta, MA and McGuire, P},
title = {Novel Lipid Formulation Increases Absorption of Oral Cannabidiol (CBD).},
journal = {Pharmaceutics},
volume = {16},
number = {12},
pages = {},
doi = {10.3390/pharmaceutics16121537},
pmid = {39771516},
issn = {1999-4923},
support = {n/a//Academic/ ; },
abstract = {Background: Cannabidiol (CBD) is an approved treatment for childhood epilepsies and a candidate treatment for several other CNS disorders. However, it has poor oral bioavailability. We investigated the effect of a novel lipid formulation on its absorption in humans and on its tissue distribution in mice. Methods: In a double-blind crossover study in fasting healthy volunteers, we compared the pharmacokinetics of a single dose of 1000 mg of CBD in the lipid formulation and in a powder formulation (ClinicalTrials.gov: NCT05032807). In a second study, male CD1 mice were administered CBD in either the lipid formulation or dissolved in water, via oral gavage (n = 1 per timepoint). The tissue distribution of CBD was assessed using matrix-assisted laser desorption/ionization mass spectrometric imaging. Results: Plasma exposure (AUC0-48) of CBD was nine times greater for the lipid formulation than the powder formulation (611.1 ng·h/mL [coefficient of variation {CV%}
: 104.6] and 66.8 ng·h/mL [CV%: 50.7], respectively). With the powder formulation, the AUC0-48 was related to the concentration of specific gastrointestinal bacteria and bile acids. These associations were attenuated with the lipid formulation. In the animal study, after treatment with the lipid formulation, measurable concentrations of CBD were identified in all organs. For the aqueous formulation, tissue concentrations of CBD were below the limit of quantification. Conclusions: Administering oral CBD in a lipid formulation was associated with an increase in its gastrointestinal absorption, as well as an attenuation of the relationship between its absorption and features of the gut microbiome.},
}
@article {pmid39771258,
year = {2024},
author = {Korshunova, T and Kuzina, E and Mukhamatdyarova, S and Iskuzhina, M and Kulbaeva, L and Petrova, S},
title = {Effect of Herbicide-Resistant Oil-Degrading Bacteria on Plants in Soil Contaminated with Oil and Herbicides.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {24},
pages = {},
pmid = {39771258},
issn = {2223-7747},
support = {23-24-00130//Russian Science Foundation/ ; },
abstract = {Biological remediation of agricultural soils contaminated with oil is complicated by the presence of residual amounts of chemical plant protection products, in particular, herbicides, which, like oil, negatively affect the soil microbiome and plants. In this work, we studied five strains of bacteria of the genera Pseudomonas and Acinetobacter, which exhibited a high degree of oil biodegradation (72-96%). All strains showed resistance to herbicides based on 2,4-D, imazethapyr and tribenuron-methyl, the ability to fix nitrogen, phosphate mobilization, and production of indole-3-acetic acid. The presence of pollutants affected the growth-stimulating properties of bacteria in different ways. The most promising strain P. citronellolis N2 was used alone and together with oat and lupine plants for soil remediation of oil, including herbicide-treated oil-contaminated soil. Combined contamination was more toxic to plants and soil microorganisms. Bacterization stimulated the formation of chlorophyll and suppressed the synthesis of abscisic acid and malonic dialdehyde in plant tissues. The combined use of bacteria and oat plants most effectively reduced the content of hydrocarbons in the soil (including in the presence of herbicides). The results obtained can be used to develop new methods for bioremediation of soils with polychemical pollution.},
}
@article {pmid39771153,
year = {2024},
author = {Mauliasari, IR and Lee, HJ and Koo, SY and Hitayezu, E and Kieu, ANT and Lee, SM and Cha, KH},
title = {Benzo(a)pyrene and Gut Microbiome Crosstalk: Health Risk Implications.},
journal = {Toxics},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/toxics12120938},
pmid = {39771153},
issn = {2305-6304},
support = {RS-2024-00396964//Ministry of Agriculture, Food and Rural Affairs/ ; 2021R1C1C1007945//National Research Foundation of Korea/ ; },
abstract = {This review delves into the impact of benzo(a)pyrene (B(a)P), which is a toxic and pervasive polycyclic aromatic hydrocarbon (PAH) and known carcinogen, on the human health risk from a gut microbiome perspective. We retrieved the relevant articles on each PAH and summarized the reporting to date, with a particular focus on benzo(a)pyrene, which has been reported to have a high risk of gut microbiome-related harm. B(a)P exposure can compromise the homeostasis of the gut microbiota, leading to dysbiosis, a state of microbial imbalance. The consequences of B(a)P-induced gut dysbiosis can be far-reaching, potentially contributing to inflammation, metabolic disorders, and an increased risk of various diseases. Additionally, due to the strong coupling between B(a)P and microparticles, the toxicity of B(a)P may be further compounded by its reaction with strong gut disruptors such as micro-/nanoplastics, which have recently become a serious environmental concern. This review summarizes current research on the impact of B(a)P on the gut microbiome, highlighting the intricate relationship between environmental exposure, gut health, and human disease. Further research is necessary to elucidate the underlying mechanisms and develop effective strategies to mitigate the adverse health effects of B(a)P exposure.},
}
@article {pmid39771069,
year = {2024},
author = {Tang, Y and Wu, X and Pang, Y and Xiao, S and Xie, L and Zhang, Y},
title = {Toxicity of Polystyrene Microplastics with Cadmium on the Digestive System of Rana zhenhaiensis Tadpoles.},
journal = {Toxics},
volume = {12},
number = {12},
pages = {},
pmid = {39771069},
issn = {2305-6304},
support = {LQ21C030002//Zhejiang Provincial Natural Science Foundation of China/ ; 32101251//National Natural Science Foundation of China/ ; },
abstract = {Microplastics pollution in freshwater systems is attracting increasing attention. However, our knowledge of its combined toxicity with heavy metals is scarce. In this study, Rana zhenhaiensis was used as the model animal to study the combined poisoning mechanism of cadmium or microplastics on the digestive systems of tadpoles in freshwater. Results showed that the exposure to cadmium and polystyrene increased the mortality and metamorphosis rate of R. zhenhaiensis tadpoles, and delayed their growth and development. Cadmium was detected in the livers and intestines, while polystyrene mainly accumulated in the gills and intestines of tadpoles. The individual exposure of cadmium or polystyrene can cause pathological damage to liver tissue, induce oxidative stress in liver, and change gene expression. Cadmium co-exposure with polystyrene can reduce the cadmium accumulation in the liver. While polystyrene can slightly increase cadmium accumulation in the intestine. Exposure to cadmium and polystyrene altered the abundance and community structure of intestinal microbiota, and polystyrene increased the dysregulation of the gut microbiome. In this study, the combined exposure of microplastics and cadmium had a negative impact on R. zhenhaiensis tadpoles, but the introduction of microplastics on the toxicity of cadmium on the tadpoles needs further investigation, due to the different characteristics of microplastics.},
}
@article {pmid39771042,
year = {2024},
author = {Karačić, A and Zonjić, J and Stefanov, E and Radolović, K and Starčević, A and Renko, I and Krznarić, &#x17d; and Ivančić, M and Šatalić, Z and Liberati Pršo, AM},
title = {Short-Term Supplementation of Sauerkraut Induces Favorable Changes in the Gut Microbiota of Active Athletes: A Proof-of-Concept Study.},
journal = {Nutrients},
volume = {16},
number = {24},
pages = {},
pmid = {39771042},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Athletes ; Male ; *Fermented Foods ; Young Adult ; Female ; Adult ; *Proof of Concept Study ; Dietary Supplements ; Sports Nutritional Physiological Phenomena ; },
abstract = {BACKGROUND: Since the gut microbiota is important for athlete health and performance, its optimization is increasingly gaining attention in sports nutrition, for example, with whole fermented foods. Sauerkraut is a traditional fermented food rich in pro-, pre-, and postbiotics, which has not yet been investigated in the field of sports nutrition.<br><br>METHODS: To determine whether sauerkraut could be used for gut microbiota optimization in sports nutrition, a proof-of-concept study was conducted. The microbiota composition of organic pasteurized sauerkraut was analyzed, and then healthy active athletes were provided with the same sauerkraut for 10 days as an intervention. The effects of sauerkraut on the athlete's gut microbiota, laboratory parameters, and bowel function were assessed.<br><br>RESULTS: Significant changes in the gut microbiota composition were seen on taxonomic and functional levels, independent of baseline microbiota composition, even after short-term supplementation. Most notably, there was an increase in several health-promoting genera of the family Lachnospiraceae, as well as significant alterations in metabolic pathways regarding cell wall synthesis and the metabolism of nucleotide bases. An increase in the proportion of lymphocytes and a decrease in B12 vitamin levels was observed, as well as a risk of indigestion in certain athletes, which significantly resolved after seven days of supplementation in all athletes. It is unclear whether the observed effects are attributable to the sauerkraut's own microbiome or its pre- and postbiotics since it is a whole food.<br><br>CONCLUSIONS: Our study has demonstrated that the concept of whole fermented foods, such as sauerkraut, could potentially be feasible and effective in sports nutrition for gut microbiota optimization.},
}
@article {pmid39771027,
year = {2024},
author = {Gruenbaum, BF and Merchant, KS and Zlotnik, A and Boyko, M},
title = {Gut Microbiome Modulation of Glutamate Dynamics: Implications for Brain Health and Neurotoxicity.},
journal = {Nutrients},
volume = {16},
number = {24},
pages = {},
pmid = {39771027},
issn = {2072-6643},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Glutamic Acid/metabolism ; *Brain-Gut Axis/physiology ; *Brain/metabolism ; Animals ; Fecal Microbiota Transplantation ; Blood-Brain Barrier/metabolism ; Neurotoxicity Syndromes/etiology/metabolism ; Depression/metabolism/microbiology ; },
abstract = {The gut-brain axis plays an integral role in maintaining overall health, with growing evidence suggesting its impact on the development of various neuropsychiatric disorders, including depression. This review explores the complex relationship between gut microbiota and glutamate (Glu) regulation, highlighting its effect on brain health, particularly in the context of depression following certain neurological insults. We discuss how microbial populations can either facilitate or limit Glu uptake, influencing its bioavailability and predisposing to neuroinflammation and neurotoxicity. Additionally, we examine the role of gut metabolites and their influence on the blood-brain barrier and neurotransmitter systems involved in mood regulation. The therapeutic potential of microbiome-targeted interventions, such as fecal microbiota transplantation, is also highlighted. While much research has explored the role of Glu in major depressive disorders and other neurological diseases, the contribution of gut microbiota in post-neurological depression remains underexplored. Future research should focus on explaining the mechanisms linking the gut microbiota to neuropsychiatric outcomes, particularly in conditions such as post-stroke depression, post-traumatic brain-injury depression, and epilepsy-associated depression. Systematic reviews and human clinical studies are needed to establish causal relationships and assess the efficacy of microbiome-targeted therapies in improving the neuropsychiatric sequalae after neurological insults.},
}
@article {pmid39770976,
year = {2024},
author = {Nohesara, S and Abdolmaleky, HM and Dickerson, F and Pinto-Tomás, AA and Jeste, DV and Thiagalingam, S},
title = {Maternal Gut Microbiome-Mediated Epigenetic Modifications in Cognitive Development and Impairments: A New Frontier for Therapeutic Innovation.},
journal = {Nutrients},
volume = {16},
number = {24},
pages = {},
pmid = {39770976},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Epigenesis, Genetic ; *Cognitive Dysfunction/microbiology/genetics ; Female ; *Cognition ; Pregnancy ; Maternal Nutritional Physiological Phenomena ; },
abstract = {Cognitive impairment in various mental illnesses, particularly neuropsychiatric disorders, has adverse functional and clinical consequences. While genetic mutations and epigenetic dysregulations of several genes during embryonic and adult periods are linked to cognitive impairment in mental disorders, the composition and diversity of resident bacteria in the gastrointestinal tract-shaped by environmental factors-also influence the brain epigenome, affecting behavior and cognitive functions. Accordingly, many recent studies have provided evidence that human gut microbiota may offer a potential avenue for improving cognitive deficits. In this review, we provide an overview of the relationship between cognitive impairment, alterations in the gut microbiome, and epigenetic alterations during embryonic and adult periods. We examine how various factors beyond genetics-such as lifestyle, age, and maternal diet-impact the composition, diversity, and epigenetic functionality of the gut microbiome, consequently influencing cognitive performance. Additionally, we explore the potential of maternal gut microbiome signatures and epigenetic biomarkers for predicting cognitive impairment risk in older adults. This article also explores the potential roles of nutritional deficiencies in programming cognitive disorders during the perinatal period in offspring, as well as the promise of gut microbiome-targeted therapeutics with epigenetic effects to prevent or alleviate cognitive dysfunctions in infants, middle-aged adults, and older adults. Unsolved challenges of gut microbiome-targeted therapeutics in mitigating cognitive dysfunctions for translation into clinical practice are discussed, lastly.},
}
@article {pmid39770970,
year = {2024},
author = {Cosier, D and Lambert, K and Charlton, K and Batterham, M and Little, RD and Wu, N and Tavakoli, P and Ghaly, S and Pipicella, JL and Connor, S and Leach, S and Lemberg, DA and Houshyar, Y and Jayawardana, T and Koentgen, S and On Behalf Of The Australian Ibd Microbiome Study Consortium, and Hold, GL},
title = {Dietary Patterns and Fibre Intake Are Associated with Disease Activity in Australian Adults with Inflammatory Bowel Disease: An Exploratory Dietary Pattern Analysis.},
journal = {Nutrients},
volume = {16},
number = {24},
pages = {},
pmid = {39770970},
issn = {2072-6643},
mesh = {Humans ; *Dietary Fiber/administration &amp; dosage ; Male ; Female ; Adult ; Australia/epidemiology ; Cross-Sectional Studies ; Middle Aged ; *Inflammatory Bowel Diseases ; *Feces/chemistry/microbiology ; *Feeding Behavior ; *Diet/statistics &amp; numerical data ; Leukocyte L1 Antigen Complex/analysis ; Biomarkers ; Crohn Disease ; Principal Component Analysis ; Dietary Patterns ; },
abstract = {BACKGROUND: Few studies have explored the relationship between habitual dietary patterns and disease activity in people with Inflammatory Bowel Disease (IBD). This cross-sectional study explored the association between dietary patterns and clinical and objective markers of inflammation in adults from the Australian IBD Microbiome Study.<br><br>METHODS: Dietary patterns were derived using principal component analysis (PCA) of baseline food frequency questionnaire data. Food intake was quantified using 3-day food record data. Associations between dietary intake and both clinical disease activity index (CDAI) and faecal calprotectin (FCP) were analysed.<br><br>RESULTS: Participants included 412 adults (IBD = 223, Healthy controls (HC) = 189). Both cohorts consumed poor-quality diets with inadequate servings of most food groups compared to Australian reference standards. IBD participants without FCP inflammation had significantly higher fibre intake than those with moderate FCP. In the Crohn's Disease group, high adherence to 'High plant diversity' and 'Meat eaters' dietary patterns were associated with increased CDAI and FCP, respectively. In the combined IBD cohort, high adherence to a 'Vegan-style' dietary pattern was associated with increased FCP.<br><br>CONCLUSIONS: There is a need for dietary modifications among Australian adults, both with and without IBD, to improve dietary fibre intake and adherence to dietary guidelines. Dietary patterns characterised by a high intake of plant foods or meat products were both positively associated with indicators of active IBD. It is possible that some participants with active IBD were modifying their diet to try to manage their disease and reduce symptoms, contributing to the association between healthier dietary patterns and active disease. Further clinical and longitudinal studies are needed to expand upon the findings. This study offers a unique contribution by utilising FCP as an objective marker of intestinal inflammation and applying dietary pattern analysis to investigate the relationship between diet and inflammatory markers.},
}
@article {pmid39770940,
year = {2024},
author = {Mareș, CR and Săsăran, MO and Mărginean, CO},
title = {Small Intestinal Bacterial Overgrowth and Childhood Malnutrition: A Comprehensive Review of Available Evidence.},
journal = {Nutrients},
volume = {16},
number = {24},
pages = {},
pmid = {39770940},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Intestine, Small/microbiology ; Infant ; Child ; Child Nutrition Disorders/microbiology ; Anti-Bacterial Agents/therapeutic use ; Child, Preschool ; Blind Loop Syndrome ; },
abstract = {The gut microbiome is essential for children's normal growth and development, with its formation aligning closely with key stages of growth. Factors like birth method, feeding practices, and antibiotic exposure significantly shape the composition and functionality of the infant gut microbiome. Small intestinal bacterial overgrowth (SIBO) involves an abnormal increase in bacteria within the small intestine. This overgrowth can interfere with digestion, impair nutrient absorption, and lead to both local and systemic inflammation, potentially contributing to malnutrition. In this review, we provide a comprehensive overview of the current understanding of the relationship between SIBO and malnutrition, with a particular focus on the pediatric population. SIBO seems to play an important role in nutrient malabsorption through the gut microbiome imbalance, local inflammation, and disruption of the mucosal intestinal barrier. Additionally, SIBO is more prevalent in digestive disorders linked to malabsorption and malnutrition. Different therapeutic strategies for addressing malnutrition-related SIBO have been proposed. While antibiotics are the primary treatment for SIBO, their effectiveness in promoting weight gain among malnourished children remains uncertain. Hence, future research directed at the impact of microbiome imbalance on nutrient intake and absorption could bring to light new strategies for the effective prevention and treatment of malnutrition.},
}
@article {pmid39770890,
year = {2024},
author = {Wells, RK and Torres, A and Mau, MK and Maunakea, AK},
title = {Racial-Ethnic Disparities of Obesity Require Community Context-Specific Biomedical Research for Native Hawaiians and Other Pacific Islanders.},
journal = {Nutrients},
volume = {16},
number = {24},
pages = {},
pmid = {39770890},
issn = {2072-6643},
support = {P20GM139753//NIH-NIGMS/ ; R01MD016593//NIH-NIMHD/ ; R56MD014630//NIH-NIMHD/ ; UG03HL169657//NIH-NHLBI/ ; },
mesh = {Humans ; *Native Hawaiian or Other Pacific Islander ; *Obesity/ethnology ; Hawaii/epidemiology ; *Biomedical Research ; Health Status Disparities ; Gastrointestinal Microbiome ; Pacific Island People ; },
abstract = {Compared to the general population of Hawai'i, Native Hawaiians and Other Pacific Islanders (NHPI) shoulder a disproportionately high risk for obesity-related cardiometabolic disorders, such as type 2 diabetes and cardiovascular disease. The gut microbiome is an area of rapid research interest for its role in regulating adjacent metabolic pathways, offering novel opportunities to better understand the etiology of these health disparities. Obesity and the gut microbiome are influenced by regional, racial-ethnic, and community-specific factors, limiting the generalizability of current literature for understudied populations. Additionally, anthropometric and directly measured obesity indices are variably predictive of adiposity and metabolic health risk in this diverse population. Thus, further NHPI-inclusive research is required to adequately characterize community-specific factors in the context of obesity-related disease etiology. Culturally responsible research ethics and scientific communication are crucial to conducting such research, especially among indigenous and understudied populations. In this review, we explore these limitations in current literature, emphasizing the urgent need for NHPI-inclusive research to assess community-specific factors accurately. Such accuracy in Indigenous health research may ensure that findings relevant to individual or public health recommendations and/or policies are meaningful to the communities such research aims to serve.},
}
@article {pmid39770870,
year = {2024},
author = {Hu, P and Xie, S and Shi, B and Tansky, CS and Circello, B and Sagel, PA and Schneiderman, E and Biesbrock, AR},
title = {The Effect of Oral Care Product Ingredients on Oral Pathogenic Bacteria Transcriptomics Through RNA-Seq.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122668},
pmid = {39770870},
issn = {2076-2607},
support = {n/a//The Procter &amp; Gamble Company/ ; },
abstract = {Various ingredients are utilized to inhibit the growth of harmful bacteria associated with cavities, gum disease, and bad breath. However, the precise mechanisms by which these ingredients affect the oral microbiome have not been fully understood at the molecular level. To elucidate the molecular mechanisms, a high-throughput bacterial transcriptomics study was conducted, and the gene expression profiles of six common oral bacteria, including two Gram-positive bacteria (Actinomyces viscosus, Streptococcus mutans) and four Gram-negative bacteria (Porphyromonas gingivalis, Tannerella forsythia, Fusobacterium nucleatum, and Prevotella pallens), were analyzed. The bacteria were exposed to nine common ingredients in toothpaste and mouthwash at different concentrations (stannous fluoride, stannous chloride, arginine bicarbonate, cetylpyridinium chloride, sodium monofluorophosphate, sodium fluoride, potassium nitrate, zinc phosphate, and hydrogen peroxide). Across 78 ingredient-microorganism pairs with 360 treatment-control combinations, significant and reproducible ingredient-based transcriptional response profiles were observed, providing valuable insights into the effects of these ingredients on the oral microbiome at the molecular level. This research shows that oral care product ingredients applied at biologically relevant concentrations manifest differential effects on the transcriptomics of bacterial genes in a variety of oral periodontal pathogenic bacteria. Stannous fluoride, stannous chloride, and cetylpyridinium chloride showed the most robust efficacy in inhibiting the growth or gene expression of various bacteria and pathogenic pathways. Combining multiple ingredients targeting different mechanisms might be more efficient than single ingredients in complex oral microbiomes.},
}
@article {pmid39770869,
year = {2024},
author = {Joura, MI and Jobbágy, A and Dunai, ZA and Makra, N and Bánvölgyi, A and Kiss, N and Sárdy, M and Sándor, SE and Holló, P and Ostorházi, E},
title = {Characteristics of the Stool, Blood and Skin Microbiome in Rosacea Patients.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122667},
pmid = {39770869},
issn = {2076-2607},
abstract = {Several research groups have confirmed that in the pathogenesis of the chronic inflammatory skin disorder rosacea, the composition of the skin and fecal microbiome of affected patients differs from that of healthy individuals. We studied the stool, blood and skin microbiomes of rosacea and control patients using 16S rRNA sequencing. Our goals were to determine 1. whether the microbiome characteristics of rosacea patients differ from that of healthy individuals, 2. whether the change experienced on the skin can be confirmed by alterations in the stool microbiome through the mediation of the blood and 3. whether the metabolic activity of the changed skin, blood or fecal microbiome can play a role in the pathogenesis of rosacea. The rosacea skin microbiome differed significantly from the healthy skin microbiome in both alpha and beta diversity, as well as in the abundance of the genera. Only a few genera abundances differed significantly in stool and blood samples. The most significant representatives of the rosacea skin microbiome, Staphylococcus, Cutibacterium, Corynebacterium and Neisseria, cannot be derived from the feces or blood. The metabolic pathways associated with healthy fecal microbiome contributed to the production of anti-inflammatory short-chain fatty acids. While the increased production of adenosylcobalamin, L-isoleucine and thiazole by the microbiome of healthy skin appeared to have a protective effect, the excessive heme and H2S production experienced in rosacea skin likely contribute to the deterioration of the pathology.},
}
@article {pmid39770857,
year = {2024},
author = {Wagner, N and Valeriano, VD and Diou-Hirtz, S and Björninen, E and Åkerström, U and Engstrand, L and Schuppe-Koistinen, I and Gillbro, JM},
title = {Microbial Dynamics: Assessing Skincare Regimens' Impact on the Facial Skin Microbiome and Skin Health Parameters.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122655},
pmid = {39770857},
issn = {2076-2607},
abstract = {The human skin microbiome, a complex ecosystem of microbes, plays a pivotal role in skin health. This study aimed to investigate the impact of two skincare regimens, with preservatives (CSPs) and preservative-free (PFPs), on the skin microbiome in correlation to skin quality. double-blind randomized cosmetic studywith a split-face design was conducted on 26 female participants. Microbial diversity and abundance were analyzed using 16S rRNA amplicon sequence data and skin quality utilizing the Antera 3D skin camera. We confirmed earlier studies on the identification of major skin microbial taxa at the genus level, including Cutibacterium acnes, Corynebacterium, and Neisseriaceae as a predominant part of the facial skin microbiome. Furthermore, microbiome profile-based subgrouping was employed, which revealed that the cluster, characterized by the Neisseriaceae family as its predominant organism, exhibited significant reduction in folds count, fine lines, and redness after application of PFP compared to CSP. A Spearman correlation analysis highlighted the correlation between changes in specific bacteria and skin quality parameters such as redness, pores, and texture in the context of comparing PFP and CSP. Overall, the PFP treatment demonstrated a greater number of significant correlations between bacterial changes and skin quality compared to the CSP treatment, suggesting a distinct impact of the preservative-free skincare regimen on the skin microbiome and skin quality. Our study provides insights into different microbiome-centered approaches to improve our understanding of the skin microbiome's interplay with skin quality but also highlights the need for larger, comprehensive research to further understand the microbiome's role in dermatology.},
}
@article {pmid39770849,
year = {2024},
author = {Wang, W and Wang, Y and Huang, P and Zhou, J and Tan, G and Zeng, J and Liu, W},
title = {Mosla Chinensis Extract Enhances Growth Performance, Antioxidant Capacity, and Intestinal Health in Broilers by Modulating Gut Microbiota.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122647},
pmid = {39770849},
issn = {2076-2607},
support = {2023YFD1301200//Peng Huang &#xff0c;Jianguo Zeng&#xff0c;Wei Liu/ ; },
abstract = {This study aimed to evaluate the effects of Mosla chinensis extract (MCE) on broiler intestinal health. A total of 240 1-day-old Arbor Acres (AA) broilers (balanced for sex) were randomly allocated into four treatment groups, each with six replicates of 10 chickens. The study comprised a starter phase (days 1-21) and a grower phase (days 22-42). The control group (C) received a basal diet, while the experimental groups were supplemented with low (S1, 500 mg/kg), medium (S2, 1000 mg/kg), and high doses (S3, 2000 mg/kg) of MCE. The results showed that MCE supplementation significantly improved average daily gain in broilers (p < 0.05) and reduced the feed-to-gain ratio in broilers. Additionally, MCE enhanced the anti-inflammatory and antioxidant capacity of broilers. In the duodenum and cecum, MCE significantly upregulated the expression of tight junction proteins Claudin-1, and Occludin, with the high-dose group showing the strongest effect on intestinal barrier protection (p < 0.05). There was no significant difference in ZO-1 in dudenum (p > 0.05). Microbial analysis indicated that MCE supplementation significantly reduced the Chao and Sobs indices in both the small and large intestines (p < 0.05). At the same time, the Coverage index of the small intestine increased, with the high-dose group demonstrating the most pronounced effect. Beta diversity analysis revealed that MCE had a significant modulatory effect on the microbial composition in the large intestine (p < 0.05), with a comparatively smaller impact on the small intestine. Furthermore, MCE supplementation significantly increased the relative abundance of Ruminococcaceae and Alistipes in the large intestine, along with beneficial genera that promote short-chain fatty acid (SCFA) production, thus optimizing the gut microecological environment. Correlation analysis of SCFAs further confirmed a significant association between the enriched microbiota and the production of acetate, propionate, and butyrate (p < 0.05). In conclusion, dietary supplementation with MCE promotes healthy growth and feed intake in broilers and exhibits anti-inflammatory and antioxidant effects. By optimizing gut microbiota composition, enhancing intestinal barrier function, and promoting SCFA production, MCE effectively maintains gut microecological balance, supporting broiler intestinal health.},
}
@article {pmid39770844,
year = {2024},
author = {Yang, F and Liu, M and Wang, X and Hong, Y and Yao, Q and Chang, X and Shi, G and Chen, W and Tian, B and Hegazy, A},
title = {Differences in the Microbial Composition and Function of the Arundo donax Rhizosphere Under Different Cultivation Conditions.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122642},
pmid = {39770844},
issn = {2076-2607},
support = {2024ZC035//Henan Academy of Agricultural Sciences/ ; CARS-24-G-15//National Characteristic Vegetable Industry Technology System/ ; 2211111110100//Key R &amp; D Projects in Henan Province/ ; 2024TD38, 2024TD43//Henan Academy of Agricultural Sciences Science and Technology Innovation Team/ ; 241100110200//Independent Innovation Project of Major Science and Technology Special Project of Henan Province/ ; },
abstract = {Rhizosphere microorganisms play an important role in the health and development of root systems. Investigating the microbial composition of the rhizosphere is central to understanding the inter-root microbial function of Arundo donax under various cultivation conditions. To complement the metagenomic study of the Arundo donax rhizosphere, here, an amplicon-based metagenomic survey of bacteria and fungi was selected as a practical approach to analyzing the abundance, diversity index, and community structure of rhizosphere bacteria and fungi, as well as to study the effects of different cultivation methods on rhizosphere microbial diversity. Next-generation sequencing and QIIME2 analysis were used. The results indicated that microbial community richness, diversity, and evenness of the hydroponic samples were lower than those of soil samples when examining the α diversity indices of bacteria and fungi using Chao1, ACE, and Shannon metrics. In particular, the relative abundances of Proteobacteria, Rhizobiales, and Incertae sedis in hydroponic materials were higher, while Basidiomycota, Ascomycota, and Actinobacteriota dominated the flora in soil materials when comparing the numbers of OTUs and the ACE community richness estimator. Furthermore, the rhizosphere of hydroponic A. donax contained a higher abundance of nitrogen-fixing bacteria and photosynthetic bacteria, which contribute to root formation. Additionally, there was a significant presence of Basidiomycota, Ascomycota, and Actinobacteriota in soil A. donax, which can form hyphae. This reveals that the microbial community composition of the A. donax rhizosphere is significantly different under various cultivation conditions, suggesting that employing two distinct culturing techniques for Arundo donax may alter the microbiome. Furthermore, it provides technical support for the synergistic interaction between Arundo donax and rhizosphere microorganisms so as to better use the relationship between Arundo donax and basic microorganisms to solve the problems of Arundo donax growth and ecological restoration.},
}
@article {pmid39770832,
year = {2024},
author = {Gouli, S and Majeed, A and Liu, J and Moseley, D and Mukhtar, MS and Ham, JH},
title = {Microbiome Structures and Beneficial Bacteria in Soybean Roots Under Field Conditions of Prolonged High Temperatures and Drought Stress.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770832},
issn = {2076-2607},
support = {LAB94575//National Institute of Food and Agriculture/ ; GR-00010744 and GR-00010803//Louisiana Soybean and Grain Research and Promotion Board/ ; 2314-209-0201//United Soybean Board/ ; RII FEC OIA-2418230 and OIA-2418232//National Science Foundation/ ; IOS-2038872//National Science Foundation/ ; },
abstract = {Drought stress has a significant impact on agricultural productivity, affecting key crops such as soybeans, the second most widely cultivated crop in the United States. Endophytic and rhizospheric microbial diversity analyses were conducted with soybean plants cultivated during the 2023 growing season amid extreme weather conditions of prolonged high temperatures and drought in Louisiana. Specifically, surviving and non-surviving soybean plants were collected from two plots of a Louisiana soybean field severely damaged by extreme heat and drought conditions in 2023. Although no significant difference was observed between surviving and non-surviving plants in microbial diversity of the rhizosphere, obvious differences were found in the structure of the endophytic microbial community in root tissues between the two plant conditions. In particular, the bacterial genera belonging to Proteobacteria, Pseudomonas and Pantoea, were predominant in the surviving root tissues, while the bacterial genus Streptomyces was conspicuously dominant in the non-surviving (dead) root tissues. Co-occurrence patterns and network centrality analyses enabled us to discern the intricate characteristics of operational taxonomic units (OTUs) within endophytic and rhizospheric networks. Additionally, we isolated and identified bacterial strains that enhanced soybean tolerance to drought stresses, which were sourced from soybean plants under a drought field condition. The 16S rDNA sequence analysis revealed that the beneficial bacterial strains belong to the genera Acinetobacter, Pseudomonas, Enterobacter, and Stenotrophomonas. Specific bacterial strains, particularly those identified as Acinetobacter pittii and Pseudomonas sp., significantly enhanced plant growth metrics and reduced drought stress indices in soybean plants through seed treatment. Overall, this study advances our understanding of the soybean-associated microbiome structure under drought stress, paving the way for future research to develop innovative strategies and biological tools for enhancing soybean resilience to drought.},
}
@article {pmid39770828,
year = {2024},
author = {Huang, CG and Lin, WN and Hsin, LJ and Huang, YS and Chuang, LP and Fang, TJ and Li, HY and Kuo, TBJ and Yang, CCH and Lee, CC and Lee, LA},
title = {Alterations in Gut Microbiota Composition Are Associated with Changes in Emotional Distress in Children with Obstructive Sleep Apnea.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770828},
issn = {2076-2607},
support = {109-2314-B-182-083-MY3//National Science and Technology Council, Taiwan/ ; CORPG3K0242, CORPG3L0481, CMRPG3F1091-3//Chang Gung Medical Foundation, Taiwan/ ; },
abstract = {Emerging evidence underscores the pivotal role of the gut microbiota in regulating emotional and behavioral responses via the microbiota-gut-brain axis. This study explores associations between pediatric obstructive sleep apnea (OSA), emotional distress (ED), and gut microbiome alterations before and after OSA treatment. Sixty-six children diagnosed with OSA via polysomnography participated, undergoing adenotonsillectomy alongside routine educational sessions. ED was assessed using the OSA-18 questionnaire, categorizing participants into high ED (scores ≥ 11, 52%) and low ED (scores < 11, 48%) groups. Gut microbiome analysis revealed significant diversity differences, with high ED linked to a reduced Shannon index (p = 0.03) and increased beta diversity (p = 0.01). Three months post-treatment, significant improvements were observed in OSA symptoms, ED scores, and gut microbiome alpha diversity metrics among 55 participants (all p < 0.04). Moreover, changes in the relative abundances of Veillonella, Bifidobacterium, Flavonifractor, and Agathobacter, as well as ultra-low frequency power and low frequency power of sleep heart rate variability, were independently associated with ED score alterations. These findings underscore the gut microbiome's critical role in the emotional and behavioral symptoms associated with pediatric OSA, suggesting that microbiome-targeted interventions could complement traditional treatments for ED reduction and emphasizing the need for further research.},
}
@article {pmid39770803,
year = {2024},
author = {Kaplan, JB and Assa, M and Mruwat, N and Sailer, M and Regmi, S and Kridin, K},
title = {Facultatively Anaerobic Staphylococci Enable Anaerobic Cutibacterium Species to Grow and Form Biofilms Under Aerobic Conditions.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770803},
issn = {2076-2607},
support = {2022//Kane Biotech (Canada)/ ; },
abstract = {Facultatively anaerobic Staphylococcus spp. and anaerobic Cutibacterium spp. are among the most prominent bacteria on human skin. Although skin microbes generally grow as multispecies biofilms, few studies have investigated the interaction between staphylococci and Cutibacterium spp. in dual-species biofilms. Here, we measured the mono- and dual-species biofilm formation of four staphylococcal species (S. epidermidis, S. hominis, S. capitis, and S. aureus) and two Cutibacterium spp. (C. acnes and C. avidum) cultured in vitro under both aerobic and anaerobic conditions. The biofilms were quantitated by rinsing them to remove planktonic cells, detaching the biofilm bacteria via sonication, and enumerating the cells by dilution plating. When cultured alone, staphylococci formed biofilms under both aerobic and anaerobic conditions, whereas Cutibacterium spp. formed biofilms only under anaerobic conditions. In co-culture, staphylococcal biofilm formation was unaffected by the presence of Cutibacterium spp., regardless of oxygen availability. However, Cutibacterium spp. biofilm formation was significantly enhanced in the presence of staphylococci, enabling robust growth under both anaerobic and aerobic conditions. Fluorescence confocal microscopy of the aerobic dual-species biofilms suggested that staphylococci create anaerobic niches at the base of the biofilm where C. acnes can grow. These findings demonstrate that staphylococci facilitate the colonization of Cutibacterium spp. in oxygen-rich environments, potentially explaining their presence in high numbers on the oxygen-exposed stratum corneum.},
}
@article {pmid39770796,
year = {2024},
author = {Enderlin, D and Bieri, U and Gadient, J and Morsy, Y and Scharl, M and Rüschoff, JH and Hefermehl, LJ and Nikitin, A and Langenauer, J and Engeler, DS and Förster, B and Obrecht, F and Surber, J and Scherer, TP and Eberli, D and Poyet, C},
title = {Towards Reliable Methodology: Microbiome Analysis of Fresh Frozen vs. Formalin-Fixed Paraffin-Embedded Bladder Tissue Samples: A Feasibility Study.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770796},
issn = {2076-2607},
support = {KFS-5308-02-2021-R//the Swiss Cancer Research foundation/ ; },
abstract = {Studies have shown that the human microbiome influences the response to systemic immunotherapy. However, only scarce data exist on the impact of the urinary microbiome on the response rates of bladder cancer (BC) to local Bacillus Calmette-Guérin instillation therapy. We launched the prospective SILENT-EMPIRE study in 2022 to address this question. We report the results of the pilot study of SILENT-EMPIRE, which aimed to compare the microbiome between fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) samples in the cancerous tissue and adjacent healthy tissue of BC patients. Our results show that alpha diversity is increased in FF samples compared to FFPE (coverage index p = 0.041, core abundance index p = 0.008). No significant differences concerning alpha diversity could be detected between cancerous and non-cancerous tissue in the same BC patients. This study demonstrates that microbiome analysis from both FF and FFPE samples is feasible. Implementing this finding could aid in the translation of research findings into clinical practice.},
}
@article {pmid39770773,
year = {2024},
author = {Pinzauti, D and De Jaegher, S and D'Aguanno, M and Biazzo, M},
title = {The Human Nasal Microbiome: A Perspective Study During the SARS-CoV-2 Pandemic in Malta.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770773},
issn = {2076-2607},
support = {16203 24102//Malta Enterprise/ ; },
abstract = {The human respiratory tract is colonized by a complex microbial community that helps maintain respiratory health and plays a crucial role in defending the host from infections. Respiratory viruses have been demonstrated to alter microbiota composition, resulting in opportunistic species expansion, and increasing the disease severity and host susceptibility to bacterial co-infections. This study aims to examine the compositional differences in the nasal microbiota between SARS-CoV-2-infected and non-infected patients. We conducted Oxford Nanopore full-length 16S rRNA sequencing on nasal swabs from 94 COVID-19 negative and 85 COVID-19 positive patients collected during the SARS-CoV-2 pandemic in Malta. Our analysis identified significant alpha and beta diversity differences in the nasal microbiota composition among our study groups. We observed a trend toward decreased microbial richness and evenness in the COVID-Positive cohort with and increased abundance of common nasal opportunistic species including Citrobacter koseri, Dolosigranulum pigrum, Haemophilus influenzae, Klebsiella pneumoniae, and Moraxella catarrhalis. The findings from this study are in line with previously published papers identifying key alterations in the nasal microbiota composition associated with SARS-CoV-2 infection. Understanding these microbiome-driven mechanisms could present novel prognostic markers or offer new approaches for disease prevention and treatment.},
}
@article {pmid39770765,
year = {2024},
author = {Cangioli, L and Tabacchioni, S and Visca, A and Fiore, A and Aprea, G and Ambrosino, P and Ercole, E and Sørensen, S and Mengoni, A and Bevivino, A},
title = {Genome Insights into Beneficial Microbial Strains Composing SIMBA Microbial Consortia Applied as Biofertilizers for Maize, Wheat and Tomato.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770765},
issn = {2076-2607},
support = {862695//European Union's Horizon 2020/ ; },
abstract = {For the safe use of microbiome-based solutions in agriculture, the genome sequencing of strains composing the inoculum is mandatory to avoid the spread of virulence and multidrug resistance genes carried by them through horizontal gene transfer to other bacteria in the environment. Moreover, the annotated genomes can enable the design of specific primers to trace the inoculum into the soil and provide insights into the molecular and genetic mechanisms of plant growth promotion and biocontrol activity. In the present work, the genome sequences of some members of beneficial microbial consortia that have previously been tested in greenhouse and field trials as promising biofertilizers for maize, tomato and wheat crops have been determined. Strains belong to well-known plant-growth-promoting bacterial genera such as Bacillus, Burkholderia, Pseudomonas and Rahnella. The genome size of strains ranged from 4.5 to 7.5 Mbp, carrying many genes spanning from 4402 to 6697, and a GC content of 0.04% to 3.3%. The annotation of the genomes revealed the presence of genes that are implicated in functions related to antagonism, pathogenesis and other secondary metabolites possibly involved in plant growth promotion and gene clusters for protection against oxidative damage, confirming the plant-growth-promoting (PGP) activity of selected strains. All the target genomes were found to possess at least 3000 different PGP traits, belonging to the categories of nitrogen acquisition, colonization for plant-derived substrate usage, quorum sensing response for biofilm formation and, to a lesser extent, bacterial fitness and root colonization. No genes putatively involved in pathogenesis were identified. Overall, our study suggests the safe application of selected strains as "plant probiotics" for sustainable agriculture.},
}
@article {pmid39770748,
year = {2024},
author = {Vaughn, SN and Eckard, EM and Kota, VK and Luber, KT and Jackson, CR},
title = {Local Scale Biogeographic Variation in the Magnolia (Magnolia grandiflora) Phyllosphere.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770748},
issn = {2076-2607},
abstract = {The phyllosphere (aerial plant surfaces colonized by microorganisms) remains an understudied ecosystem in terms of bacterial biogeography, particularly at intermediate or local spatial scales. This study characterized the phyllosphere bacterial community on the leaves of 87 Magnolia grandiflora trees sampled throughout a small town, encompassing an area of approximately 60 km[2]. Sequencing of the 16S ribosomal RNA gene revealed the dominant bacterial phyla to be Alphaproteobacteria, Bacteroidetes, and Acidobacteria, consistent with other studies of the phyllosphere. There was a small but significant relationship between the phyllosphere community similarity and the distance between the trees (i.e., trees further apart were more likely to have dissimilar bacterial communities). There was also a relationship between the assigned categories of tree height (low, medium, high) and the phyllosphere bacterial community composition, with the trees in the high category having more diverse bacterial communities on their leaves than the shorter trees. This study provides insight into the relationship between phyllosphere community composition and host tree characteristics and shows that the distance between M. grandiflora trees has a significant, albeit low, influence on bacterial composition. These findings contribute to a deeper understanding of phyllosphere microbiome biogeography, highlighting how individual tree characteristics and spatial proximity shape phyllosphere bacterial communities.},
}
@article {pmid39770743,
year = {2024},
author = {Peng, X and Li, S and Dou, W and Li, M and Gontcharov, AA and Peng, Z and Qi, B and Wang, Q and Li, Y},
title = {Metagenomic Insight into the Associated Microbiome in Plasmodia of Myxomycetes.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770743},
issn = {2076-2607},
support = {31770011//National Natural Science Foundation of China/ ; },
abstract = {During the trophic period of myxomycetes, the plasmodia of myxomycetes can perform crawling feeding and phagocytosis of bacteria, fungi, and organic matter. Culture-based studies have suggested that plasmodia are associated with one or several species of bacteria; however, by amplicon sequencing, it was shown that up to 31-52 bacteria species could be detected in one myxomycete, suggesting that the bacterial diversity associated with myxomycetes was likely to be underestimated. To fill this gap and characterize myxomycetes' microbiota and functional traits, the diversity and functional characteristics of microbiota associated with the plasmodia of six myxomycetes species were investigated by metagenomic sequencing. The results indicate that the plasmodia harbored diverse microbial communities, including eukaryotes, viruses, archaea, and the dominant bacteria. The associated microbiomes represented more than 22.27% of the plasmodia genome, suggesting that these microbes may not merely be parasitic or present as food but rather may play functional roles within the plasmodium. The six myxomycetes contained similar bacteria, but the bacteria community compositions in each myxomycete were species-specific. Functional analysis revealed a highly conserved microbial functional profile across the six plasmodia, suggesting they may serve a specific function for the myxomycetes. While the host-specific selection may shape the microbial community compositions within plasmodia, functional redundancy ensures functional stability across different myxomycetes.},
}
@article {pmid39770742,
year = {2024},
author = {Park, SH and Lee, JH and Lee, S and Shin, J and Cha, B and Hong, JT and Kwon, KS},
title = {Factors for Treatment Failure After Fecal Microbiota Transplantation in Clostridioides difficile Infection.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770742},
issn = {2076-2607},
support = {2023AR05//Seoul Clinical Laboratories/ ; },
abstract = {Recently, fecal microbiota transplantation (FMT) has been introduced as an effective treatment option for Clostridioides difficile infection (CDI). However, the risk factors associated with FMT treatment failure have not been well demonstrated. Therefore, we aimed to investigate the risk factors of treatment failure or recurrence after FMT for CDI. This retrospective study included 124 patients with CDI who underwent FMT at Inha University Hospital between November 2017 and August 2021 and were followed up for 8 weeks after FMT for symptoms of CDI. FMT failure was defined as diarrhea recurrence or a positive stool test. We assessed the risk factors for treatment failure, including comorbidities, antibiotic use pre- and post-FMT, and the number of CDI episodes before FMT. Ninety-three patients (75%) experienced symptom improvement <7 days after FMT, while treatment failure occurred in 40 patients (32.3%). Multivariate analysis revealed that males had a lower symptom improvement rate <7 days after FMT (p = 0.049). Patients using antibiotics after FMT showed a higher rate of recurrence or treatment failure in <8 weeks (p = 0.032). Patients requiring antibiotics after FMT should be considered at higher risk of treatment failure. Careful antibiotic stewardship, particularly minimizing non-essential antibiotic use before and after FMT, may significantly enhance treatment outcomes. Further large-scale prospective studies are warranted to confirm these findings and develop targeted antibiotic management protocols for improving the efficacy of FMT in CDI treatment.},
}
@article {pmid39770729,
year = {2024},
author = {García, G and Soto, J and Netherland, M and Hasan, NA and Buchaca, E and Martínez, D and Carlin, M and de Jesus Cano, R},
title = {Evaluating the Effects of Sugar Shift[®] Symbiotic on Microbiome Composition and LPS Regulation: A Double-Blind, Placebo-Controlled Study.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770729},
issn = {2076-2607},
support = {No Grant Number//The BioCollective Foundation/ ; },
abstract = {(1) Background: This study evaluated the effects of BiotiQuest[®] Sugar Shift[®], a novel probiotic formulation, for its impact on gut microbiome composition and metabolic health in type 2 diabetes mellitus (T2D). T2D is characterized by chronic inflammation and gut microbiome imbalances, yet the therapeutic potential of targeted probiotics remains underexplored. (2) Methods: In a 12-week randomized, double-blind, placebo-controlled trial, 64 adults with T2D received either Sugar Shift or placebo capsules twice daily. Each dose provided 18 billion CFU of eight GRAS-certified bacterial strains and prebiotics. Clinical samples were analyzed for metabolic markers, and microbiome changes were assessed using 16S rRNA sequencing and metagenomics. (3) Results: Sugar Shift significantly reduced serum lipopolysaccharide (LPS) levels, improved insulin sensitivity (lower HOMA-IR scores), and increased short-chain fatty acid (SCFA)-producing genera, including Bifidobacterium, Faecalibacterium, Fusicatenibacter, and Roseburia. Pro-inflammatory taxa like Enterobacteriaceae decreased, with reduced LPS biosynthesis genes and increased SCFA production genes. The Lachnospiraceae:Enterobactericeae ratio emerged as a biomarker of reduced inflammation. (4) Conclusions: These findings demonstrate the potential of Sugar Shift to restore gut homeostasis, reduce inflammation, and improve metabolic health in T2D. Further studies are warranted to explore its long-term efficacy and broader application in metabolic disease management.},
}
@article {pmid39770715,
year = {2024},
author = {Johnson, BT and White, BJ and Amachawadi, RG and Kleinhenz, MD and Farney, JK and Shippy, TD and Larson, RL},
title = {Determining the Effect of Varied Proportions of Cohort Administered Tulathromycin at Arrival on Nasopharyngeal Microbiota and Performance Characteristics in Yearling Steers in the First 56 Days on Feed.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770715},
issn = {2076-2607},
abstract = {Metaphylaxis or treating the entire population of cattle at arrival with an antimicrobial has been studied extensively in the cattle industry; however, little information is available on the impacts of treating only a proportion of the population with antimicrobials at arrival. The study objective was to determine potential associations between the proportion of animals in a pen treated with antimicrobial therapy with pen performance and nasopharyngeal microbiome. Yearling steers (n = 160) were randomly allocated to study pens (n = 40) and pens were systematically randomized to one of two antimicrobial treatments (META: all four head received tulathromycin; MIXED: two of four head randomly selected to receive tulathromycin). The study was conducted in conjunction with an essential oil feeding trial. Deep nasal pharyngeal (DNP) swabs were collected from every steer at Days 0, 14, 28, and 56. All DNP swabs were individually cultured for Pasteurella multocida and Mannheimia haemolytica. Samples of DNA were extracted from DNP swabs, pooled by pen, and analyzed by metagenomic shotgun sequencing to compare nasopharyngeal microbiome composition and quantity of resistance genes between test groups. Neither antimicrobial nor essential oil treatment groups had any significant associations with performance or DNP microbiome. Sampling day was significantly associated with alpha and beta diversity at the species level. Shannon's diversity and Inverse Simpson diversity were significantly lower on Day 14 versus both Day 0 and Day 56. These data indicated a shift in microbial populations across study days; however, the microbiome diversity and relative abundance were not significantly different between antimicrobial treatment groups.},
}
@article {pmid39770709,
year = {2024},
author = {Wang, M and Xing, X and Zhang, Y and Sui, X and Zheng, C},
title = {Geographic Distribution Pattern Determines Soil Microbial Community Assembly Process in Acanthopanax senticosus Rhizosphere Soil.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122506},
pmid = {39770709},
issn = {2076-2607},
support = {No.20230202//Heilongjiang Province Seed Industry Innovation and Development Funding Program/ ; },
abstract = {The geographic distribution patterns of soil microbial communities associated with cultivated Acanthopanax senticosus plants in Northeast China were investigated. High-throughput sequencing revealed that the diversity and community assembly of bacterial and fungal communities in the inter-root soil varied significantly with geographic location. The study found that bacterial communities were predominantly assembled through stochastic processes at most sites, while fungal communities showed greater variation, with both stochastic and deterministic processes involved. The complexity of bacterial-fungal co-occurrence networks also varied with longitude and latitude, demonstrating both positive and negative interactions. PICRUSt 2.0 and FUNGuild were used to predict the potential functions of soil bacterial and fungal microbiota, respectively, during different land use patterns. The average taxonomic distinctness (AVD) index indicated varying degrees of community stability across sites. Key microbial taxa contributing to community variability were identified through Random Forest modeling, with Bacteriap25 and Sutterellaceae standing out among bacteria, and Archaeorhizomyces and Clavaria among fungi. Soil chemical properties, including pH, TN, TP, EC, and SOC, significantly correlated with microbial diversity, composition, and co-occurrence networks. Structural equation modeling revealed that geographic distribution patterns directly and indirectly influenced soil chemical properties and microbial communities. Overall, the study provides insights into the geographic distribution patterns of soil microbial communities associated with A. senticosus and highlights the need for further research into the underlying mechanisms shaping these patterns.},
}
@article {pmid39770703,
year = {2024},
author = {Islam, MZ and Jozipovic, D and Lopez, PA and Krych, L and Correia, BSB and Bertram, HC and Hansen, AK and Hansen, CHF},
title = {Wild-Mouse-Derived Gut Microbiome Transplantation in Laboratory Mice Partly Alleviates House-Dust-Mite-Induced Allergic Airway Inflammation.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122499},
pmid = {39770703},
issn = {2076-2607},
support = {R288-2018-1123//Lundbeck Foundation/ ; N/A//Sigrid Rigmor Morans Mindefond/ ; },
abstract = {Laboratory mice are instrumental for preclinical research but there are serious concerns that the use of a clean standardized environment for specific-pathogen-free (SPF) mice results in poor bench-to-bedside translation due to their immature immune system. The aim of the present study was to test the importance of the gut microbiota in wild vs. SPF mice for evaluating host immune responses in a house-dust-mite-induced allergic airway inflammation model without the influence of pathogens. The wild mouse microbiome reduced histopathological changes and TNF-α in the lungs and serum when transplanted to microbiota-depleted mice compared to mice transplanted with the microbiome from SPF mice. Moreover, the colonic gene expression of Gata3 was significantly lower in the wild microbiome-associated mice, whereas Muc1 was more highly expressed in both the ileum and colon. Intestinal microbiome and metabolomic analyses revealed distinct profiles associated with the wild-derived microbiome. The wild-mouse microbiome thus partly reduced sensitivity to house-dust-mite-induced allergic airway inflammation compared to the SPF mouse microbiome, and preclinical studies using this model should consider using both 'dirty' rewilded and SPF mice for testing new therapeutic compounds due to the significant effects of their respective microbiomes and derived metabolites on host immune responses.},
}
@article {pmid39770702,
year = {2024},
author = {Wu, W and Xue, F and Huang, C and Zhou, Y and Lan, G and Bi, W and Liu, J and Yu, X and Li, Z and Zhang, L and Feng, F and Gu, J and Ma, R and Qi, D},
title = {Low Reproductivity of Giant Pandas May Be Associated with Increased Vaginal Escherichia-Shigella.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122500},
pmid = {39770702},
issn = {2076-2607},
support = {U21A20193//National Natural Science Foundation of China/ ; 32400405//National Natural Science Foundation of China/ ; 2023NSFSC1156//Sichuan Science and Technology Program/ ; 2024NSFSC0023//Sichuan Science and Technology Program/ ; 2023-YF09-00017-SN//Chengdu Science and Technology Bureau/ ; 2024CPB-A23//Chengdu Giant Panda Breeding Research Foundation/ ; 2024CPB-Y05//Chengdu Giant Panda Breeding Research Foundation/ ; 2025CPB-C13//Chengdu Giant Panda Breeding Research Foundation/ ; },
abstract = {The poor reproductive capacity of giant pandas significantly hinders the development of captive populations, with 80.88% of adult individuals being unable to successfully become pregnant and deliver offspring. The disturbance of vaginal microbiota has been proven to potentially lead to miscarriage, abortion, and stillbirth in mammals. To elucidate the potential relationship between the vaginal microbiota and the reproductive capacity of giant pandas, we performed high-throughput sequencing of vaginal microbiota at the time of fertilization and conducted comparative analyses based on different pregnancy outcomes. We found that the microbial diversity in the delivery (D) group exceeded that in the non-delivery (ND) group and the vaginal microbial community structure was statistically different between the two groups. The vaginal microbiota in the delivery pandas consisted of unclassified Pseudomonadaceae which was gradually replaced by the Escherichia-Shigella type of vaginal microbiota in the ND group. A function predictions analysis showed that infectious disease, glycan biosynthesis, and metabolism were significantly enriched in the ND group. Additionally, an analysis of the microbial community phenotypic categories indicated that the ND group exhibited a significantly higher abundance of Gram-negative bacteria, facultative anaerobes, potential pathogens, and stress-tolerant species compared to the D group, predominantly driven by the elevated abundance of Escherichia-Shigella. Escherichia-Shigella can be used within LDA and ROC analyses to diagnostically distinguish the vaginal microflora associated with bad pregnancy outcomes during estrus. Our results will help to identify potential pathogens causing reproductive tract diseases, reduce the number of reproductive tract disease infections in pandas, and increase the birth rate of giant pandas in conservation breeding programs.},
}
@article {pmid39770690,
year = {2024},
author = {Olotu, T and Ferrell, JM},
title = {Lactobacillus sp. for the Attenuation of Metabolic Dysfunction-Associated Steatotic Liver Disease in Mice.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122488},
pmid = {39770690},
issn = {2076-2607},
support = {1R01DK044442-26A1/NH/NIH HHS/United States ; 1R01AA015951-17A1/NH/NIH HHS/United States ; 01//University Hospitals-NEOMED Faculty Scholar/ ; },
abstract = {Probiotics are studied for their therapeutic potential in the treatment of several diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD). Part of the significant progress made in understanding the pathogenesis of steatosis has come from identifying the complex interplay between the gut microbiome and liver function. Recently, probiotics have shown beneficial effects for the treatment and prevention of steatosis and MASLD in rodent models and in clinical trials. Numerous studies have demonstrated the promising potential of lactic acid bacteria, especially the genus Lactobacillus. Lactobacillus is a prominent bile acid hydrolase bacterium that is involved in the biotransformation of bile acids. This genus' modulation of the gut microbiota also contributes to overall gut health; it controls gut microbial overgrowth, shapes the intestinal bile acid pool, and alleviates inflammation. This narrative review offers a comprehensive summary of the potential of Lactobacillus in the gut-liver axis to attenuate steatosis and MASLD. It also highlights the roles of Lactobacillus in hepatic lipid metabolism, insulin resistance, inflammation and fibrosis, and bile acid synthesis in attenuating MASLD.},
}
@article {pmid39770676,
year = {2024},
author = {Wang, Z and Liu, X and Zhao, M and Ma, W and Wang, Y and Jia, Y and Ge, G},
title = {Effect of Spirulina on the Rumen Microbiota and Serum Biochemical Parameters of Lambs.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122473},
pmid = {39770676},
issn = {2076-2607},
abstract = {Spirulina (Arthrospira platensis) is rich in a variety of fermentable fibers and prebiotics, which can promote the proliferation of beneficial flora in the intestinal tract of ruminants and optimize the balance of microorganisms in the rumen. The aim of this study was to evaluate whether dietary supplementation with Spirulina has a beneficial effect on the rumen microbial community and serum indices in lambs. For this purpose, 36 lambs with a mean weight of 21.68 kg (standard deviation 1.04 kg) and an age of approximately 5 months (standard deviation 4 days) were selected for the study. The same scale was used for age standard deviation, i.e., 4 days/30.5 days (1 month) = 0.13 months. All lambs were randomly assigned into two treatments, and received non-Spirulina diet as the control (CK treatment) and the Spirulina added diet (Spirulina was added at a rate of 3% of the fresh weight of the diet). The results indicated that the triacylglycerol (p < 0.0001), alanine transaminase (ALT) (p < 0.0001), aspartate aminotransferase (AST) (p < 0.0001), glucose (p < 0.0001), immunoglobulin G (p = 0.0066) and insulin (p = 0.0025) levels were markedly increased in the Spirulina treatment compared to those in the CK treatment. The principal coordinates analysis showed that the bacterial community did not cluster separately between the CK and Spirulina treatments. Firmicutes, Bacteroidetes and Actinobacteria were the dominant members of the community in two treatments. Prevotella were the primary genera, followed by the Lachnospiraceae_NK3A20_group, Olsenella, Succinivibrionaceae_UCG-001 and Ruminococcus, and a significant (p < 0.05) difference was found in Olsenella between the two treatments. These results suggest that the addition of Spirulina is more beneficial for serum biochemical parameters and rumen microbiota of lambs. Overall, these findings contribute to the development of strategies to improve rumen microbial communities for healthy ecosystems on the Mongolian Plateau and provide a scientific basis for the use of Spirulina in feed.},
}
@article {pmid39770661,
year = {2024},
author = {Fu, Y and Cheng, Y and Ma, L and Zhou, Q},
title = {Longitudinal Microbiome Investigations Reveal Core and Growth-Associated Bacteria During Early Life Stages of Scylla paramamosain.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770661},
issn = {2076-2607},
support = {2023YFD2402000//the National Key R. &amp; D. Program of China/ ; 2023TD31//the Special Scientific Research Funds for Central Non-profit Institutes, Chinese Academy of Fish-ery Sciences/ ; T2023214//the Shanghai Agriculture Science and Technology Innovation Project/ ; CARS-48//the earmarked fund for China Agriculture Research System/ ; },
abstract = {In animals, growth and development are strongly correlated with the gut microbiota. The gut of the economically important marine crab (Scylla paramamosain) harbors a diverse microbial community, yet its associations with the surrounding environment, growth performance, and developmental stages remain obscure. In this study, we first characterized stage-specific microbiomes and shifts in the contributions of live feed and water via SourceTracker. We observed decreased microbial diversity and increased priority effects along zoea stages. Psychobacter was identified as the core genus, whereas Lactobacillus was the hub genus connecting different stages. Second, microbial correlations with various stage-specific growth traits were observed under interventions generating enhanced (probiotic mixture enrichment), normal (control), and reduced (antibiotic treatment) microbiomes. By combining machine learning regression and bioinformatics analysis, we identified four candidate growth performance-associated probiotics belonging to Rhodobacterales, Sulfitobacter, Confluentimicrobium, and Lactobacillus, respectively. Our study interpreted the dynamics and origins of the Scylla paramamosain zoea microbiome and underscored the importance of optimizing potential probiotics to increase growth performance during early life stages in marine invertebrates for effective larviculture.},
}
@article {pmid39770654,
year = {2024},
author = {Maldonado-Ruiz, P},
title = {The Tick Microbiome: The "Other Bacterial Players" in Tick Biocontrol.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770654},
issn = {2076-2607},
abstract = {Hard ticks (family Ixodidae) are one of the most predominant arthropod disease vectors worldwide, second only to mosquitoes. In addition to harboring animal and human pathogens, ticks are known to carry a microbial community constituted of non-pathogenic organisms, which includes maternally inherited intracellular endosymbionts and other environmentally acquired extracellular microorganisms. These microbial communities, which include bacteria, viruses, protozoans, and fungi-with often commensal, mutualistic, or parasitic associations with the tick-comprise the tick microbiome, bacteria being the most studied community. Many bacterial taxa frequently reported in ticks include soil, plant, and animal-associated microbes, suggesting many are environmentally acquired, including members with known entomopathogenic potential, such as Bacillus thuringiensis, Bacillus spp., and Pseudomonas spp. It has been reported that microbial community composition can impact pathogen persistence, dissemination, and fitness in ticks. In the United States, Ixodes scapularis (northeast) and I. pacificus (west) are the predominant vectors of Borrelia burgdorferi, the causal agent of Lyme disease. Amblyomma americanum is another important tick vector in the U.S. and is becoming an increasing concern as it is the leading cause of alpha-gal syndrome (AGS, or red meat allergy). This condition is caused by tick bites containing the galactose alpha 1,3 galactose (alpha-gal) epitope in their saliva. In this paper, we present a summary of the tick microbiome, including the endosymbiotic bacteria and the environmentally acquired (here referred to as the non-endosymbiotic community). We will focus on the non-endosymbiotic bacteria from Ixodes spp. and Amblyomma americanum and discuss their potential for novel biocontrol strategies.},
}
@article {pmid39770642,
year = {2024},
author = {Lucaciu, SR and Domokos, B and Puiu, R and Ruta, V and Motoc, SN and Rajnoveanu, R and Todea, D and Stoia, AM and Man, AM},
title = {Lung Microbiome in Lung Cancer: A Systematic Review.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770642},
issn = {2076-2607},
abstract = {UNLABELLED: To date, the percentage composition of the lung microbiome in bronchopulmonary cancer has not been summarized. Existing studies on identifying the lung microbiome in bronchopulmonary cancer through 16S rRNA sequencing have shown variable results regarding the abundance of bacterial taxa.<br><br>OBJECTIVE: To identify the predominant bacterial taxa at the phylum and genus levels in bronchopulmonary cancer using samples collected through bronchoalveolar lavage and to determine a potential proportional pattern that could contribute to the diagnosis of bronchopulmonary cancer.<br><br>DATA SOURCES: A systematic review of English articles using MEDLINE, Embase, and Web of Science. Search terms included lung microbiome, lung cancer, and bronchoalveolar lavage.<br><br>STUDY SELECTION: Studies that investigated the lung microbiome in bronchopulmonary cancer with samples collected via bronchoalveolar lavage.<br><br>DATA EXTRACTION: Independent extraction of articles using predefined data fields, including study quality indicators.<br><br>DATA SYNTHESIS: Nine studies met the inclusion criteria, focusing on those that utilized a percentage expression of the microbiome at the phylum or genus level. There was noted heterogeneity between studies, both in terms of phylum and genus, with a relatively constant percentage of the Firmicutes phylum and the genera Streptococcus and Veillonella being mentioned. Significant differences were also observed regarding the inclusion criteria for study participants, the method of sample collection, and data processing.<br><br>CONCLUSIONS: To date, there is no consistent percentage pattern at the phylum or genus level in bronchopulmonary cancer, with the predominance of a phylum or genus varying across different patient cohorts, resulting in non-overlapping outcomes.},
}
@article {pmid39770639,
year = {2024},
author = {Peraza, P and Fernández-Calero, T and Naya, H and Sotelo-Silveira, J and Navajas, EA},
title = {Exploring the Linkage Between Ruminal Microbial Communities on Postweaning and Finishing Diets and Their Relation to Residual Feed Intake in Beef Cattle.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770639},
issn = {2076-2607},
support = {FSA_1_2018_1_152872//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; },
abstract = {Feed efficiency significantly impacts the economics of beef production and is influenced by biological and environmental factors. The rumen microbiota plays a crucial role in efficiency, with studies increasingly focused on its relationship with different rearing systems. This study analyzed 324 rumen samples from bulls and steers categorized as high and low efficiency based on residual feed intake. The animals were fed two diets (postweaning and finishing) and rumen samples were sequenced using a reduced representation sequencing (RRS) based approach. The results indicated that diet significantly affected microbial diversity and abundance. In postweaning diets, Actinomycetota, particularly Bifidobacterium, were prevalent, aiding carbohydrate fermentation. In contrast, Acetoanaerobium was identified in finishing diets, likely contributing to acetate production. Additionally, Bacteroides and Butyrivibrio were abundant during postweaning, known for fiber degradation and volatile fatty acid production. Notably, Prevotella and Fibrobacter succinogenes were associated with high feed intake and nutrient utilization, indicating their potential as microbial biomarkers. However, alpha diversity indices showed no significant relationship with feed efficiency, suggesting that diversity alone may not adequately reflect the complexity of feed efficiency phenotypes. These findings highlight the importance of diet and microbial interactions on feed efficiency and suggest further research to explore these microbial contributions to precision feeding strategies.},
}
@article {pmid39770627,
year = {2024},
author = {Ricchezze, G and Buratti, E and De Micco, F and Cingolani, M and Scendoni, R},
title = {Medico-Legal Applications of the Human Microbiome and Critical Issues Due to Environmental Transfer: A Review.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770627},
issn = {2076-2607},
support = {ECS00000041 - VITALITY - CUP n&#xb0; D83C22000710005//European Union - NextGenerationEU under the Italian Ministry of University and Research (MUR) National Innovation Ecosystem/ ; },
abstract = {Microbiome has recently seen an increase in its forensic applications. It could be employed to identify a suspect when DNA is not available; it can be used to establish postmortem interval (PMI). Furthermore, it could prove to be fundamental in cases of sexual assault. One of the most interesting aspects to study is how microbiomes are transferred. The aim of this review is to analyze the existing literature focusing on the potential transfer of microbiome from humans to environment. Searches on PubMed, Scopus, and Web of Science identified a total of 348 articles. Furthermore, from the bibliographies of the included articles, an additional publication was selected, in accordance with the established inclusion and exclusion criteria. This study has shown the potential of utilizing microbiomes as trace evidence, particularly in connecting individuals to specific environments or objects. However, the variability and dynamics of microbial transfer and persistence need to be carefully addressed.},
}
@article {pmid39770624,
year = {2024},
author = {Li, J and Zuo, Y and Zhang, J},
title = {Rhizosphere Shifts: Reduced Fungal Diversity and Microbial Community Functionality Enhance Plant Adaptation in Continuous Cropping Systems.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770624},
issn = {2076-2607},
support = {31760360//National Natural Science Foundation of China/ ; 202301AT070007//Natural Science Foundation of Yunnan Province of China/ ; 202101BD070001-078//Natural Science Agricultural Joint Foundation of Yunnan Province of China/ ; },
abstract = {Continuous cropping problems constitute threats to perennial plant health and survival. Soil conditioners have the potential to enhance plant disease resistance in continuous cropping systems. However, how microbes and metabolites of the rhizosphere respond to soil conditioner addition remains largely unknown, but this knowledge is paramount to providing innovative strategies to enhance plant adaptation in continuous cropping systems. Here, we found that a biochar conditioner significantly improved plant survival rates in a continuous cropping system. The biochar-induced rhizosphere significantly alters the fungal community, causing a decline in fungal diversity and the downregulation of soil microbial community functionality. Specifically, the biochar-induced rhizosphere causes a reduction in the relative abundance of pathogenic Fusarium sp. and phenolic acid concentration, whose variations are the primary causes of continuous cropping problems. Conversely, we observed an unexpected bacterial diversity increase in rhizospheric and non-rhizospheric soils. Our research further identified key microbial taxa in the biochar-induced rhizosphere, namely, Monographella, Acremonium, Geosmithia, and Funneliformis, which enhance soil nutrient availability, suppress Fusarium sp., mitigate soil acidification, and reduce phenolic acid concentrations. Collectively, we highlight the critical role of regular microbial communities and metabolites in determining plant health during continuous cropping and propose a synthetic microbial community framework for further optimizing the ecological functions of the rhizosphere.},
}
@article {pmid39770612,
year = {2024},
author = {Yang, B and Yang, J and Chen, R and Chai, J and Wei, X and Zhao, J and Zhao, Y and Deng, F and Li, Y},
title = {Metagenome-Assembled Genomes of Pig Fecal Samples in Nine European Countries: Insights into Antibiotic Resistance Genes and Viruses.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770612},
issn = {2076-2607},
support = {2023YFE0124400//the National Key Research and Development Program of China/ ; 2022A1515110819//Youth Project of Guangdong Foshan joint fund of the Guangdong Natural Science Foundation/ ; 2019B030301010//Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding/ ; },
abstract = {Gut microbiota plays a crucial role in the health and productivity of pigs. However, the spread of antibiotic resistance genes (ARGs) and viruses within the pig intestinal microbiota poses significant threats to animal and public health. This study utilized 181 pig samples from nine European countries and employed metagenomic assembly methods to investigate the dynamics and distribution of ARGs and viruses within the pig intestinal microbiota, aiming to observing their associations with potential bacterial hosts. We identified 4605 metagenome-assembled genomes (MAGs), corresponding to 19 bacterial phyla, 97 families, 309 genera, and a total of 449 species. Additionally, 44 MAGs were classified as archaea. Analysis of ARGs revealed 276 ARG types across 21 ARG classes, with Glycopeptide being the most abundant ARG class, followed by the class of Multidrug. Treponema D sp016293915 was identified as a primary potential bacterial host for Glycopeptide. Aligning nucleotide sequences with a viral database, we identified 1044 viruses. Among the viral genome families, Peduoviridae and Intestiviridae were the most prevalent, with CAG-914 sp000437895 being the most common potential host species for both. These findings highlight the importance of MAGs in enhancing our understanding of the gut microbiome, revealing microbial diversity, antibiotic resistance, and virus-bacteria interactions. The data analysis for the article was based on the public dataset PRJEB22062 in the European Nucleotide Archive.},
}
@article {pmid39770592,
year = {2024},
author = {Gonzalez-Escalona, N and Kwon, HJ and Chen, Y},
title = {Nanopore Sequencing Allows Recovery of High-Quality Completely Closed Genomes of All Cronobacter Species from Powdered Infant Formula Overnight Enrichments.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770592},
issn = {2076-2607},
support = {This research was funded by the Food and Drug Administration Foods Program Intramural Funds//United States Food and Drug Administration/ ; },
abstract = {Precision metagenomic approaches using Oxford Nanopore Technology (ONT) sequencing has been shown to allow recovery of complete genomes of foodborne bacteria from overnight enrichments of agricultural waters. This study tests the applicability of a similar approach for Cronobacter genome recovery from powdered infant formula (PIF) overnight enrichments, where Cronobacter typically dominates the overall microbiome (>90%). This study aimed to test whether using ONT sequencing of overnight PIF enrichments could recover a completely closed Cronobacter genome for further genomic characterization. Ten PIF samples, each inoculated with different Cronobacter strains, covering Cronobacter sakazakii, C. muytjensii, C. dublinensis, C. turicensis, and C. universalis, were processed according to the Bacteriological Analytical Manual (BAM) protocol. Real-time quantitative PCR (qPCR) was used for initial screening (detection and quantification) of the overnight enrichments and confirmed that the inoculated PIF samples after the overnight enrichment had high levels of Cronobacter (10[7] to 10[9] CFU/mL). DNA from overnight PIF enrichments was extracted from the enrichment broth and sequenced using ONT. Results showed that ONT sequencing could accurately identify, characterize, and close the genomes of Cronobacter strains from overnight PIF enrichments in 3 days, much faster than the nearly 2 weeks required by the current BAM method. Complete genome recovery and species differentiation were achieved. This suggests that combining qPCR with ONT sequencing provides a rapid, cost-effective alternative for detecting and characterizing Cronobacter in PIF, enabling timely corrective actions during outbreaks.},
}
@article {pmid39770567,
year = {2024},
author = {Czarnowski, M and Wnorowska, U and Łuckiewicz, M and Dargiewicz, E and Spałek, J and Okła, S and Sawczuk, B and Savage, PB and Bucki, R and Piktel, E},
title = {Natural Antimicrobial Peptides and Their Synthetic Analogues for Effective Oral Microflora Control and Oral Infection Treatment-The Role of Ceragenins in the Development of New Therapeutic Methods.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {17},
number = {12},
pages = {},
pmid = {39770567},
issn = {1424-8247},
support = {B.SUB.23.328//medical university of bia&#x142;ystok/ ; },
abstract = {Oral diseases, both acute and chronic, of infectious or non-infectious etiology, represent some of the most serious medical problems in dentistry. Data from the literature increasingly indicate that changes in the oral microbiome, and therefore, the overgrowing of pathological microflora, lead to a variety of oral-localized medical conditions such as caries, gingivitis, and periodontitis. In recent years, compelling research has been devoted to the use of natural antimicrobial peptides as therapeutic agents in the possible treatment of oral diseases. This review focuses on the potential of ceragenins (CSAs), which are lipid analogs of natural antimicrobial peptides, as molecules for the development of new methods for the prevention and treatment of oral diseases. Studies to date indicate that ceragenins, with their spectrum of multidirectional biological activities, including antimicrobial, tissue regeneration-stimulating, anti-inflammatory, and immunomodulatory properties, are strong candidates for further development of oral formulations. However, many of the beneficial properties of ceragenins require confirmation in experimental conditions reproducing the oral environment to fully determine their application potential. Their transition to practical use also requires more advanced testing of these molecules in clinical trials, which have only been conducted in limited numbers to date.},
}
@article {pmid39770543,
year = {2024},
author = {Vitetta, L and Nation, T and Oldfield, D and Thomsen, M},
title = {Medicinal Cannabis and the Intestinal Microbiome.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {17},
number = {12},
pages = {},
pmid = {39770543},
issn = {1424-8247},
abstract = {Historically, the multiple uses of cannabis as a medicine, food, and for recreational purposes as a psychoactive drug span several centuries. The various components of the plant (i.e., seeds, roots, leaves and flowers) have been utilized to alleviate symptoms of inflammation and pain (e.g., osteoarthritis, rheumatoid arthritis), mood disorders such as anxiety, and intestinal problems such as nausea, vomiting, abdominal pain and diarrhea. It has been established that the intestinal microbiota progresses neurological, endocrine, and immunological network effects through the gut-microbiota-brain axis, serving as a bilateral communication pathway between the central and enteric nervous systems. An expanding body of clinical evidence emphasizes that the endocannabinoid system has a fundamental connection in regulating immune responses. This is exemplified by its pivotal role in intestinal metabolic and immunity equilibrium and intestinal barrier integrity. This neuromodulator system responds to internal and external environmental signals while also serving as a homeostatic effector system, participating in a reciprocal association with the intestinal microbiota. We advance an exogenous cannabinoid-intestinal microbiota-endocannabinoid system axis potentiated by the intestinal microbiome and medicinal cannabinoids supporting the mechanism of action of the endocannabinoid system. An integrative medicine model of patient care is advanced that may provide patients with beneficial health outcomes when prescribed medicinal cannabis.},
}
@article {pmid39770481,
year = {2024},
author = {Zhu, W and Zhang, X and Wang, D and Yao, Q and Ma, GL and Fan, X},
title = {Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]): Current Developments, Applications, and Future Prospects.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {17},
number = {12},
pages = {},
pmid = {39770481},
issn = {1424-8247},
support = {U23A20513//National Natural Science Foundation of China/ ; 2024C03106//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; 2022030309//Ningbo Top Medical and Health Research Program/ ; 226-2024-00001; 226-2024-00149//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {The human gastrointestinal microbiota plays a vital role in maintaining host health and preventing diseases, prompting the creation of simulators to replicate this intricate system. The Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]), a multicompartment dynamic simulator, has emerged as a pivotal in vitro model for studying the interactions and interferences within the human gut microbiota. The continuous and real-time monitoring hallmarks, along with the programmatically flexible setup, bestow SHIME[®] with the ability to mimic the entire human intestinal ecosystem with high dynamics and stability, allowing the evaluation of various treatments on the bowel microbiota in a controlled environment. This review outlines recent developments in SHIME[®] systems, including the M-SHIME[®], Twin-SHIME[®], Triple-SHIME[®], and Toddle SHIME[®] models, highlighting their applications in the fields of food and nutritional science, drug development, gut health research, and traditional Chinese medicine. Additionally, the prospect of SHIME[®] integrating with other advanced technologies is also discussed. The findings underscore the versatility of SHIME[®] technology, demonstrating its significant contributions to current gut ecosystem research and its potential for future innovation in microbiome-related fields.},
}
@article {pmid39770384,
year = {2024},
author = {Thaker, S and Chan, JYH and Thaker, KN and Takele, RA and Newlands, AF and Maxwell, K and Bhanji, Y and Kramer, M and Scotland, KB},
title = {Public Interest in Online Information on Recurrent Urinary Tract Infections Is Greatest for Information with the Poorest Publication Quality.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
pmid = {39770384},
issn = {2076-0817},
mesh = {*Urinary Tract Infections/epidemiology/microbiology ; Humans ; *Internet ; *Social Media ; Recurrence ; Surveys and Questionnaires ; },
abstract = {Background: Urinary tract infections (UTIs) are among the most prevalent bacterial infections. With many patients turning to the Internet as a health resource, this study seeks to understand public engagement with online resources concerning recurrent UTIs (rUTIs), assess their reliability, and identify common questions/concerns about rUTIs. Methods: Social media analysis tool BuzzSumo was used to calculate online engagement (likes, shares, comments, views) with information on rUTIs. The reliability of highly engaged articles was evaluated using the DISCERN questionnaire. Highly engaged categories were entered as keywords in Google Trends to quantify search interest. To categorize patient-specific concerns, a database containing anonymously collected patient questions about rUTIs was created. Results: BuzzSumo revealed four search categories: general information, treatment, causes, and herbal remedies. DISCERN scores indicated moderate reliability overall; however, the "herbal remedies" category demonstrated poor reliability despite high engagement. Google Trends analysis highlighted "causes" and "treatment" searches as highest in relative interest. The 10 most popular categories of concern were antibiotics, microbiome, vaccines, prevention, pelvic pain, sex, testing, symptoms, diet/lifestyle, and hormones. Conclusions: People living with rUTIs demonstrate key concerns and often seek information online, yet articles with high engagement often contain unreliable information. Healthcare professionals may consider counteracting misinformation by providing evidence-based information online about rUTIs.},
}
@article {pmid39770361,
year = {2024},
author = {Ulas, M and Hussey, S and Broderick, A and Fitzpatrick, E and Dunne, C and Cooper, S and Dominik, A and Bourke, B},
title = {FISH-Flow Cytometry Reveals Microbiome-Wide Changes in Post-Translational Modification and Altered Microbial Abundance Among Children with Inflammatory Bowel Disease.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/pathogens13121102},
pmid = {39770361},
issn = {2076-0817},
support = {C/19/1//Children's Medical and Research Foundation Dublin/ ; },
mesh = {Humans ; Child ; *In Situ Hybridization, Fluorescence/methods ; *Inflammatory Bowel Diseases/microbiology/immunology ; *Flow Cytometry/methods ; Male ; *Gastrointestinal Microbiome ; Female ; Adolescent ; *Protein Processing, Post-Translational ; Child, Preschool ; Phosphorylation ; Feces/microbiology ; Bacteria/classification/isolation &amp; purification/metabolism/genetics ; Tyrosine/metabolism ; Microbiota ; },
abstract = {Metaproteomic analysis of microbiome post-translation modifications (PTMm) is challenging, and little is known about the effects of inflammation on the bacterial PTM landscape in IBD. Here, we adapted and optimised fluorescence in situ hybridisation-flow cytometry (FISH-FC) to study microbiome-wide tyrosine phosphorylation (p-Tyr) in children with and without inflammatory bowel disease (IBD). Microbial p-Tyr signal was significantly higher in children with IBD, compared to those without. Faecalibacterium prausnitzii, Bacteroidota, Gammaproteobacteria and Bifidobacteria tended to be more abundant in IBD than in non-IBD control children but there were only minor differences in p-Tyr among these bacterial communities in those with and without IBD. p-Tyr was significantly lower in non-IBD children older than 9 yrs compared with those less than 9 yrs, and the effect was seen in all four bacterial subgroups studied. The opposite trend was seen in patients with IBD. p-Tyr overall is higher in children with IBD but the effects of inflammation on p-Tyr vary according to the bacterial community. The overall microbiome p-Tyr signal changes with age in healthy children. FISH-FC can be used to study the microbiome-wide PTM landscape.},
}
@article {pmid39770288,
year = {2024},
author = {Brigida, M and Saviano, A and Petruzziello, C and Manetti, LL and Migneco, A and Ojetti, V},
title = {Gut Microbiome Implication and Modulation in the Management of Recurrent Urinary Tract Infection.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
pmid = {39770288},
issn = {2076-0817},
mesh = {Humans ; *Urinary Tract Infections/microbiology/drug therapy/therapy ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; Urinary Tract/microbiology ; Recurrence ; Anti-Bacterial Agents/therapeutic use ; Escherichia coli ; Female ; Escherichia coli Infections/microbiology/therapy ; },
abstract = {Urinary tract infections (UTIs) are one of the most common bacterial infections, affecting more than 150 million people each year in the world. UTIs have grown exponentially in the last few years. They represent a major load for both individuals and society. The highest incidence (about 55-60%) concerns women. Many pathogens are involved in UTIs, most of which are derived from the gut. Recent studies, together with recent diagnostic techniques (such as quantitative culture of urine or next-generation sequencing), have improved the knowledge of microbial communities in the urinary tract. It turned out that gut dysbiosis is strictly involved in the pathogenesis of UTIs. In particular, the human gut is the natural habitat for Escherichia coli (E. coli), the main bacterium responsible for UTIs. The overgrowth of E. coli pathogenic strains represents a risk factor for them. Furthermore, the human gut microbiota acts as a "global reservoir" for genes conferring resistance to clinically relevant antibiotics, thus influencing the treatment of UTIs. In addition, differently from the past, the idea of a sterile urinary environment has been replaced by the characterization of a urinary microbiome. The aim of our review is to explore recent studies on the association between gut microbiota and urinary microbiome and to summarize the current knowledge about the effects of interactions between gut and urinary microbial communities in the pathogenesis of UTIs, considering UTIs more as a "gut disease" and not only a urinary disease and providing new insight into the therapeutic options such as the use of probiotics.},
}
@article {pmid39769409,
year = {2024},
author = {Nedelyaeva, OI and Khramov, DE and Balnokin, YV and Volkov, VS},
title = {Functional and Molecular Characterization of Plant Nitrate Transporters Belonging to NPF (NRT1/PTR) 6 Subfamily.},
journal = {International journal of molecular sciences},
volume = {25},
number = {24},
pages = {},
pmid = {39769409},
issn = {1422-0067},
support = {theme No. 122042700044-6//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Nitrate Transporters ; *Anion Transport Proteins/genetics/metabolism/chemistry ; *Phylogeny ; *Plant Proteins/genetics/metabolism ; Nitrates/metabolism ; Plants/metabolism/genetics ; Multigene Family ; Gene Expression Regulation, Plant ; Stress, Physiological/genetics ; },
abstract = {Plant nitrate transporters in the NPF (NRT1) family are characterized by multifunctionality and their involvement in a number of physiological processes. The proteins in this family have been identified in many monocotyledonous and dicotyledonous species: a bioinformatic analysis predicts from 20 to 139 members in the plant genomes sequenced so far, including mosses. Plant NPFs are phylogenetically related to proton-coupled oligopeptide transporters, which are evolutionally conserved in all kingdoms of life apart from Archaea. The phylogenetic analysis of the plant NPF family is based on the amino acid sequences present in databases; an analysis identified a separate NPF6 clade (subfamily) with the first plant nitrate transporters studied at the molecular level. The available information proves that proteins of the NPF6 clade play key roles not only in the supply of nitrate and its allocation within different parts of plants but also in the transport of chloride, amino acids, ammonium, and plant hormones such as auxins and ABA. Moreover, members of the NPF6 family participate in the perception of nitrate and ammonium, signaling, plant responses to different abiotic stresses, and the development of tolerance to these stresses and contribute to the structure of the root-soil microbiome composition. The available information allows us to conclude that NPF6 genes are among the promising targets for engineering/editing to increase the productivity of crops and their tolerance to stresses. The present review summarizes the available published data and our own results on members of the NPF6 clade of nitrate transporters, especially under salinity; we outline their molecular, structural, and functional characteristics and suggest potential lines for future research.},
}
@article {pmid39769396,
year = {2024},
author = {Magaña-Gómez, JA and González-Ochoa, G and Rosas-Rodríguez, JA and Stephens-Camacho, NA and Flores-Mendoza, LK},
title = {Sucralose-Enhanced Adipogenesis on Preadipocyte Human Cell Line During Differentiation Process.},
journal = {International journal of molecular sciences},
volume = {25},
number = {24},
pages = {},
doi = {10.3390/ijms252413635},
pmid = {39769396},
issn = {1422-0067},
mesh = {Humans ; *Adipogenesis/drug effects ; *Sucrose/analogs &amp; derivatives/pharmacology ; *Cell Differentiation/drug effects ; *Adipocytes/drug effects/metabolism/cytology ; Cell Line ; Cytokines/metabolism ; Sweetening Agents/pharmacology ; Gene Expression Regulation/drug effects ; },
abstract = {Sucralose, a commonly nonnutritive sweetener used in daily products of habitual diet, is related to impairing the gut microbiome by disrupting inflammatory response, promoting weight gain by increasing adipose tissue and promoting chronic inflammatory processes. Considering the impact of sucralose in the development of metabolic diseases, in this work, we focused on the impact of sucralose on the adipocyte differentiation process to determine if sucralose can promote adipogenesis and increase adipose tissue depots in PCS 210 010 human preadipocytes cell line. Sucralose at 25 (S25) and 100 ng/µL (S100) concentrations were tested against control with no edulcorant (NS) during the adipocyte differentiation process at 48 h and 96 h. The genetic expression of adipogenesis markers such as CEBP-α, PPARγ, EBF-2, UCP-1, and lipogenesis regulator ACC was determined by qPCR. A panel of human cytokines related to inflammatory response was measured by a flow cytometer using the kit Legend Plex Human Cytokine panel of BIOLUMINEX. Our results indicate that sucralose increased the expression of white adipocyte differentiation marker CEBP-α and lipogenesis regulator ACC at 96 h before complete differentiation. Also, sucralose triggers an inflammatory response by synthesizing adiponectin, resistin, IL-6, IL-8, and Il-1B. To summarize, sucralose stimulates the expression of genes related to adipogenesis and negatively affects the secretion of inflammatory cytokines and adipokines during preadipocyte differentiation.},
}
@article {pmid39769394,
year = {2024},
author = {Altamura, S and Lombardi, F and Palumbo, P and Cinque, B and Ferri, C and Del Pinto, R and Pietropaoli, D},
title = {The Evolving Role of Neutrophils and Neutrophil Extracellular Traps (NETs) in Obesity and Related Diseases: Recent Insights and Advances.},
journal = {International journal of molecular sciences},
volume = {25},
number = {24},
pages = {},
doi = {10.3390/ijms252413633},
pmid = {39769394},
issn = {1422-0067},
mesh = {Humans ; *Extracellular Traps/metabolism/immunology ; *Neutrophils/metabolism/immunology ; *Obesity/metabolism/immunology ; Animals ; *Gastrointestinal Microbiome ; Inflammation/metabolism/immunology ; Adipose Tissue/metabolism/immunology ; },
abstract = {Obesity is a chronic, multifactorial disease characterized by persistent low-grade tissue and systemic inflammation. Fat accumulation in adipose tissue (AT) leads to stress and dysfunctional adipocytes, along with the infiltration of immune cells, which initiates and sustains inflammation. Neutrophils are the first immune cells to infiltrate AT during high-fat diet (HFD)-induced obesity. Emerging evidence suggests that the formation and release of neutrophil extracellular traps (NETs) play a significant role in the progression of obesity and related diseases. Additionally, obesity is associated with an imbalance in gut microbiota and increased intestinal barrier permeability, resulting in the translocation of live bacteria, bacterial deoxyribonucleic acid (DNA), lipopolysaccharides (LPS), and pro-inflammatory cytokines into the bloodstream and AT, thereby contributing to metabolic inflammation. Recent research has also shown that short-chain fatty acids (SCFAs), produced by gut microbiota, can influence various functions of neutrophils, including their activation, migration, and the generation of inflammatory mediators. This review comprehensively summarizes recent advancements in understanding the role of neutrophils and NET formation in the pathophysiology of obesity and related disorders while also focusing on updated potential therapeutic approaches targeting NETs based on studies conducted in humans and animal models.},
}
@article {pmid39769364,
year = {2024},
author = {Grzyb, T and Szulc, J},
title = {Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition.},
journal = {International journal of molecular sciences},
volume = {25},
number = {24},
pages = {},
pmid = {39769364},
issn = {1422-0067},
mesh = {*Microbiota ; *Bacteria/genetics/classification/metabolism ; *Plants/microbiology ; Biodiversity ; Ecosystem ; Phosphorus/metabolism ; Nitrogen/metabolism ; Symbiosis ; Nutrients/metabolism ; },
abstract = {While gaining increasing attention, plant-microbiome-environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron-elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology.},
}
@article {pmid39769349,
year = {2024},
author = {Guzowska, M and Dziendzikowska, K and Kopiasz, &#x141; and Gajewska, M and Wilczak, J and Harasym, J and Czerwińska, M and Gromadzka-Ostrowska, J},
title = {Oat Beta-Glucans Modulate the Gut Microbiome, Barrier Function, and Immune Responses in an In Vivo Model of Early-Stage Colorectal Cancer.},
journal = {International journal of molecular sciences},
volume = {25},
number = {24},
pages = {},
pmid = {39769349},
issn = {1422-0067},
support = {2018/29/B/NZ9/01060//National Science Center/ ; Science development fund//Warsaw University of Life Sciences - SGGW/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/immunology/pathology/metabolism ; *beta-Glucans/pharmacology ; Rats ; Male ; Intestinal Mucosa/drug effects/metabolism/immunology/microbiology ; Disease Models, Animal ; Dietary Supplements ; Azoxymethane ; Akkermansia ; },
abstract = {Oat beta-glucans (OBGs) are known for their beneficial effects on gut health, including anti-inflammatory and prebiotic effects. The aim of this study was to evaluate the impact of two doses (1% or 3% w/w) of dietary low-molar-mass OBG supplementation on colorectal cancer (CRC) development, immune cell profiles, intestinal barrier protein expression, and microbiota composition in a rat model of CRC induced by azoxymethane (AOM). Microbiome analysis revealed significant differences between the control and CRC groups. OBG supplementation influenced microbial diversity and abundance, particularly increasing the population of beneficial bacteria, such as Lachnospiraceae and Ruminococcaceae, associated with butyrate production. However, higher doses of OBG (3%) led to a decrease in butyrate-producing bacteria and a shift toward higher levels of Akkermansia muciniphila and Enterococcus faecalis. Immune cell profiling showed a higher percentage of T lymphocytes (CD3+) in rats fed a diet supplemented with 3% OBG, both in the intraepithelial (IEL) and lamina propria lymphocytes (LPLs). Immunohistochemical analysis of the large intestine revealed a significantly elevated expression of intestinal barrier proteins, i.e., claudin 3 and 4 in rats receiving 1% OBG, while claudin 7 expression was reduced in early-stage CRC. Gene expression analysis also revealed a significant downregulation of Cldn1 in CRC rats. These findings suggest that dietary OBG supplementation modulates the gut microbiota, immune response, and intestinal barrier integrity, with potential implications for nutritional CRC development prevention and treatment strategies.},
}
@article {pmid39769296,
year = {2024},
author = {Chantanaskul, T and Patumcharoenpol, P and Roytrakul, S and Kingkaw, A and Vongsangnak, W},
title = {Exploring Protein Functions of Gut Bacteriome and Mycobiome in Thai Infants Associated with Atopic Dermatitis Through Metaproteomic and Host Interaction Analysis.},
journal = {International journal of molecular sciences},
volume = {25},
number = {24},
pages = {},
pmid = {39769296},
issn = {1422-0067},
support = {N42A650235//National Research Council of Thailand/ ; //Kasetsart University through the Graduate School Fellowship Program, Kasetsart University./ ; },
mesh = {Humans ; *Dermatitis, Atopic/microbiology/metabolism ; *Gastrointestinal Microbiome ; Infant ; Thailand ; *Mycobiome ; *Proteomics/methods ; Male ; Proteome/metabolism ; Female ; Protein Interaction Maps ; Lactobacillus acidophilus ; Southeast Asian People ; },
abstract = {Atopic dermatitis (AD), a prevalent allergic skin condition in children, has been closely associated with imbalances in the gut microbiome. To investigate these microbial alterations and their functional implications, we investigated protein expression, functions and interactions of the gut bacteriome and mycobiome as well as the human proteome in Thai infants with AD using integrative metaproteomic and host interaction analysis. As we observed, probiotic species, such as Lactobacillus acidophilus and Bacteroides salyersiae, were reduced in abundance in the AD group while key pathogenic bacteria and fungi, such as Streptococcus constellatus and Penicillium chrysogenum, increased in abundance. Additionally, the functional analysis of expressed proteins was enriched in response to stress and DNA repair in the bacteriome and ribosome biogenesis-related processes in the mycobiome of the AD group, potentially associated to increased reactive oxygen species (ROS), intestinal inflammation, fungal growth and microbial dysbiosis. Further, a protein-protein interactions (PPIs) network analysis incorporating the human proteome revealed 10 signature proteins related to stress and immune system processes associated with AD. Our findings propose the interactions of the key species and signature protein functions between the gut microbes and the human host in response to AD in Thai infants. To our knowledge, this study serves as the first framework for monitoring bacteriome-mycobiome-human gut studies associated with AD and other allergic diseases in infants.},
}
@article {pmid39769292,
year = {2024},
author = {Sagmeister, A and Matter, CM and Stähli, BE and Scharl, M},
title = {The Gut-Heart Axis: Effects of Intestinal Microbiome Modulation on Cardiovascular Disease-Ready for Therapeutic Interventions?.},
journal = {International journal of molecular sciences},
volume = {25},
number = {24},
pages = {},
pmid = {39769292},
issn = {1422-0067},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Cardiovascular Diseases/prevention &amp; control/microbiology ; *Probiotics/therapeutic use/administration &amp; dosage/pharmacology ; Life Style ; Diet ; Risk Factors ; },
abstract = {Recent reports demonstrate an association between distinct bacteria or bacteria-derived metabolites originating from the gut microbiome and the onset or progression of cardiovascular disease (CVD). This raises the opportunity to modulate the gut microbiome to prevent or treat CVD. To investigate whether intestinal microbiome modulation can prevent or treat CVD, this systematic literature review includes all randomized clinical trials on microbiome modulation and its effects on CVD risk published between August 2018 and August 2023. Within this review, we report the modulation of the gut microbiome by a variety of interventions and their effects on CVD, focusing on cardiovascular risk factors and risk markers of CVD. Beneficial effects were observed upon lifestyle intervention and probiotics use. The most promising diets for reducing risk factors of CVD were the Mediterranean diet, high-fiber diets, polyphenol-rich diets, and diets containing polyunsaturated fatty acids. Among drug interventions, only empagliflozin showed beneficial effects on CVD risk factors. Many dietary interventions were less conclusive because of the heterogeneity of study populations, small sample sizes, and short intervention windows or follow-up. Diet, lifestyle, probiotics, or drug interventions can modulate the gut microbiome and decrease risk markers or risk factors related to CVD. Yet, their effects on clinical endpoints remain to be determined.},
}
@article {pmid39769276,
year = {2024},
author = {Todorovic, N and Martinelli, S and Nannini, G and Weiskirchen, R and Amedei, A},
title = {Etiology-Dependent Microbiome Differences in Hepatocellular Carcinoma Development.},
journal = {International journal of molecular sciences},
volume = {25},
number = {24},
pages = {},
pmid = {39769276},
issn = {1422-0067},
support = {the European Union-NextGenerationEU-National Recovery and Resilience Plan, Mission 4 Component 2-Investment 1.5-THE-Tuscany Health Ecosystem-ECS00000017-CUP B83C22003920001; #NEXTGENERATIONEU (NGEU) and funded by the Ministry of University and Research (M//the European Union-NextGenerationEU-National Recovery and Resilience Plan, Mission 4 Component 2-Investment 1.5-THE-Tuscany Health Ecosystem-ECS00000017-CUP B83C22003920001; #NEXTGENERATIONEU (NGEU) and funded by the Ministry of University and Research (M/ ; },
mesh = {Humans ; *Carcinoma, Hepatocellular/microbiology/etiology/pathology ; *Liver Neoplasms/microbiology/etiology/pathology ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Animals ; Non-alcoholic Fatty Liver Disease/microbiology/pathology ; Microbiota ; },
abstract = {Chronic liver disease is characterised by persistent inflammation, tissue damage, and regeneration, which leads to steatosis, fibrosis, and, lastly, cirrhosis and hepatocellular carcinoma (HCC). HCC, the most prevalent form of primary liver cancer, is one of the leading causes of cancer-related mortality worldwide. The gut microbiota plays a fundamental role in human physiology, and disturbances in its critical balance are widely recognised as contributors to various pathological conditions, including chronic liver diseases, both infectious and non-infectious in nature. Growing interest in microbiota research has recently shifted the focus towards the study of intratumoural microbiota, referred to as the "oncobiome", which can significantly impact the development and progression of HCC. In this review, we discuss existing research and provide an overview of the microbiota influence on viral hepatitis, particularly in shaping the progression of liver disease caused by the hepatitis B and hepatitis C viruses. We also explore microbial dysbiosis and its contribution to the silent and dangerous progression of non-alcoholic fatty liver disease. Additionally, we address the impact of alcohol on the liver and its interaction with the microbiota, tracing the pathway from inflammation to cirrhosis and cancer. The review emphasises the most common etiologies of hepatocellular carcinoma.},
}
@article {pmid39769095,
year = {2024},
author = {Mohan, B and Majeed, A and Thingujam, D and Burton, SS and Cowart, KE and Pajerowska-Mukhtar, KM and Mukhtar, MS},
title = {Amplicon Sequencing Analysis of Submerged Plant Microbiome Diversity and Screening for ACC Deaminase Production by Microbes.},
journal = {International journal of molecular sciences},
volume = {25},
number = {24},
pages = {},
doi = {10.3390/ijms252413330},
pmid = {39769095},
issn = {1422-0067},
support = {IOS-2038872//National Science Foundation/ ; 2418230//National Science Foundation/ ; },
mesh = {*Carbon-Carbon Lyases/genetics/metabolism ; *Microbiota/genetics ; *Plants/microbiology ; Bacteria/genetics/classification/enzymology ; Metagenomics/methods ; Phylogeny ; Biodiversity ; },
abstract = {Submerged plants can thrive entirely underwater, playing a crucial role in maintaining water quality, supporting aquatic organisms, and enhancing sediment stability. However, they face multiple challenges, including reduced light availability, fluctuating water conditions, and limited nutrient access. Despite these stresses, submerged plants demonstrate remarkable resilience through physiological and biochemical adaptations. Additionally, their interactions with microbial communities are increasingly recognized as pivotal in mitigating these environmental stresses. Understanding the diversity of these microbial communities is crucial for comprehending the complex interactions between submerged plants and their environments. This research aims to identify and screen microbes from submerged plant samples capable of producing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and to explore microbial diversity through metagenomic analysis. Microbes were isolated and screened for ACC deaminase production, and metagenomic techniques, including co-occurrence network analysis, were used to examine microbial diversity and interactions within the communities. ACC deaminase-producing microbes can significantly enhance plant metabolism under stress conditions. The identification of the culturable bacteria revealed that most of these microbes belong to the genera Pseudomonas, Bacillus, and Acinetobacter. A total of 177 microbial strains were cultured, with molecular identification revealing 79 reductant, 86 non-reductant, and 12 uncultured strains. Among 162 samples screened for ACC deaminase activity, 50 tested positive. To further understand microbial dynamics, samples were collected from both natural sources and artificial pond reservoirs to assess the impact of the location on flood-associated microbiomes in submerged plants. Metagenomic analysis was conducted on both the epiphytic and endophytic samples. By exploring the overall composition and dynamics of microbial communities associated with submerged plants, this research seeks to deepen our understanding of plant-microbe interactions in aquatic environments. The microbial screening helped to identify the diverse microbes associated with ACC deaminase activity in submerged plants and amplicon sequencing analysis paved the way towards identifying the impact of the location in shaping the microbiome and the diversity associated with endophytic and epiphytic microbes. Co-occurrence network analysis further highlighted the intricate interactions within these microbial communities. Notably, ACC deaminase activity was observed in plant-associated microbes across different locations, with distinct variations between epiphytic and endophytic populations as identified through co-occurrence network analysis.},
}
@article {pmid39769081,
year = {2024},
author = {Li, Y and Fan, H and Li, B and Liu, X},
title = {Environmental Impact of Xenobiotic Aromatic Compounds and Their Biodegradation Potential in Comamonas testosteroni.},
journal = {International journal of molecular sciences},
volume = {25},
number = {24},
pages = {},
pmid = {39769081},
issn = {1422-0067},
support = {30922010305//Fundamental Research Funds for the Central Universities/ ; 1225011021289//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Biodegradation, Environmental ; *Xenobiotics/metabolism ; *Comamonas testosteroni/metabolism/genetics ; Hydrocarbons, Aromatic/metabolism ; Environmental Pollutants/metabolism ; Biofilms/drug effects/growth &amp; development ; Microbiota ; },
abstract = {Xenobiotic aromatic compounds are the raw materials of necessities in modern life, such as plastics, pesticides, and antibiotics. To meet the global requirements, their production and consumption have continually increased, and thus, the vast amount of waste generated results in prominent environmental pollution. Fortunately, some microorganisms (e.g., Comamonas spp.) can specially use these pollutants as substrates for growth, allowing for the development of bioremediation technology to achieve sustainable development goals. Here, we describe common xenobiotic aromatic compounds used in our daily life, discuss their impact on the environment, and review their biodegradation strategies by Comamonas testosteroni, as an example. Finally, we argue that microbiome engineering opens up the avenue to future biofilm-based biodegradation technology to improve aromatic compound bioremediation.},
}
@article {pmid39769067,
year = {2024},
author = {Wang, Q and Wang, BY and Williams, S and Xie, H},
title = {Diversity and Characteristics of the Oral Microbiome Associated with Self-Reported Ancestral/Ethnic Groups.},
journal = {International journal of molecular sciences},
volume = {25},
number = {24},
pages = {},
pmid = {39769067},
issn = {1422-0067},
support = {U54MD007586; R16GM149359; UG3HG013248; 1OT2OD032581/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/genetics ; Male ; Female ; Adult ; Mouth/microbiology ; Dental Plaque/microbiology ; Black or African American/genetics ; Middle Aged ; White People/genetics ; Self Report ; Periodontitis/microbiology/genetics ; Hispanic or Latino/genetics ; Ethnicity/genetics ; Bacteria/genetics/classification ; Biofilms/growth &amp; development ; Gingivitis/microbiology/genetics ; RNA, Ribosomal, 16S/genetics ; White ; },
abstract = {Periodontitis disproportionately affects genetic ancestral/ethnic groups. To characterize the oral microbiome from different genetic ancestral/ethnic groups, we collected 161 dental plaque samples from self-identified African Americans (AAs), Caucasian Americans (CAs), and Hispanic Americans (HAs) with clinical gingival health or biofilm-induced gingivitis on an intact periodontium. DNA was extracted from these samples, and then DNA libraries were prepared and sequenced using an Illumina NovaSeq high-throughput sequencer. We found significant differences in the diversity and abundance of microbial taxa among dental plaque samples of the AA, CA, and HA groups. We also identified unique microbial species in a self-reported ancestral/ethnic group. Moreover, we revealed variations in functional potentials of the oral microbiome among the three ancestral/ethnic groups, with greater diversity and abundance of antibiotic-resistant genes in the oral microbiome and significantly more genes involved in the modification of glycoconjugates and oligo- and polysaccharides in AAs than in CAs and HAs. Our observations suggest that the variations in the oral microbiome associated with ancestral/ethnic backgrounds may directly relate to their virulence potential including their abilities to induce host immune responses and to resist antibiotic treatment. These finding can be a steppingstone for developing precision medicine and personalized periodontal prevention/treatment and for reducing oral health disparities.},
}
@article {pmid39768848,
year = {2024},
author = {Jovandaric, MZ and Jovanović, K and Raus, M and Babic, S and Igic, T and Kotlica, B and Milicevic, S},
title = {The Significance of Plant Nutrition in the Creation of the Intestinal Microbiota-Prevention of Chronic Diseases: A Narrative Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {60},
number = {12},
pages = {},
pmid = {39768848},
issn = {1648-9144},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Chronic Disease/prevention &amp; control ; Dysbiosis/prevention &amp; control ; Dietary Fiber/administration &amp; dosage ; Diet, Vegetarian ; },
abstract = {Dysbiosis of the gastrointestinal tract is the most common cause of disease in childhood and adulthood. The formation of the intestinal microbiome begins in utero, and composition modification during life depends mainly on various genetic, nutritional, and environmental factors. The main cause of intestinal dysbiosis is improper nutrition due to a short period of breastfeeding, insufficient intake of fresh fruits and vegetables, and/or consumption of a large amount of processed food. The benefits of a diet based on grains, legumes, fruits, and vegetables are reflected in reducing the risk of cancer, cardiovascular diseases, myocardial infarction, stroke, rheumatoid arthritis, high blood pressure, asthma, allergies, and kidney stones. Anaerobic fermentation of fibers produces short-chain fatty acids (SCFA) that have an anti-inflammatory role and great importance in shaping the intestinal microbiota. Factors associated with high fiber in a plant-based diet promote increased insulin sensitivity. Insulin and insulin-like growth factor 1 (IGF-I) act as promoters of most normal and pre-neoplastic tissues. Conclusion: A plant-based diet high in fiber prevents disease by creating metabolites in the gut that reduce oxidative stress.},
}
@article {pmid39768409,
year = {2024},
author = {Shalmon, G and Ibrahim, R and Israel-Elgali, I and Grad, M and Shlayem, R and Shapira, G and Shomron, N and Youngster, I and Scheinowitz, M},
title = {Differential Gut Microbiome Profiles in Long-Distance Endurance Cyclists and Runners.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
pmid = {39768409},
issn = {2075-1729},
abstract = {We recently have shown that the gut microbiota composition in female and male runners positively correlates with sports, and female runners show similar gut microbiome diversity to male runners. However, gut microbiota composition has not yet been fully investigated in other endurance athletes, such as cyclists. Therefore, in the current study, we investigated the gut microbiome profiles in competitive, non-professional female and male cyclists compared to what we have shown in runners. We aim to understand (1) whether the gut microbiome signature is sport-specific; (2) whether there is a microbiome difference between female and male cyclists and runners; and (3) whether the gut bacteria expressed in cyclists and runners correlates with exercise performance. Our study included 58 subjects: 18 cyclists (9 males), 22 runners (13 males), and 18 control subjects (9 males). Fecal samples were obtained and subjected to taxonomic analysis to assess the relative abundances of species across subjects based on 16S rRNA sequencing results. Both alpha and beta diversity of the bacterial communities were evaluated to identify compositional variations between the groups. Each participant completed a maximal oxygen consumption test and a time-to-exhaustion test at 85% of the measured VO2max. Cyclists performed the test on an SRM ergometer, while runners used a motorized treadmill. Blood lactate levels were measured at 5 min intervals throughout the time-to-exhaustion trials. Alpha diversity demonstrated a significant difference (p-adj < 0.001) between cyclists and runners. Male cyclists showed significantly lower alpha diversity than runners (p-adj < 0.001). The taxonomic analysis of gut microbiota composition between cyclists, runners, and controls showed a lower or higher abundance of fifteen different bacteria. In cyclists, there was a significant positive correlation between six bacteria, and in runners, there was a significant positive correlation between eight bacteria, with weekly training volume, time-to-exhaustion, VO2max, and blood lactate levels. This study suggests potential sport-specific characteristics in long-distance cyclists' and runners' gut microbiome signatures. These findings emphasize the differences in gut microbiota between cyclists and runners, probably due to the difference in physiological and biomechanical conditions related to the activity mode during each sport.},
}
@article {pmid39768402,
year = {2024},
author = {Kesim, B and Tezcan Ülger, S and Aslan, G and Üstün, Y and Avcı, AT and Küçük, M&#xd6;},
title = {Effects of Sequential Antimicrobial Phases on Root Canal Microbiome Dynamics in Two-Visit Treatment of Primary Apical Periodontitis: A Longitudinal Experimental Study.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
pmid = {39768402},
issn = {2075-1729},
support = {2022-SA.DH.BP/24//Nuh Naci Yazgan University Scientific Research Projects Department/ ; },
abstract = {BACKGROUND: Effective management of primary apical periodontitis depends on understanding the dynamic interactions within the root canal microbiome. This study aimed to investigate the effect of sequential antimicrobial phases on the root canal microbiome during a two-visit treatment approach, with a focus on calcium hydroxide medication.<br><br>METHODS: Samples were collected from three teeth across four treatment phases: initial infection (S1), after chemomechanical preparation (S2), after intracanal medication (S3), and after a final flush (S4). DNA was extracted, and the V3-V4 regions of the 16S rRNA gene were sequenced using Illumina MiSeq. Sequencing data were analyzed with QIIME 2, and differentially abundant taxa were identified using linear discriminant analysis effect size (LEfSe).<br><br>RESULTS: While microbial community composition did not differ significantly between phases, the Firmicutes/Bacteroidetes ratio decreased after the antimicrobial stages. LEfSe analysis revealed higher abundances of Lactobacillales, Arthrobacter, and Veillonella in the untreated (CMP) group. Bifidobacterium longum was relatively more abundant in the intracanal medication (ICM) phase, and Dorea formicigenerans was more abundant in the final-flush (FF) phase.<br><br>CONCLUSIONS: Although calcium hydroxide treatment did not induce statistically significant changes in overall root canal microbial composition, trends such as a reduction in the Firmicutes/Bacteroidetes ratio and a relative increase in Bifidobacterium longum numbers suggest potential ecological shifts. The observed relative increase in Bifidobacterium longum numbers may represent a hypothesis-driven observation reflecting indirect ecological effects rather than direct pH modulation. While visual patterns (e.g., PCA clustering) were observed, they lacked statistical support. Further studies with larger sample sizes are needed to validate these observations and assess the potential role of beneficial bacteria in root canal treatments.},
}
@article {pmid39768401,
year = {2024},
author = {Chung, J and Lee, JC and Oh, H and Kim, Y and Lim, S and Lee, C and Shim, YG and Bang, EC and Baek, JH},
title = {Gut Microbiota Regulates the Homeostasis of Dendritic Epidermal T Cells.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
pmid = {39768401},
issn = {2075-1729},
support = {2021R111A3059820//National Research Foundation of Korea (Ministry of Education)/ ; },
abstract = {Dendritic epidermal T cells (DETCs) are a γδ T cell subset residing in the skin epidermis. Although they have been known for decades, the fate of DETCs has largely remained enigmatic. Recent studies have highlighted the relationship between the gut microbiome and γδ T cells in various epithelial and non-epithelial tissues, such as the small intestine, lung, liver, gingiva, and testis. While the skin microbiota has been shown to impact skin γδ T cells, a direct relationship between the gut microbiota and DETCs remains unexplored. In this study, we investigated whether DETCs are regulated by the gut microbiota in the steady-state skin epidermis. We examined the occurrence of DETCs in Balb/c mice, which have a skin epidermis barely populated with DETCs, compared to C57BL/6 mice, under different housing conditions. Our findings reveal that local skin inflammation markedly increases DETC numbers in the ear epidermis of Balb/c mice and that DETCs are activated by environmental factors. Furthermore, an investigation of the gut microbiota under different housing conditions revealed distinct microbial compositions and functional profiles. Taken together, these results suggest a strong connection between DETCs and gut microbiota.},
}
@article {pmid39768341,
year = {2024},
author = {Maffia, A and Scotti, R and Wood, T and Muscolo, A and Lepore, A and Acocella, E and Celano, G},
title = {Transforming Agricultural and Sulfur Waste into Fertilizer: Assessing the Short-Term Effects on Microbial Biodiversity via a Metagenomic Approach.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
pmid = {39768341},
issn = {2075-1729},
support = {FARB2023//University of Salerno and the doctoral research funds of the Mediterranean University of Reggio Calabria./ ; },
abstract = {Fungi and soil bacteria are vital for organic matter decomposition and biogeochemical cycles, but excessive synthetic fertilizer use contributes to soil degradation and loss of biodiversity. Despite this, about 97% of soil microorganisms are unculturable, making them difficult to study. Metagenomics offers a solution, enabling the direct extraction of DNA from soil to uncover microbial diversity and functions. This study utilized metagenomics to analyze the rhizosphere of two-year-old Tonda di Giffoni hazelnut saplings treated with synthetic NPK, composted olive pomace, and an innovative fertilizer derived from sulfur-based agro-industrial waste stabilized with bentonite clay. Using 16S rDNA for bacteria and ITS2 for fungi, Illumina sequencing provided insights into microbial responses to different fertilizer treatments. The results highlighted a significant increase in the abundance of beneficial microorganisms such as Thiobacillus, Pseudoxanthomonas, and Thermomyces, especially when organic materials were included. Additionally, microbial biodiversity improved with organic inputs, as shown by increased species richness (Chao1) and diversity (Bray-Curtis) greater than 20% compared with NPK and unfertilized soils (CTR). These findings emphasize the importance of organic fertilization in enhancing soil microbial health, offering a sustainable approach to improving soil quality and hazelnut productivity.},
}
@article {pmid39768299,
year = {2024},
author = {Brahmbhatt, Y and Alqaderi, H and Chinipardaz, Z},
title = {Association Between Severe Periodontitis and Cognitive Decline in Older Adults.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
pmid = {39768299},
issn = {2075-1729},
abstract = {(1) Background: Periodontal disease, a progressive inflammatory condition, disrupts the oral microbiome and releases inflammatory cytokines, leading to systemic issues, including cognitive decline. This study investigates the association between severe periodontitis and cognitive decline, exploring the role of alkaline phosphatase (ALP), an enzyme linked to systemic inflammation, as an effect modifier. (2) Methods: We analyzed cross-sectional data from the 2013-2014 National Health and Nutrition Examination Survey (NHANES). Severe periodontitis was defined using the Centers for Disease Control and Prevention (CDC) and the American Academy of Pediatrics (AAP) case definition. A weighted multivariable logistic regression model assessed the association between severe periodontitis and cognitive decline. An interaction term examined ALP's role as an effect modifier. (3) Results: This study included 1265 participants aged 65 and older. After adjusting for confounders, each one-point increase in cognitive function score was associated with a 2% decrease in the odds of severe periodontitis (OR = 0.98; 95% CI = 0.97-0.99; p = 0.008). ALP was a significant effect modifier in the relationship between severe periodontitis and cognitive decline. (4) Conclusions: This study, using a representative U.S. adult population aged 65 and over, suggests that lower cognitive performance correlates with higher likelihood of severe periodontitis. ALP enhances the association between severe periodontitis and cognitive decline.},
}
@article {pmid39768284,
year = {2024},
author = {Mohamed Rasheed, ZB and Sheng, CW and Norfitriah, E and Nasruddin, NS and Yazid, F},
title = {Oral Microbiome Dynamics in Treated Childhood Caries: A Comparative Study.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
pmid = {39768284},
issn = {2075-1729},
support = {DD-2020-006//Faculty of Dentistry Research Incentive Grant/ ; },
abstract = {BACKGROUND: Dental caries is a multifactorial disease that results from interactions of susceptible host, cariogenic microorganisms, and fermentable carbohydrate sources. Our study explored oral microbiome shifts in children before and after dental treatment.<br><br>METHODS: Initial saliva samples were collected from caries free, moderate caries, and severe caries children based on the decayed, missing, and filled teeth index (DMFT/dmft) index. After three months of dental treatment, second saliva samples were gathered from the moderate and severe caries groups. The microbiota was analyzed by 16S rRNA gene-based high-throughput sequencing.<br><br>RESULTS: Most children with caries were between seven and eight years of age (40%), from middle-income group families (61%), highly educated parents (18% secondary level and 75% tertiary level) with good oral hygiene practices. There was a significant increase in alpha-diversity post-dental intervention. Firmicutes, Bacteroidota, and Proteobacteria were abundant across all samples. Post-treatment, Actinobacteria, and Firmicutes significantly decreased (p < 0.05) while Fusobacteria, Proteobacteria, Spirochaetota, and Synergistota significantly increased (p < 0.05). At genus level, a decreased trend was seen in Streptococcus, Prevotella_7, and Rothia and an increased trend was seen in Fusobacterium, Neisseria, Haemophilus, and Leptotrichia, but was not statistically significant.<br><br>CONCLUSIONS: This study on Malaysian children highlights that dental caries are influenced by factors like age, socioeconomic status, and diet, with oral microbiome diversity increasing post-treatment, though some harmful bacteria persist, indicating a need for targeted oral health education and further research on probiotics' role in caries prevention.},
}
@article {pmid39767777,
year = {2024},
author = {Yu, X and Yu, Z and Chen, X and Liu, M and Yang, F and Cheung, KCP},
title = {Research Progress on the Relationship Between Artificial Sweeteners and Breast Cancer.},
journal = {Biomedicines},
volume = {12},
number = {12},
pages = {},
pmid = {39767777},
issn = {2227-9059},
support = {12101023//the General Research Fund (GRF) under Grant 160/ ; F-161 HKBU201/22, PROCORE//the France/Hong Kong Joint Research Scheme under Grant/ ; AY2020/21//the Research Committee's Startup Grant (Tier 1) for the Academic 162 Year 2020/21 with Grant/ ; },
abstract = {Artificial sweeteners, as low-calorie sugar substitutes, have attracted much attention in recent years, especially in terms of their potential health effects. Although they add almost no calories, studies have shown that artificial sweeteners may affect metabolism by stimulating insulin secretion and changing the intestinal microbiota, increasing the risk of metabolic syndrome and type 2 diabetes. Breast cancer, as the most common cancer in the world, is related to multiple factors such as genetics and hormone levels. The results of studies on artificial sweeteners and breast cancer risk are conflicting, with some showing a positive correlation between the two and others failing to confirm it. Differences in study design, participant characteristics, and the types of sweeteners have led to this ambiguity. Although some studies have focused on mechanisms such as hormone disorders, insulin response, and changes in the intestinal microbiota, further exploration is needed to establish a causal relationship. Our review aims to comprehensively analyze the potential association between artificial sweeteners and breast cancer and its mechanisms, as well as encourage future studies to reveal its long-term health effects.},
}
@article {pmid39767699,
year = {2024},
author = {Medina, CK and Aykut, B},
title = {Gut Microbial Dysbiosis and Implications in Solid Organ Transplantation.},
journal = {Biomedicines},
volume = {12},
number = {12},
pages = {},
pmid = {39767699},
issn = {2227-9059},
abstract = {The gut microbiome has been shown to play a significant role in solid organ transplantation, potentially influencing graft function and patient outcomes. Dysbiosis, characterized by reduced microbial diversity and an increase in pathogenic taxa, has been linked to higher incidences of allograft rejection, graft dysfunction, and post-transplant mortality. Several studies suggest that the gut microbiome might be able to serve as both a biomarker and a therapeutic target, potentially guiding personalized immunosuppressive therapies and other interventions to improve outcomes after solid organ transplantation. As summarized in this review, clinical studies have shown that specific microbial shifts correlate with adverse outcomes, including acute rejection and chronic allograft dysfunction. As research surrounding the relationship between the gut microbiome and solid organ transplant progresses, the integration of microbial analysis into clinical practice has the potential to revolutionize post-transplant care, offering new avenues to improve graft survival and patient quality of life. This review aims to provide a comprehensive overview of the relationship between gut microbial dysbiosis and transplantation outcomes, emphasizing the impact on kidney, liver, lung, and heart transplant recipients.},
}
@article {pmid39767682,
year = {2024},
author = {Farhadi Rad, H and Tahmasebi, H and Javani, S and Hemati, M and Zakerhamidi, D and Hosseini, M and Alibabaei, F and Banihashemian, SZ and Oksenych, V and Eslami, M},
title = {Microbiota and Cytokine Modulation: Innovations in Enhancing Anticancer Immunity and Personalized Cancer Therapies.},
journal = {Biomedicines},
volume = {12},
number = {12},
pages = {},
pmid = {39767682},
issn = {2227-9059},
abstract = {The gut microbiota plays a crucial role in modulating anticancer immunity, significantly impacting the effectiveness of various cancer therapies, including immunotherapy, chemotherapy, and radiotherapy. Its impact on the development of cancer is complex; certain bacteria, like Fusobacterium nucleatum and Bacteroides fragilis, can stimulate the growth of tumors by causing immunological evasion and inflammation, while advantageous strains, like Faecalibaculum rodentium, have the ability to suppress tumors by modifying immune responses. Cytokine activity and immune system regulation are intimately related. Cytokines including TGF-β, IL-6, and IL-10 promote tumor development by inhibiting efficient immune surveillance. The gut microbiome exhibits a delicate balance between pro- and anti-tumorigenic factors, as evidenced by the enhancement of anti-tumor immunity by cytokines such as IL-12 and IFN-γ. Improved immunotherapy responses are linked to a diverse microbiota, which is correlated with higher tumor infiltration and cytotoxic T-cell activation. Because microbial metabolites, especially short-chain fatty acids, affect cytokine expression and immune cell activation inside the tumor microenvironment, this link highlights the need to maintain microbial balance for optimal treatment effects. Additionally, through stimulating T-cell activation, bacteria like Lactobacillus rhamnosus and Bifidobacterium bifidum increase cytokine production and improve the efficacy of immune checkpoint inhibitors (ICIs). An option for overcoming ICI resistance is fecal microbiota transplantation (FMT), since research suggests that it improves melanoma outcomes by increasing CD8+ T-cell activation. This complex interaction provides an opportunity for novel cancer therapies by highlighting the possibility of microbiome modification as a therapeutic approach in personalized oncology approaches.},
}
@article {pmid39767664,
year = {2024},
author = {Santilli, A and Han, Y and Yan, H and Sangwan, N and Cresci, GAM},
title = {The Gut-Lung Axis During Ethanol Exposure and a Pseudomonas aeruginosa Bacterial Challenge.},
journal = {Biomedicines},
volume = {12},
number = {12},
pages = {},
pmid = {39767664},
issn = {2227-9059},
support = {R01AA028043/NH/NIH HHS/United States ; },
abstract = {Background: Susceptibility to and severity of pulmonary infections increase with ethanol consumption. We have previously shown that ethanol-induced changes in the gut microbiome disrupt gut homeostasis, allowing for the translocation of proinflammatory mediators into the circulation and eliciting an immune response in the lung. Additionally, targeting the gut with butyrate supplementation not only rescues ethanol-induced disruptions to gut health but also reverses aspects of immune dysregulation in the lungs. Here, we assessed the impact of this connection on a subsequent infectious challenge. Methods: To assess if ethanol-induced alterations to the gut microbiome could also impact the host response to a pulmonary infectious challenge, we employed a chronic-binge ethanol-feeding mouse model followed by a nasal instillation of Pseudomonas aeruginosa. Results: In addition to altering gut microbiome composition and metabolism, ethanol consumption also disrupted the local immune response as demonstrated by suppressed cecal SIgA levels, a decreased presence of CD3[+]CD8a[+] cytotoxic T cells in the proximal colon mucosa, and depleted CD3[+]CD8a[+] T cells and CD11c[+]CD8a[+] dendritic cells in the mesenteric lymph nodes. Circulatory Ly6G[+]CD11b[+] neutrophils increased, indicating a systemic change in immune-cell presence with ethanol exposure. Ethanol exposure increased CD11c[+]CD64[+] macrophages and Ly6G[+]CD11b[+] neutrophils in the lungs, with neutrophil populations being further exacerbated during a bacterial challenge with Pseudomonas aeruginosa. Lipocalin 2, a marker of oxidative stress, was also elevated with ethanol consumption, though not with infection. Conclusions: These data suggest that ethanol-induced changes in the gut microbiome and immune environment are linked to dysfunctional immune responses in the intestine, blood, and the lungs, compromising the pulmonary immune response during an infectious challenge in mice.},
}
@article {pmid39767626,
year = {2024},
author = {Dulai, AS and Min, M and Sivamani, RK},
title = {The Gut Microbiome's Influence on Incretins and Impact on Blood Glucose Control.},
journal = {Biomedicines},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/biomedicines12122719},
pmid = {39767626},
issn = {2227-9059},
abstract = {Obesity and type 2 diabetes mellitus (T2DM) have been increasing in prevalence, causing complications and strain on our healthcare systems. Notably, gut dysbiosis is implicated as a contributing factor in obesity, T2DM, and chronic inflammatory diseases. A pharmacology exists which modulates the incretin pathway to improve glucose control; this has proven to be beneficial in patients with obesity and T2DM. However, it is unclear how the gut microbiome may regulate insulin resistance, glucose control, and metabolic health. In this narrative review, we aim to discuss how the gut microbiome can modulate incretin pathways and related mechanisms to control glucose. To investigate this, Google Scholar and PubMed databases were searched using key terms and phrases related to the microbiome and its effects on insulin and glucose control. Emerging research has shown that several bacteria, such as Akkermansia and MN-Gup, have GLP-1-agonistic properties capable of reducing hyperglycemia. While more human research is needed to prove clinical benefit and identify long-term implications on health, the usage of pre-, pro-, and postbiotics has the potential to improve glucose control.},
}
@article {pmid39767593,
year = {2024},
author = {Anaclerio, F and Minelli, M and Antonucci, I and Gatta, V and Stuppia, L},
title = {Microbiota and Autism: A Review on Oral and Gut Microbiome Analysis Through 16S rRNA Sequencing.},
journal = {Biomedicines},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/biomedicines12122686},
pmid = {39767593},
issn = {2227-9059},
abstract = {Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with multifactorial etiologies, including genetic, environmental, and microbiological factors. In recent years, increasing attention has been given to the role of the gut microbiota in ASD. Emerging evidence suggests that gut microbiota dysbiosis may influence the central nervous system through the gut-brain axis, potentially impacting behavior and neurodevelopment. The use of 16S rRNA gene sequencing has become a pivotal tool in profiling the microbial communities associated with ASD, offering valuable insights into bacterial diversity, composition, and potential functional roles. This review aims to provide a comprehensive analysis of current findings on the relationship between the gut and oral microbiota with ASD, and a particular focus on studies utilizing 16S rRNA sequencing. We will explore how gut microbiome alterations may contribute to ASD pathophysiology, discuss the limitations of existing research, and propose future directions for the integration of microbiome analysis in ASD diagnostics and treatment strategies. These findings underscore the potential role of microbiota in modulating ASD symptoms. The data suggest that specific bacterial taxa are consistently altered in ASD, which may have implications for understanding the gut-brain axis and its influence on neurodevelopment.},
}
@article {pmid39767560,
year = {2024},
author = {Li, L and Meng, Z and Huang, Y and Xu, L and Chen, Q and Qiao, D and Yue, X},
title = {Chronic Sleep Deprivation Causes Anxiety, Depression and Impaired Gut Barrier in Female Mice-Correlation Analysis from Fecal Microbiome and Metabolome.},
journal = {Biomedicines},
volume = {12},
number = {12},
pages = {},
pmid = {39767560},
issn = {2227-9059},
support = {2023A1515011601//Natural Science Foundation of Guangdong Province/ ; },
abstract = {BACKGROUND: Chronic sleep deprivation (CSD) plays an important role in mood disorders. However, the changes in the gut microbiota and metabolites associated with CSD-induced anxiety/depression-like behavior in female mice have not been determined. Due to the influence of endogenous hormone levels, females are more susceptible than males to negative emotions caused by sleep deprivation. Here, we aim to investigate how CSD changes the gut microbiota and behavior and uncover the relationship between CSD and gut microbiota and its metabolites in female mice.<br><br>METHODS: We used a 48-day sleep deprivation (SD) model using the modified multiple platform method (MMPM) to induce anxiety/depression-like behavior in female C57BL/6J mice and verified our results using the open field test, elevated plus maze, novel object recognition test, forced swim test, and tail suspension test. We collected fecal samples of mice for 16S rDNA sequencing and untargeted metabolomic analysis and colons for histopathological observation. We used Spearmen analysis to find the correlations between differential bacterial taxa, fecal metabolites, and behaviors.<br><br>RESULTS: Our study demonstrates that CSD induced anxiety/depressive-like behaviors in female mice. The results of 16S rDNA sequencing suggested that the relative abundance of the harmful bacteria g_ Rothia, g_ Streptococcus, g_ Pantoea, and g_ Klebsiella were significantly increased, while the beneficial bacteria g_ Rikenella, g_ Eubacterium]-xylanophilum-group, and g_ Eisenbergiella were significantly decreased after SD. Glycerophospholipid metabolism and glutathione metabolism were identified as key pathways in the fecal metabolism related to oxidative stress and inflammatory states of the intestine. Histological observation showed hyperplasia of epithelial cells, a decrease in goblet cells, and glandular atrophy of the colon in SD mice. There were correlations between some of the differential bacterial taxa, fecal metabolites, and behaviors.<br><br>CONCLUSION: In summary, we found that CSD induced anxiety/depression-like behavior, caused gut microbiota dysbiosis, altered fecal metabolism, and damaged the colon barrier in female mice.},
}
@article {pmid39767090,
year = {2024},
author = {Lamm, KW and Idun, A and Lu, P},
title = {Critical Issues Faced by Industries Associated with Food Science and Technology: A Delphi Analysis.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {24},
pages = {},
pmid = {39767090},
issn = {2304-8158},
abstract = {As the foundation of human health, the food system is arguably a cornerstone of society. However, despite the criticality of a safe and productive food value chain there are numerous critical issues faced by industries associated with food science and technology. Using a three round Delphi process, this study identified the most critical issues faced by these industries. Based on input from expert panelists representing industry, policy makers, and academics, a total of 120 critical issues were identified in the first round. Through a consensus-building process in two subsequent rounds, 38 issues were retained. The retained issues were then analyzed using the constant comparative method to identify themes. A total of eight themes emerged from the analysis, including the following (alphabetically): (1) education, training, and workforce development; (2) emerging technologies in food sciences; (3) food safety and public health; (4) fresh produce and raw food operations; (5) microbiome and pathogens; (6) product innovation and development; (7) quality assurance and systems management; and (8) sustainability and climate resilience. These results provide a robust foundation to help guide and inform strategic priorities and actions within the food industry.},
}
@article {pmid39767077,
year = {2024},
author = {Nelios, G and Prapa, I and Mitropoulou, G and Kompoura, V and Balafas, E and Kostomitsopoulos, N and Yanni, AE and Kourkoutas, Y},
title = {Assessment of Immobilized Lacticaseibacillus rhamnosus OLXAL-1 Cells on Oat Flakes for Functional Regulation of the Intestinal Microbiome in a Type-1 Diabetic Animal Model.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {24},
pages = {},
pmid = {39767077},
issn = {2304-8158},
support = {Project Number: HFRI-FM17-2496, acronym: iFUNcultures//Hellenic Foundation for Research and Innovation (H.F.R.I.)/ ; Project Number: HFRI-FM17-2496, acronym: iFUNcultures//Hellenic Foundation for Research and Innovation (H.F.R.I.)/ ; },
abstract = {The aim of this study was to examine the effect of free or immobilized Lacticaseibacillus rhamnosus OLXAL-1 cells on oat flakes on the gut microbiota and metabolic and inflammatory markers in a streptozotocin (STZ)-induced Type-1 Diabetes Mellitus (T1DM) animal model. Forty-eight male Wistar rats were assigned into eight groups (n = 6): healthy or diabetic animals that received either a control diet (CD and DCD), an oat-supplemented diet (OD and DOD), a diet supplemented with free L. rhamnosus OLXAL-1 cells (CFC and DFC), or a diet supplemented with immobilized L. rhamnosus OLXAL-1 cells on oat flakes (CIC and DIC). Neither L. rhamnosus OLXAL-1 nor oat supplementation led to any significant positive effects on body weight, insulin levels, plasma glucose concentrations, or lipid profile parameters. L. rhamnosus OLXAL-1 administration resulted in a rise in the relative abundances of Lactobacillus and Bifidobacterium, as well as increased levels of lactic, acetic, and butyric acids in the feces of the diabetic animals. Additionally, supplementation with oat flakes significantly reduced the microbial populations of E. coli, Enterobacteriaceae, coliforms, staphylococci, and enterococci and lowered IL-1β levels in the blood plasma of diabetic animals. These findings suggested that probiotic food-based strategies could have a potential therapeutic role in managing dysbiosis and inflammation associated with T1DM.},
}
@article {pmid39766866,
year = {2024},
author = {Borrego-Ruiz, A and Borrego, JJ},
title = {Epigenetic Mechanisms in Aging: Extrinsic Factors and Gut Microbiome.},
journal = {Genes},
volume = {15},
number = {12},
pages = {},
pmid = {39766866},
issn = {2073-4425},
mesh = {Humans ; *Epigenesis, Genetic ; *Gastrointestinal Microbiome/genetics ; *Aging/genetics ; DNA Methylation ; Animals ; },
abstract = {BACKGROUND/OBJECTIVES: Aging is a natural physiological process involving biological and genetic pathways. Growing evidence suggests that alterations in the epigenome during aging result in transcriptional changes, which play a significant role in the onset of age-related diseases, including cancer, cardiovascular disease, diabetes, and neurodegenerative disorders. For this reason, the epigenetic alterations in aging and age-related diseases have been reviewed, and the major extrinsic factors influencing these epigenetic alterations have been identified. In addition, the role of the gut microbiome and its metabolites as epigenetic modifiers has been addressed.<br><br>RESULTS: Long-term exposure to extrinsic factors such as air pollution, diet, drug use, environmental chemicals, microbial infections, physical activity, radiation, and stress provoke epigenetic changes in the host through several endocrine and immune pathways, potentially accelerating the aging process. Diverse studies have reported that the gut microbiome plays a critical role in regulating brain cell functions through DNA methylation and histone modifications. The interaction between genes and the gut microbiome serves as a source of adaptive variation, contributing to phenotypic plasticity. However, the molecular mechanisms and signaling pathways driving this process are still not fully understood.<br><br>CONCLUSIONS: Extrinsic factors are potential inducers of epigenetic alterations, which may have important implications for longevity. The gut microbiome serves as an epigenetic effector influencing host gene expression through histone and DNA modifications, while bidirectional interactions with the host and the underexplored roles of microbial metabolites and non-bacterial microorganisms such as fungi and viruses highlight the need for further research.},
}
@article {pmid39766862,
year = {2024},
author = {Lin, H and Perkins, NJ and Nkoy, F and Stanford, JB and Schliep, KC and Peddada, SD},
title = {A Study of Short-Chain Fatty Acids During the Canalicular and Early Saccular Phases of Fetal Lung Development and Childhood Asthma.},
journal = {Genes},
volume = {15},
number = {12},
pages = {},
pmid = {39766862},
issn = {2073-4425},
support = {This study was supported by the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Early Career Award granted to HL. The research of NP and SDP was also supported in part by the Division of Population Health Research o//Intramural Programs at NICHD and NIEHS./ ; },
mesh = {*Asthma/blood ; Humans ; Female ; Pregnancy ; *Fatty Acids, Volatile/metabolism/blood ; *Lung/metabolism/embryology ; Adult ; Child ; Fetal Development ; Male ; Acetates/blood/metabolism ; },
abstract = {BACKGROUND: Emerging literature indicates that the microbiome and its byproducts, such as short-chain fatty acids (SCFAs), play an important role in childhood diseases such as allergies and asthma. Specifically, there is evidence suggesting that SCFAs play a critical role in fetal immunoprogramming during the late saccular phase of fetal lung development. An increase in acetate during the late saccular phase is known to play a critical role in inhibiting histone deacetylases (HDACs), resulting in a cascade of events, including Treg immune regulation, involved in fetal immunoprogramming, and reduction in the asthma phenotype. However, it is not known whether changes in SCFA levels, especially acetate, occurred during the canalicular or early saccular phase among pregnant women whose children did not develop asthma.<br><br>METHODS: In this research, we investigated this question using plasma samples obtained from mothers during the 20th and 28th weeks of pregnancy. Mothers whose children developed asthma were categorized as cases, while those whose children did not were categorized as controls. The specimens were assayed for a panel of SCFAs consisting of acetate, propionate, butyrate, valerate, isobutyrate, and isovalerate.<br><br>RESULTS: The resulting data indicated no significant differences between the cases and controls, either at week 20 or week 28, in any of the SCFAs measured, despite the vascularization during these phases.<br><br>CONCLUSIONS: We did not find differences in measured SCFAs at week 20 or at week 28. A larger prospective study covering multiple time points is necessary to confirm the findings of this preliminary study. Such a study, together with the published literature regarding later time points, may help discover critical windows during pregnancy when simple manipulation of diet will result in healthier outcomes for infants.},
}
@article {pmid39766628,
year = {2024},
author = {Ma, Q and Xiang, X and Ma, Y and Li, G and Liu, X and Jia, B and Yang, W and Yin, H and Zhang, B},
title = {Identification and Bioactivity Analysis of a Novel Bacillus Species, B. maqinnsis sp. nov. Bos-x6-28, Isolated from Feces of the Yak (Bos grunniens).},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
pmid = {39766628},
issn = {2079-6382},
support = {31960642//National Natural Science Foundation of China/ ; 2023-ZJ-939M//Natural Science Foundation of Qinghai province, China/ ; },
abstract = {Background: The identification of novel bacterial species from the intestines of yaks residing on the Qinghai-Tibet Plateau is pivotal in advancing our understanding of host-microbiome interactions and represents a promising avenue for microbial drug discovery. Methods: In this study, we conducted a polyphasic taxonomic analysis and bioactive assays on a Bacillus strain, designated Bos-x6-28, isolated from yak feces. Results: The findings revealed that strain Bos-x6-28 shares a high 16S rRNA gene sequence similarity (98.91%) with B. xiamenensis HYC-10[T] and B. zhangzhouensis DW5-4[T], suggesting close phylogenetic affinity. Physiological and biochemical characterizations demonstrated that Bos-x6-28 could utilize nine carbon sources, including D-galactose, inositol, and fructose, alongside nine nitrogen sources, such as threonine, alanine, and proline. Analysis of biochemical markers indicated that Bos-x6-28's cell wall hydrolysates contained mannose, glucose, and meso-2,6-diaminopimelic acid, while menaquinone-7 (MK-7), phosphatidylethanolamine (PE), phosphatidylcholine (PC), and phosphatidylglycerol (DPG) were found in the cell membrane. The primary cellular fatty acids included C16:0 (28.00%), cyclo-C17:0 (19.97%), C14:0 (8.75%), cyclo-C19:0 (8.52%), iso-C15:0 (5.49%), anteiso-C15:0 (4.61%), and C12:0 (3.15%). Whole-genome sequencing identified a genome size of 3.33 Mbp with 3353 coding genes. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses confirmed Bos-x6-28 as a novel species, hereby named B. maqinnsis Bos-x6-28 (MCCC 1K09379). Further genomic analysis unveiled biosynthetic gene clusters encoding bioactive natural compounds, including β-lactones, sactipeptides, fengycin, and lichenysin analogs. Additionally, in vitro assays demonstrated that this strain exhibits antibacterial and cytotoxic activities. Conclusions: These findings collectively indicate the novel Bacillus species B. maqinnsis Bos-x6-28 as a promising source for novel antibiotic and antitumor agents.},
}
@article {pmid39766625,
year = {2024},
author = {Domán, M and Pintér, K and Pollák, BD and Pintér, &#xc1; and Wehmann, E and Tenk, M and Magyar, T},
title = {Comparative Genome Analysis of Canine Frederiksenia canicola Isolates.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
pmid = {39766625},
issn = {2079-6382},
support = {EK&#xd6;P-2024//EK&#xd6;P-2024 University Researcher Scholarship Program of the Ministry for Culture and Innovation/ ; RRF-2.3.1-21-2022-00001//National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety/ ; },
abstract = {Background/Objectives: The One Health approach is crucial for managing and controlling the spread of antimicrobial resistance. Frederiksenia canicola is a recently identified bacterial species that seems to be a component of the oral microbiota of dogs; however, its pathogenic nature is questionable. Methods: In this study, the antibacterial susceptibility of F. canicola isolates was determined using the disk diffusion and broth microdilution methods. Genome-wide comparative analyses were performed to identify the genetic factors driving virulence and antimicrobial drug resistance (e.g., virulence factors, antimicrobial resistance genes (ARGs) and prophage-related sequences). Results: Most of the F. canicola isolates lacked virulence-associated genes. F. canicola is likely resistant to clindamycin, lincomycin and neomycin, but susceptible to penicillin, erythromycin and enrofloxacin. Antimicrobial resistance genes were not found in the F. canicola genomes, but prophage-related sequences were identified, suggesting its potential in the transfer of genes associated with drug resistance between bacteria in the oral microbiome. Conclusions: F. canicola is presumably a commensal organism with low virulence potential, as evidenced by the absence of virulence-associated genes. As F. canicola can colonize a wide range of hosts, including humans, further investigation with a greater number of isolates is needed to better understand the role of F. canicola in disease development and the spread of drug resistance.},
}
@article {pmid39766607,
year = {2024},
author = {Schwebs, T and Kieninger, AK and Podpera Tisakova, L and Oberbauer, V and Berdaguer, R and Mtshali, A and Mzobe, G and Rompalo, A and Mindel, A and Letsoalo, M and Garrett, N and Ngcapu, S and Corsini, L},
title = {Evaluation of Metronidazole Resistance of Vaginal Swab Isolates from South African Women Treated for Bacterial Vaginosis.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
pmid = {39766607},
issn = {2079-6382},
support = {INV-033691/GATES/Bill &amp; Melinda Gates Foundation/United States ; AI116759//South African Medical Research Council and National Institute of Health/ ; },
abstract = {Background/Objectives: The high recurrence rate of bacterial vaginosis (BV) after antibiotic treatment is at least partially attributed to resistant bacteria. The CAPRISA 083 (CAP083) study investigated the influence of metronidazole (MTZ) treatment on the vaginal microbiome in 56 South African women diagnosed with BV. To explore the etiology of recurrent BV in this cohort, we retrospectively analyzed vaginal swabs collected in CAP083 before and after MTZ treatment. Methods: We isolated over 1200 bacterial strains, including Gardnerella, Lactobacillus, Prevotella, and Fannyhessa, and determined the minimum inhibitory concentration (MIC) of MTZ and the resistance status according to CLSI and EUCAST guidelines. Results: At baseline, 64% (CLSI) of Gardnerella isolates were resistant to MTZ, rising to 80% after MTZ treatment by the 12-week visit. Lactobacillus species consistently exhibited resistance of 100%, while Fannyhessea vaginae maintained resistance rates of 78-91% across visits. Prevotella strains varied, showing two susceptible isolates at baseline and one resistant isolate at the 6-week visit. Susceptible and resistant Gardnerella isolates were often isolated from the same swab, and 70% (CLSI) of participants had at least one resistant Gardnerella strain already at baseline. Sensitive Gardnerella isolates were not a predictor of an MTZ-mediated reduction in Gardnerella abundance. Conclusions: Our data indicate that the 23% cure rate in CAP083 was associated with a combination of a high share of MTZ-resistant bacteria at baseline, a potentially insufficient MTZ dose regimen, and a constantly high average abundance of Gardnerella. Future research should explore novel therapeutic strategies to enhance treatment efficacy and combat antibiotic resistance.},
}
@article {pmid39766500,
year = {2024},
author = {Tran, AT and Ghanem, AS and Móré, M and Nagy, AC and Tóth, &#xc1;},
title = {Efficacy of Prophylactic Antibiotics in COPD: A Systematic Review.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
pmid = {39766500},
issn = {2079-6382},
abstract = {Background/Objectives: Chronic obstructive pulmonary disease (COPD) is a global health problem and the third leading contributor to mortality worldwide. This systematic review aims to summarize the results of previous studies tackling the question of the efficacy of long-term prophylaxis of antibiotics in COPD patients, with particular regard to exacerbation rate, time to first exacerbation, health status, airway bacterial load, inflammatory markers, cell counts in sputum samples, and potential adverse events. Results: Four studies found significant improvement in the exacerbation rate in patients receiving antibiotic intervention. One study found doxycycline to have negative effects on patients' exacerbation outcomes. Two studies recorded a reduction in total airway bacterial load using quantitative culture of sputum samples, but the prevalence of antibiotic-resistant bacteria increased in all studies that measured it. No change in inflammatory markers was observed; however, there was a decline in neutrophil cell counts and, subsequently, reductions in neutrophil elastase concentrations. Methods: PubMed and Web of Science databases were searched for English-language studies presenting data on the prophylactic use of antibiotics in COPD management. All included studies are randomized controlled trials (RCTs) and meet the inclusion criteria. Conclusions: Based on current evidence from RCTs, the prophylactic antibiotic approach utilizing macrolides is the most effective in reducing the incidence of COPD exacerbation. However, the emergence of antibiotic-resistant pathogens is notable. Whether the beneficial effects of macrolides on exacerbation are due to their antibacterial or immunomodulant properties is still inconclusive. Future studies are needed to better understand the interactions between antibiotics and the airway microbiome during COPD exacerbation.},
}
@article {pmid39766429,
year = {2024},
author = {Bortoletto, R and Garzitto, M and Piscitelli, F and Fornasaro, S and Scipioni, C and Sepulcri, O and Fabris, M and Curcio, F and Balestrieri, M and Colizzi, M},
title = {The Endocannabinoid Activity Remodulation for Psychosis Liability in Youth (EARLY) Study: An Open-Label Feasibility Trial of Ultramicronized-Palmitoylethanolamide Oral Supplementation in Clinical High-Risk State for Psychosis.},
journal = {Brain sciences},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/brainsci14121230},
pmid = {39766429},
issn = {2076-3425},
abstract = {To date, no psychotropic medication has shown to effectively halt progression to psychosis among individuals at Clinical High-Risk for psychosis (CHR), fueling the search for novel therapeutic agents. Recent evidence supports Palmitoylethanolamide (PEA) signaling as a potential psychosis biomarker, also indicating a therapeutic role for its supplementation in the treatment of psychotic disorders. Nonetheless, the effect of sustained PEA intake in CHR subjects has never been explored so far. We will assess the feasibility of enrolling 20 CHR young adults presenting with attenuated psychotic symptoms (APS) in a 12-week, open-label, investigator-initiated, proof-of-concept, single-arm trial of ultramicronized-PEA (um-PEA) 600 mg/day. Once completed the 12-week phase, participants will be proposed to enter a 24-week extension phase of the study. We will examine um-PEA ability to reduce APS and psychic distress, um-PEA safety and tolerability, and the biological basis of um-PEA effect in terms of modulation of inflammatory response, endocannabinoid (eCB) signaling, and microbiome composition. Our trial aims to address an unmet clinical need in CHR subjects, providing an initial solid basis for the development of future studies evaluating the efficacy and tolerability of PEA supplementation in this group of patients.},
}
@article {pmid39766423,
year = {2024},
author = {Menezes, AA and Shah, ZA},
title = {A Review of the Consequences of Gut Microbiota in Neurodegenerative Disorders and Aging.},
journal = {Brain sciences},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/brainsci14121224},
pmid = {39766423},
issn = {2076-3425},
support = {R01NS112642/NS/NINDS NIH HHS/United States ; },
abstract = {Age-associated alterations in the brain lead to cognitive deterioration and neurodegenerative disorders (NDDs). This review with a particular focus on Alzheimer's disease (AD), emphasizes the burgeoning significance of the gut microbiota (GMB) in neuroinflammation and its impact on the gut-brain axis (GBA), a communication conduit between the gut and the central nervous system (CNS). Changes in the gut microbiome, including diminished microbial diversity and the prevalence of pro-inflammatory bacteria, are associated with AD pathogenesis. Promising therapies, such as fecal microbiota transplantation (FMT), probiotics, and prebiotics, may restore gut health and enhance cognitive performance. Clinical data remain insufficient, necessitating further research to elucidate causes, enhance therapy, and consider individual variances. This integrative approach may yield innovative therapies aimed at the GMB to improve cognitive function and brain health in older people.},
}
@article {pmid39766350,
year = {2024},
author = {Zhao, Y and Zhu, S and Dong, Y and Xie, T and Chai, Z and Gao, X and Dai, Y and Wang, X},
title = {The Role of Gut Microbiome in Irritable Bowel Syndrome: Implications for Clinical Therapeutics.},
journal = {Biomolecules},
volume = {14},
number = {12},
pages = {},
pmid = {39766350},
issn = {2218-273X},
support = {National Natural Science Foundation of China under Grant No. 82192914//Xiumei Gao/ ; },
mesh = {*Irritable Bowel Syndrome/microbiology/metabolism/therapy ; *Gastrointestinal Microbiome ; Humans ; *Brain-Gut Axis ; Animals ; },
abstract = {Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder (FGID) characterized by chronic or recurrent gastrointestinal symptoms without organic changes, and it is also a common disorder of gut-brain interaction (DGBIs).. The symptoms of IBS not only affect the quality of life for individual patients but also place a significant burden on global healthcare systems. The lack of established and universally applicable biomarkers for IBS, along with the substantial variability in symptoms and progression, presents challenges in developing effective clinical treatments. In recent years, preclinical and clinical studies have linked the pathogenesis of IBS to alterations in the composition and function of the intestinal microbiota. Within the complex microbial community of the gut, intricate metabolic and spatial interactions occur among its members and between microbes and their hosts. Amid the multifaceted pathophysiology of IBS, the role of intestinal microenvironment factors in symptom development has become more apparent. This review aims to delve into the changes in the composition and structure of the gut microbiome in individuals with IBS. It explores how diet-mediated alterations in intestinal microbes and their byproducts play a role in regulating the pathogenesis of IBS by influencing the "brain-gut" axis, intestinal barrier function, immune responses, and more. By doing so, this review seeks to lay a theoretical foundation for advancing the development of clinical therapeutics for IBS.},
}
@article {pmid39766312,
year = {2024},
author = {Estevan-Morió, E and Ramírez-Larrota, JS and Bushi, E and Eckhard, U},
title = {Dissecting Cytophagalysin: Structural and Biochemical Studies of a Bacterial Pappalysin-Family Metallopeptidase.},
journal = {Biomolecules},
volume = {14},
number = {12},
pages = {},
pmid = {39766312},
issn = {2218-273X},
support = {RYC2020-029773-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; PID2021-128682OA-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; PRE2020-096731//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; JAEINT_22_02654//Consejo Superior de Investigaciones Cient&#xed;ficas/ ; 2021SGR00423//Government of Catalonia/ ; },
mesh = {*Metalloproteases/chemistry/metabolism/genetics ; Bacterial Proteins/chemistry/metabolism/genetics ; Catalytic Domain ; Amino Acid Sequence ; Models, Molecular ; },
abstract = {Cytophaga is a genus of Gram-negative bacteria occurring in soil and the gut microbiome. It is closely related to pathogenic Flavobacterium spp. that cause severe diseases in fish. Cytophaga strain L43-1 secretes cytophagalysin (CPL1), a 137 kDa peptidase with reported collagenolytic and gelatinolytic activity. We performed highly-confident structure prediction calculations for CPL1, which identified 11 segments and domains, including a signal peptide for secretion, a prosegment (PS) for latency, a metallopeptidase (MP)-like catalytic domain (CD), and eight immunoglobulin (Ig)-like domains (D3-D10). In addition, two short linkers were found at the D8-D9 and D9-D10 junctions, and the structure would be crosslinked by four disulfide bonds. The CPL1 CD was found closest to ulilysin from Methanosarcina acetivorans, which assigns CPL1 to the lower-pappalysin family within the metzincin clan of MPs. Based on the structure predictions, we aimed to produce constructs spanning the full-length enzyme, as well as PS+CD, PS+CD+D3, and PS+CD+D3+D4. However, we were successful only with the latter three constructs. We could activate recombinant CPL1 by PS removal employing trypsin, and found that both zymogen and mature CPL1 were active in gelatin zymography and against a fluorogenic gelatin variant. This activity was ablated in a mutant, in which the catalytic glutamate described for lower pappalyins and other metzincins was replaced by alanine, and by a broad-spectrum metal chelator. Overall, these results proved that our recombinant CPL1 is a functional active MP, thus supporting the conclusions derived from the structure predictions.},
}
@article {pmid39766175,
year = {2024},
author = {Okuyama, K and Yanamoto, S},
title = {Saliva in Balancing Oral and Systemic Health, Oral Cancer, and Beyond: A Narrative Review.},
journal = {Cancers},
volume = {16},
number = {24},
pages = {},
pmid = {39766175},
issn = {2072-6694},
abstract = {Saliva plays a multifaceted role in oral health and systemic well-being. It supports digestion, protects oral tissues, maintains a healthy oral microbiome, and facilitates wound healing. Additionally, saliva serves as a diagnostic tool that reflects systemic health and disease/therapeutic states. Furthermore, although saliva shows a protective effect against oral cancer development, once tumor formation occurs, it may be involved in tumor progression and metastasis via exosomes and microRNAs. This review discusses the essential role of saliva; its relationship with the development, progression, and metastasis of head and neck squamous cell carcinoma (HNSCC); liquid biopsy tools for early diagnosis and monitoring of HNSCC; and the potential of exosomes as therapeutic agents.},
}
@article {pmid39766170,
year = {2024},
author = {Ciernikova, S and Sevcikova, A and Novisedlakova, M and Mego, M},
title = {Insights into the Relationship Between the Gut Microbiome and Immune Checkpoint Inhibitors in Solid Tumors.},
journal = {Cancers},
volume = {16},
number = {24},
pages = {},
pmid = {39766170},
issn = {2072-6694},
support = {1/0071/24//Scientific Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic and Slovak Academy of Sciences (VEGA)/ ; 2/0069/22//Scientific Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic and Slovak Academy of Sciences (VEGA)/ ; },
abstract = {Immunotherapy with immune checkpoint inhibitors represents a revolutionary approach to the treatment of solid tumors, including malignant melanoma, lung cancer, and gastrointestinal malignancies. Anti-CTLA-4 and anti-PD-1/PDL-1 therapies provide prolonged survival for cancer patients, but their efficacy and safety are highly variable. This review focuses on the crucial role of the gut microbiome in modulating the efficacy and toxicity of immune checkpoint blockade. Studies suggest that the composition of the gut microbiome may influence the response to immunotherapy, with specific bacterial strains able to promote an anti-tumor immune response. On the other hand, dysbiosis may increase the risk of adverse effects, such as immune-mediated colitis. Interventions aimed at modulating the microbiome, including the use of probiotics, prebiotics, fecal microbial transplantation, or dietary modifications, represent promising strategies to increase treatment efficacy and reduce toxicity. The combination of immunotherapy with the microbiome-based strategy opens up new possibilities for personalized treatment. In addition, factors such as physical activity and nutritional supplementation may indirectly influence the gut ecosystem and consequently improve treatment outcomes in refractory patients, leading to enhanced patient responses and prolonged survival.},
}
@article {pmid39766077,
year = {2024},
author = {Dovrolis, N and Spathakis, M and Collins, AR and Pandey, VK and Uddin, MI and Anderson, DD and Kaminska, T and Paspaliaris, V and Kolios, G},
title = {Pan-Cancer Insights: A Study of Microbial Metabolite Receptors in Malignancy Dynamics.},
journal = {Cancers},
volume = {16},
number = {24},
pages = {},
pmid = {39766077},
issn = {2072-6694},
abstract = {BACKGROUND/OBJECTIVES: The role of the gut microbiome in cancer biology has become an increasingly prominent area of research, particularly regarding the role of microbial metabolites and their receptors (MMRs). These metabolites, through the various gut-organ axes, have been proven to influence several pathogenetic mechanisms. This study conducted a comprehensive pan-cancer analysis of MMR transcriptomic profiles across twenty-three cancer types, exploring the mechanisms through which they can influence cancer development and progression.<br><br>METHODS: Utilizing both cancer cell lines from CCLE (Cancer Cell Line Encyclopedia) and human tumor samples from TCGA (The Cancer Gene Atlas), we analyzed 107 MMRs interacting with microbial metabolites such as short-chain fatty acids, bile acids, indole derivatives, and others while studying their interactions with key known cancer genes.<br><br>RESULTS: Our results revealed that certain MMRs, such as GPR84 and serotonin receptors, are consistently upregulated in various malignancies, while others, like ADRA1A, are frequently downregulated, suggesting diverse roles in cancer pathophysiology. Furthermore, we identified significant correlations between MMR expression and cancer hallmark genes and pathways, including immune evasion, proliferation, and metastasis.<br><br>CONCLUSIONS: These findings suggest that the interactions between microbial metabolites and MMRs may serve as potential biomarkers for cancer diagnosis, prognosis, and therapy, highlighting their therapeutic potential. This study underscores the significance of the microbiota-cancer axis and provides novel insights into microbiome-based strategies for cancer treatment.},
}
@article {pmid39766032,
year = {2024},
author = {Altrawy, A and Khalifa, MM and Abdelmaksoud, A and Khaled, Y and Saleh, ZM and Sobhy, H and Abdel-Ghany, S and Alqosaibi, A and Al-Muhanna, A and Almulhim, J and El-Hashash, A and Sabit, H and Arneth, B},
title = {Metabolites in the Dance: Deciphering Gut-Microbiota-Mediated Metabolic Reprogramming of the Breast Tumor Microenvironment.},
journal = {Cancers},
volume = {16},
number = {24},
pages = {},
pmid = {39766032},
issn = {2072-6694},
abstract = {Breast cancer (BC), a major cause of death among women worldwide, has traditionally been linked to genetic and environmental factors. However, emerging research highlights the gut microbiome's significant role in shaping BC development, progression, and treatment outcomes. This review explores the intricate relationship between the gut microbiota and the breast tumor microenvironment, emphasizing how these microbes influence immune responses, inflammation, and metabolic pathways. Certain bacterial species in the gut either contribute to or hinder BC progression by producing metabolites that affect hormone metabolism, immune system pathways, and cellular signaling. An imbalance in gut bacteria, known as dysbiosis, has been associated with a heightened risk of BC, with metabolites like short-chain fatty acids (SCFAs) and enzymes such as β-glucuronidase playing key roles in this process. Additionally, the gut microbiota can impact the effectiveness of chemotherapy, as certain bacteria can degrade drugs like gemcitabine and irinotecan, leading to reduced treatment efficacy. Understanding the complex interactions between gut bacteria and BC may pave the way for innovative treatment approaches, including personalized microbiome-targeted therapies, such as probiotics and fecal microbiota transplants, offering new hope for more effective prevention, diagnosis, and treatment of BC.},
}
@article {pmid39765860,
year = {2024},
author = {Mignini, I and Galasso, L and Piccirilli, G and Calvez, V and Termite, F and Esposto, G and Borriello, R and Miele, L and Ainora, ME and Gasbarrini, A and Zocco, MA},
title = {Interplay of Oxidative Stress, Gut Microbiota, and Nicotine in Metabolic-Associated Steatotic Liver Disease (MASLD).},
journal = {Antioxidants (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/antiox13121532},
pmid = {39765860},
issn = {2076-3921},
abstract = {Oxidative stress has been described as one of the main drivers of intracellular damage and metabolic disorders leading to metabolic syndrome, a major health problem worldwide. In particular, free radicals alter lipid metabolism and promote lipid accumulation in the liver, existing in the hepatic facet of metabolic syndrome, the metabolic dysfunction-associated steatotic liver disease (MASLD). Recent literature has highlighted how nicotine, especially if associated with a high-fat diet, exerts a negative effect on the induction and progression of MASLD by upregulating inflammation and increasing oxidative stress, abdominal fat lipolysis, and hepatic lipogenesis. Moreover, considerable evidence shows the central role of intestinal dysbiosis in the pathogenesis of MASLD and the impact of nicotine-induced oxidative stress on the gut microbiome. This results in an intricate network in which oxidative stress stands at the intersection point between gut microbiome, nicotine, and MASLD. The aim of this review is to delve into the molecular mechanisms linking tobacco smoking and MASLD, focusing on nicotine-induced microbiota modifications and their impact on MASLD development.},
}
@article {pmid39765826,
year = {2024},
author = {Liu, CY and Tsai, TY and Liu, TH and Chang, TC and Chen, YW and Tsao, CW},
title = {Lactiplantibacillus plantarum 1008 Promotes Reproductive Function and Cognitive Activity in Aged Male Mice with High-Fat-Diet-Induced Obesity by Altering Metabolic Parameters and Alleviating Testicular Oxidative Damage, Inflammation and Apoptosis.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
pmid = {39765826},
issn = {2076-3921},
support = {NSTC 112-2314-B-016-030//the National Science and Technology Council of Taiwan/ ; },
abstract = {The effects of Lactiplantibacillus plantarum 1008 (LP1008) on age-related cognitive impairment and skeletal muscle atrophy have been reported previously. However, its role in obesity- and age-related hypogonadism has yet to be explored. This study investigates the therapeutic efficacy of low- and high-dose LP1008 in a high-fat-diet-fed male mouse model. Mice at 37 weeks of age were fed a standard diet (n = 8) or a 45% high-fat diet for 28 weeks, and the high-fat-diet-fed mice were divided into vehicle, low-dose and high-dose LP1008 groups (n = 8 per group) on the basis of the treatment administered for an additional 8 weeks. We found that LP1008 suppressed the increases in total cholesterol levels and liver function parameters and alleviated histological changes in the brain, ileum, gastrocnemius muscle and testes. In terms of reproductive function, LP1008 attenuated the decreases in sperm quality, sperm maturity, testosterone levels and levels of enzymes involved in testosterone biosynthesis. Furthermore, LP1008 altered impairments in spatial learning and memory and induced slight alterations in the gut microbiota. Moreover, LP1008 exerted antioxidant, anti-inflammatory and anti-apoptotic effects in aged, obese male mice. LP1008 reversed diet-induced obesity, age-related reproductive dysfunction and pathological damage by increasing testosterone levels and altering the gut microbiome through the regulation of mediators involved in oxidative stress, apoptosis and inflammation.},
}
@article {pmid39765792,
year = {2024},
author = {Liu, X and Sun, C and Zhou, Q and Zheng, X and Jiang, S and Wang, A and Han, Y and Xu, G and Liu, B},
title = {Ferulic Acid Relieves the Oxidative Stress Induced by Oxidized Fish Oil in Oriental River Prawn (Macrobrachium nipponense) with an Emphasis on Lipid Metabolism and Gut Microbiota.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
pmid = {39765792},
issn = {2076-3921},
support = {CARS-48//China Agriculture Research System of MOF and MARA/ ; CX (22)3077//the project of the Jiangsu Province Agricultural Science and Technology Independent Innovation Fund/ ; CAFS (2023TD63, 2022XT0401)//Central Public-interest Scientific Institution Basal Research Fund/ ; JATS [2023]470//Jiangsu modern agricultural industry technology system shrimp nutrition and feed innovation team/ ; },
abstract = {To investigate the potential of ferulic acid (FA) in attenuating the deleterious effects of oxidized fish oil (OF) on Macrobrachium nipponense, four experimental diets were formulated: 3% fresh fish oil (CT group, peroxide value: 2.2 mmol/kg), 3% oxidized fish oil (OF group, peroxide value: 318 mmol/kg), and 3% OF with an additional 160 and 320 mg/kg of FA (OF+FA160 group and OF+FA320 group, respectively). M. nipponense (initial weight: 0.140 ± 0.015 g) were randomly divided into four groups with six replicates (60 individuals per replicate) and reared for a period of 10 weeks. The results showed that the OF treatments significantly reduced the growth performance, the expression of antioxidant genes in the hepatopancreas, the levels of low-density lipoprotein cholesterol, and the gene expression levels of ACC, FAS, FABP10, ACBP, G6PDH, and SCD in the hepatopancreas (p < 0.05). OF supplementation significantly increased the levels of high-density lipoprotein cholesterol in hemolymph and the gene expression levels of CPT1 (p < 0.05). Addition of FA to the OF group significantly increased total bile acids (p < 0.05). In addition, it was found by Oil Red staining that the proportion of lipid droplets was significantly increased in the OF group (p < 0.05). However, the lipid droplets were alleviated by FA supplementation in the diet. OF was found to significantly reduce the diversity of intestinal microbiota by 16S rDNA sequencing and significantly increase the Firmicutes/Bacteroidetes (F/B) ratio (p < 0.05). Functional analysis of gut microbiota also showed that OF reduced lipolysis and led to fat deposition, which is related to gut microbiota. However, this study found that the composition of the gut microbiome of M. nipponense was changed by the addition of FA in the diet, including an increase in the abundance of Ruminococcaceae UCG-005 and Lachnospiraceae, a reduction in the F/B ratio, and an improvement in lipid metabolism. In conclusion, the OF induced oxidative stress, disturbed the balance of intestinal microbiota, promoted lipid accumulation, and caused disorders of lipid metabolism in M. nipponense by increasing lipid synthesis and reducing β-oxidation. However, the results of this study highlighted the potential of FA supplementation to modulate intestinal microbial composition, promote bile acid production, and activate genes related to lipid metabolism in the hepatopancreas, ultimately leading to a reduction in lipid deposition in M. nipponense.},
}
@article {pmid39765782,
year = {2024},
author = {Arendshorst, WJ and Vendrov, AE and Kumar, N and Ganesh, SK and Madamanchi, NR},
title = {Oxidative Stress in Kidney Injury and Hypertension.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
pmid = {39765782},
issn = {2076-3921},
abstract = {Hypertension (HTN) is a major contributor to kidney damage, leading to conditions such as nephrosclerosis and hypertensive nephropathy, significant causes of chronic kidney disease (CKD) and end-stage renal disease (ESRD). HTN is also a risk factor for stroke and coronary heart disease. Oxidative stress, inflammation, and activation of the renin-angiotensin-aldosterone system (RAAS) play critical roles in causing kidney injury in HTN. Genetic and environmental factors influence the susceptibility to hypertensive renal damage, with African American populations having a higher tendency due to genetic variants. Managing blood pressure (BP) effectively with treatments targeting RAAS activation, oxidative stress, and inflammation is crucial in preventing renal damage and the progression of HTN-related CKD and ESRD. Interactions between genetic and environmental factors impacting kidney function abnormalities are central to HTN development. Animal studies indicate that genetic factors significantly influence BP regulation. Anti-natriuretic mechanisms can reset the pressure-natriuresis relationship, requiring a higher BP to excrete sodium matched to intake. Activation of intrarenal angiotensin II receptors contributes to sodium retention and high BP. In HTN, the gut microbiome can affect BP by influencing energy metabolism and inflammatory pathways. Animal models, such as the spontaneously hypertensive rat and the chronic angiotensin II infusion model, mirror human essential hypertension and highlight the significance of the kidney in HTN pathogenesis. Overproduction of reactive oxygen species (ROS) plays a crucial role in the development and progression of HTN, impacting renal function and BP regulation. Targeting specific NADPH oxidase (NOX) isoforms to inhibit ROS production and enhance antioxidant mechanisms may improve renal structure and function while lowering blood pressure. Therapies like SGLT2 inhibitors and mineralocorticoid receptor antagonists have shown promise in reducing oxidative stress, inflammation, and RAAS activity, offering renal and antihypertensive protection in managing HTN and CKD. This review emphasizes the critical role of NOX in the development and progression of HTN, focusing on its impact on renal function and BP regulation. Effective BP management and targeting oxidative stress, inflammation, and RAAS activation, is crucial in preventing renal damage and the progression of HTN-related CKD and ESRD.},
}
@article {pmid39765689,
year = {2024},
author = {Vetrova, AA and Ivanova, AA and Petrikov, KV and Gavrichkova, O and Korneykova, MV and Sazonova, OI},
title = {Antibiotic Resistance as a Functional Characteristic of Urban Dust Particles' Microbial Communities.},
journal = {Biology},
volume = {13},
number = {12},
pages = {},
pmid = {39765689},
issn = {2079-7737},
support = {grant #FMRM-2022-0014//Ministry of Science and Higher Education of the Russian Federation/ ; 19-77-30012//Russian Science Foundation/ ; },
abstract = {Urban dust samples were collected in Moscow (Russia) in June 2021. The samples were collected in three functional zones of Moscow (traffic, residential, and recreational) and included air microparticles, leaf dust, and paved dust. Data on the taxonomic composition of bacterial communities were obtained for dust samples, and their functional characteristics were predicted using PICRUSt2 2.5.0 and FAPROTAX 1.8.0 software. The culturable part of the bacterial community was examined for the presence of antibiotic-resistant strains with respect to β-lactams, tetracyclines, amphenicols, and aminoglycosides. The presence of bacteria resistant to ceftazidime, cefepime, and tetracycline was detected in all dust samples. The presence of bacteria resistant to meropenem and amikacin was only observed in the dust collected from leaves in the residential and traffic zones. The overall abundance of cultured antibiotic-resistant bacteria from the total heterotrophs ranged from 0.03% to 1.88%, with the highest percentage observed in dust from the residential zone. Notably, strains resistant to all antibiotics tested were observed in the leaf dust bacterial community.},
}
@article {pmid39765681,
year = {2024},
author = {Laevens, GCS and Dolson, WC and Drapeau, MM and Telhig, S and Ruffell, SE and Rose, DM and Glick, BR and Stegelmeier, AA},
title = {The Good, the Bad, and the Fungus: Insights into the Relationship Between Plants, Fungi, and Oomycetes in Hydroponics.},
journal = {Biology},
volume = {13},
number = {12},
pages = {},
pmid = {39765681},
issn = {2079-7737},
abstract = {Hydroponic systems are examples of controlled environment agriculture (CEA) and present a promising alternative to traditional farming methods by increasing productivity, profitability, and sustainability. In hydroponic systems, crops are grown in the absence of soil and thus lack the native soil microbial community. This review focuses on fungi and oomycetes, both beneficial and pathogenic, that can colonize crops and persist in hydroponic systems. The symptomatology and mechanisms of pathogenesis for Botrytis, Colletotrichum, Fulvia, Fusarium, Phytophthora, Pythium, and Sclerotinia are explored for phytopathogenic fungi that target floral organs, leaves, roots, and vasculature of economically important hydroponic crops. Additionally, this review thoroughly explores the use of plant growth-promoting fungi (PGPF) to combat phytopathogens and increase hydroponic crop productivity; details of PGP strategies and mechanisms are discussed. The benefits of Aspergillus, Penicillium, Taloromyces, and Trichoderma to hydroponics systems are explored in detail. The culmination of these areas of research serves to improve the current understanding of the role of beneficial and pathogenic fungi, specifically in the hydroponic microbiome.},
}
@article {pmid39765642,
year = {2024},
author = {Deryabin, D and Kosyan, D and Vlasenko, L and Lazebnik, C and Zatevalov, A and Karimov, I and Duskaev, G},
title = {Macro, Trace and Toxic Element Composition in Liver and Meat of Broiler Chicken Associated with Cecal Microbiome Community.},
journal = {Biology},
volume = {13},
number = {12},
pages = {},
pmid = {39765642},
issn = {2079-7737},
support = {22-16-00036//Russian Science Foundation/ ; FNWZ-2022-0010//research project/ ; },
abstract = {The current study presents a meta-analysis of the detailed relationship between the composition of 25 essential and toxic elements in chicken tissues examined by ICP-MS and the gut microbial community analyzed using NGS techniques. The examination of chicken liver and meat revealed typical elemental compositions, called the "elementomes". The α-elementomes showed high contents of macro elements (Na, K, Mg, Ca, P), majority trace elements (Sr, Se, Mn, Fe, Co, Cu, Zn) and some toxic elements (B, Pb, Ni, Cd); β-elementomes indicated accumulation of Si, V and Cr; γ-elementomes indicated accumulation of Al, As and Hg. Characterization of the microbiomes' structure showed two distinct enterotypes, designated "microbiome patterns"; the first was enriched in the phylum Bacteroidota, and the second was dominated by Bacillota and coupled with members of the phyla Actinomycetota, Cyanobacteriota and Thermodesulfobacteriota. A comparison of elementomes and microbiomes demonstrated a clear correspondence between the α- and γ-elementomes belonging to the Bacteroidota-enriched pattern, while the β-elementome was predominantly found in chicken groups belonging to the Bacillota + ACT pattern. This insight proposes a novel strategy to improve deficiency or excess of certain elements in the host by gut microbiome modulation, which needs to be verified with further in vivo experiments.},
}
@article {pmid39765622,
year = {2024},
author = {Lamichhane, G and Olawale, F and Liu, J and Lee, DY and Lee, SJ and Chaffin, N and Alake, S and Lucas, EA and Zhang, G and Egan, JM and Kim, Y},
title = {Curcumin Mitigates Gut Dysbiosis and Enhances Gut Barrier Function to Alleviate Metabolic Dysfunction in Obese, Aged Mice.},
journal = {Biology},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/biology13120955},
pmid = {39765622},
issn = {2079-7737},
support = {1-503351//OTTOGI HAM TAIHO Foundation/ ; n/a//Intramural Research Program of the National Institute on Aging/ ; },
abstract = {The gut microbiome plays a critical role in maintaining gut and metabolic health, and its composition is often altered by aging and obesity. This study aimed to investigate the protective effects of curcumin on gut dysbiosis, gut barrier integrity, and bile acid homeostasis in aged mice fed a high-fat, high-sugar diet (HFHSD). Eighteen- to twenty-one-month-old male C57BL/6 mice were divided into groups fed a normal chow diet or HFHSD, with or without curcumin supplementation (0.4% w/w) for 8 and 15 weeks. We assessed body weight, food intake, insulin sensitivity, gut microbiota composition, and gene expression in the gut and liver and performed histological analysis of gut tissues. Curcumin supplementation prevented HFHSD-induced weight gain and metabolic disturbances. In the gut, curcumin-treated mice showed a higher abundance of beneficial bacterial genera, such as Lachnospiraceae, Akkermansia, Mucispirillum, and Verrucomicrobiota, alongside a lower abundance of harmful bacterial genera like Desulfobacteria, Alistipes, and Muribaculaceae compared to control. This shift in gut microbiota was associated with improved gut integrity, as demonstrated by increased expression of the tight junction protein occludin and reduced levels of the pro-inflammatory marker interleukin-1β in the ileum. Additionally, curcumin modulated hepatic gene expression involved in bile acid homeostasis, suggesting a positive effect on liver health. Curcumin supplementation can alleviate the negative effects of aging and an HFHSD on the gut microbiome, improve gut barrier integrity, and maintain bile acid homeostasis. These findings highlight curcumin's potential as a dietary intervention for managing obesity- and age-associated gut health issues.},
}
@article {pmid39765547,
year = {2024},
author = {Zhang, J and Guo, D and Zhang, L and Li, D and Deng, B},
title = {Dietary Supplementation with Methylsulfonylmethane and Myo-Inosito Supports Hair Quality and Fecal Microbiome in Poodles.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {24},
pages = {},
pmid = {39765547},
issn = {2076-2615},
support = {32472927//National Natural Science Foundation of China/ ; 2021YFD1300400//the National Key R&amp;D Program of China/ ; 2023YFD1301900//the National Key R&amp;D Program of China/ ; },
abstract = {This study aimed to investigate the effects of dietary supplementation with methylsulfonylmethane (MSM) and myo-inositol (MI) on hair quality, fecal microbiota, and metabolome in poodles. Thirty-two adult poodles categorized based on initial body weight and sex were randomly assigned to four groups. These groups (designated the CON, MSM, MI, and MSM + MI groups) received a basal diet, the same diet supplemented with 0.2% MSM + 0% MI, the same diet supplemented with 0% MSM + 0.2% MI, or the same diet supplemented with 0.2% MSM + 0.2% MI, respectively. The study lasted for 65 days. During the entire study period, body weight, average daily weight gain, feed intake, energy intake, and fecal output were normal in all the animals and did not differ significantly among the treatment groups. Hair scale thickness was lower in the MI and MSM + MI groups than in the CON group on Day 65 (p < 0.05). An amino acid analysis of the hair revealed higher sulfur content in the MI and MSM + MI groups on Day 65 than on Day 0 (p < 0.05). Moreover, the poodles in the MSM, MI, and MSM + MI groups presented significantly lower levels of Proteobacteria_unclassified and Candidatus Phytoplasma than did those in the CON group. The relative abundance of Gammaproteobacteria_unclassified was greater in the MSM and MI groups than in the CON group (p < 0.05). The MSM group presented a greater abundance of Glucerabacter than the CON group (p < 0.05). Compared with those in the CON and MSM + MI groups, the abundances of Paramuribaculum and Hafnia in the MSM group were greater (p < 0.05). The abundances of Enterobacter and Kineothrix were greater (p < 0.05) in the MI group than in the CON and MSM + MI groups. The poodles in the MI group presented significantly greater abundances of Bacteroidales_unclassified, Halanaerobium, Mycobacterium, and Erysipelotrichaceae_unclassified than did poodles in the CON, MSM, and MSM + MI groups. Fecal metabolomics analysis revealed that MSM, MI, and MSM + MI treatment markedly affected carbohydrate metabolism. MSM + MI treatment also influenced lipid metabolism. These findings suggest that dietary supplementation with MSM and MI can improve the hair quality of poodles.},
}
@article {pmid39765538,
year = {2024},
author = {Rong, W and Wei, Y and Chen, Y and Huang, L and Huang, S and Lv, Y and Guan, D and Li, X},
title = {16S rRNA Sequencing Analysis Uncovers Dose-Dependent Cupric Chloride Effects on Silkworm Gut Microbiome Composition and Diversity.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {24},
pages = {},
pmid = {39765538},
issn = {2076-2615},
support = {2020XJZC002//the Research Project of Hechi University/ ; 2023GXCSSC04//the Special Project of Guangxi Collaborative Innovation Center of Modern Sericulture and Silk/ ; 2023GCC017//the Scientific research project of Hechi University/ ; Heke ZY230301//the Local Science and Technology Development Fund project guided by the central government/ ; },
abstract = {Copper-based pesticides are extensively used in agriculture, yet their impacts on beneficial insects remain poorly understood. Here, we investigate how cupric chloride exposure affects the gut microbiome of Bombyx mori, a model organism crucial for silk production. Using 16S rRNA sequencing, we analyzed the gut bacterial communities of fifth-instar silkworm larvae exposed to different concentrations of cupric chloride (0, 4, and 8 g/kg) in an artificial diet. The high-dose exposure dramatically altered the microbial diversity and community structure, where the Bacteroidota abundance decreased from 50.43% to 23.50%, while Firmicutes increased from 0.93% to 18.92%. A network analysis revealed complex interactions between the bacterial genera, with Proteobacteria and Firmicutes emerging as key players in the community response to copper stress. The functional prediction indicated significant shifts in metabolic pathways and genetic information processing in the high-dose group. Notably, the low-dose treatment induced minimal changes in both the taxonomic composition and predicted functions, suggesting a threshold effect in the microbiome response to copper exposure. Our findings provide novel insights into how agricultural chemicals influence insect gut microbiota and highlight potential implications for silkworm health and silk production. This work contributes to understanding the ecological impacts of copper-based pesticides and may inform evidence-based policies for their use in sericulture regions.},
}
@article {pmid39765529,
year = {2024},
author = {Kou, X and Liu, Y and Xiang, F and Zhang, X and Khan, MZ and Wu, B and Wang, H and Gong, Y and Wang, C and Ma, Q and Li, Y},
title = {Insights into the Donkey Hindgut Microbiome Using Metagenome-Assembled Genomes.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {24},
pages = {},
pmid = {39765529},
issn = {2076-2615},
support = {32102564//National Natural Science Foundation of China/ ; },
abstract = {The gut microbiota plays an important role in the digestion, absorption, and metabolism of nutrients, as well as in the immunity, health, and behavior of donkeys. While reference genomes and gut microbial gene catalogs have been helpful in understanding the composition of the donkey, there is still a significant gap in sequencing and understanding the functional aspects of donkey gut microbial genomes. In this study, we analyzed metagenomic sequencing data from 26 donkeys' gut samples and successfully assembled 844 microbial metagenome-assembled genomes (MAGs). Surprisingly, 678 (80.33%) of these MAGs appear to belong to previously unidentified species. Our analysis further revealed a total of 292,980 predicted carbohydrate-active enzymes (CAZymes) and 257,893 polysaccharide utilization loci (PULs). Interestingly, these enzymes and loci displayed relatively low similarity matches in public databases. We found that the higher abundances of 36 MAGs in the cecum (such as Prevotella, Desulfovibrio, Alistipes, and Treponema_D) and 9 MAGs in the dorsal colon (such as Limimorpha, Saccharofermentans, and Lactobacillus) were associated with a diverse array of carbohydrate-degrading pathways. Network analysis identified Prevotella and Dysosmobacter as connectors, while Saccharofermentans and Akkermansia were shown as provincial hubs. This suggests their crucial roles in complex carbohydrate degradation and hindgut metabolism in donkeys. These findings underscore the complexity of hindgut metabolism in donkeys and expand our understanding of their gut microbiome. Overall, this study provides a comprehensive catalog of donkey gut microbial genes, revealing novel carbohydrate-degrading enzymes and offering new insights for future research on the donkey gut microbiome.},
}
@article {pmid39765519,
year = {2024},
author = {Xiong, X and Yu, C and Qiu, M and Zhang, Z and Hu, C and Zhu, S and Yang, L and Peng, H and Song, X and Chen, J and Xia, B and Wang, J and Qing, Y and Yang, C},
title = {Genomic and Gut Microbiome Evaluations of Growth and Feed Efficiency Traits in Broilers.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {24},
pages = {},
pmid = {39765519},
issn = {2076-2615},
support = {YSCX2035-004//Original Innovation Project of Sichuan Academy of Agricultural Sciences/ ; CARS-41//National Modern Agricultural Industrial Technology System Construction Project/ ; 2021YFYZ0031//Sichuan Science and Technology Program/ ; SASA2024CZYX002//Sichuan Provincial Financial Operation Special Project/ ; },
abstract = {In this study, we combined genomic and gut microbiome data to evaluate 13 economically important growth and feed efficiency traits in 407 Dahen broilers, including body weight (BW) at four, six, nine, and ten weeks of age (BW4, BW6, BW9, and BW10), as well as the average daily gain (ADG6, ADG9, and ADG10), feed conversion ratio (FCR6, FCR9, and FCR10), and residual feed intake (RFI6, RFI9, and RFI10) for the three growing ages. The highest ADG and lowest FCR were observed at nine and six weeks of age, respectively. We obtained 47,872 high-quality genomic single-nucleotide polymorphisms (SNPs) by sequencing the genomes and 702 amplicon sequence variants (ASVs) of the gut microbiome by sequencing the 16S rRNA gene, both of which were used for analyses of linear mixed models. The heritability estimates (± standard error, SE) ranged from 0.103 ± 0.072 to 0.156 ± 0.079 for BW, 0.154 ± 0.074 to 0.276 ± 0.079 for the ADG, 0.311 ± 0.076 to 0.454 ± 0.076 for the FCR, and 0.413 ± 0.077 to 0.609 ± 0.076 for the RFI traits. We consistently observed moderate and low negative genetic correlations between the BW traits and the FCR and RFI traits (r = -0.562 to -0.038), whereas strong positive correlations were observed between the FCR and RFI traits (r = 0.564 to 0.979). For the FCR and RFI traits, strong positive correlations were found between the measures at the three ages. In contrast to the genomic contribution, we did not detect a gut microbial contribution to all of these traits, as the estimated microbiabilities did not confidently deviate from zero. We systematically evaluated the contributions of host genetics and gut microbes to several growth and feed efficiency traits in Dahen broilers, and the results show that only the host genetics had significant effects on the phenotypic variations in a flock. The parameters obtained in this study, based on the combined use of genomic and gut microbiota data, may facilitate the implementation of efficient breeding schemes in Dahen broilers.},
}
@article {pmid39765499,
year = {2024},
author = {Chen, Y and Ma, J and Yong, YS and Chen, Y and Chen, B and Cao, J and Peng, K and Wang, G and Huang, H and Loh, JY},
title = {Impacts of Black Soldier Fly (Hermetia illucens) Larval Meal on Intestinal Histopathology and Microbiome Responses in Hybrid Grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂): A Comprehensive Analysis.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {24},
pages = {},
pmid = {39765499},
issn = {2076-2615},
support = {ZDYF2022XDNY331//2022 Key Science and Technology planned project of Yazhou Bay Innovation Institute of Hainan Tropical Ocean University, and the 2023 Hainan Province's Key Research and Development Project/ ; },
abstract = {This study examined the diversity and responses of intestinal microbiota in hybrid grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂) fed diets with varying levels of fishmeal replaced by black soldier fly larvae (BSFL). The 10% BSFL substitution (BSFL10) group showed the highest levels of trypsin and amylase. Substituting fishmeal with 30% and 50% BSFL weakened the intestinal wall, resulting in vacuoles, sparse striatal boundaries, and fewer villi. Microbiota diversity, measured through Shannon's index, was higher in the BSFL10 and BSFL50 groups than in the control. 16S rRNA amplicon data revealed the dominance of Firmicutes, Proteobacteria, Bacteroidetes, Spirochaetota, and Verrucomicrobia phyla. The BSFL-replacement groups showed an increase in Proteobacteria, Bacteroidetes, and Spirochaetota compared to the control, but fewer Firmicutes. PICRUSt analysis indicated significant alterations in microbial function, particularly enhanced protein, carbohydrate, lipid, and energy metabolisms in the BSFL-fed group. Substituting 10% fishmeal with BSFL enhanced nutrient metabolism and gut microbiota in juvenile hybrid grouper. Further research is needed to explore factors affecting the efficacy of insect feed as a sustainable aquaculture diet.},
}
@article {pmid39765228,
year = {2024},
author = {Whidbey, C},
title = {The right tool for the job: Chemical biology and microbiome science.},
journal = {Cell chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chembiol.2024.12.004},
pmid = {39765228},
issn = {2451-9448},
abstract = {Microbiomes exist in ecological niches ranging from the ocean and soil to inside of larger organisms like plants and animals. Within these niches, microbes play key roles in biochemical processes that impact larger phenomena, such as biogeochemical cycling or health. By understanding of how these processes occur at the molecular level, it may be possible to develop new interventions to address global problems. The complexity of these systems poses challenges to more traditional techniques. Chemical biology can help overcome these challenges by providing tools that are broadly applicable and can obtain molecular-level information about complex systems. This primer is intended to serve as a brief introduction to chemical biology and microbiome science, to highlight some of the ways that these two disciplines complement each other, and to encourage dialog and collaboration between these fields.},
}
@article {pmid39765121,
year = {2025},
author = {Zhu, B and Zhang, Z and Xie, Y and Huang, M and Chen, Y and Yang, Y and Shi, X and Han, J and Yang, L and Zhao, M},
title = {Effects of environmental bisphenol S exposure on male rat reproductive health and gut-blood-testicular axis integrity.},
journal = {Ecotoxicology and environmental safety},
volume = {289},
number = {},
pages = {117646},
doi = {10.1016/j.ecoenv.2024.117646},
pmid = {39765121},
issn = {1090-2414},
abstract = {In this study, male Sprague-Dawley (SD) rats were exposed to bisphenol S (BPS) at environmentally relevant concentrations to investigate its reproductive toxicity and evaluate its effects on the gut-blood-testicular axis. After 28 days of exposure to BPS (0.05 and 20 mg/kg), the results showed a reduction in weight gain and the induction of reproductive toxicity in male rats, including decreased sperm parameters, lower sperm viability, and increased abnormal sperm density and mortality. These observations were made by counting with a hemocytometer under the optical microscope. 16S rRNA and untargeted metabolomic elucidated potential impacts on the gut-blood-testicular axis: BPS impaired the physical barrier, evoked inflammation, and resulted in dysbiosis of the gut microbiota. Additionally, BPS altered serum metabolites, including phosphatidic acid and diacylglycerol, which are involved in Fc gamma R-mediated phagocytosis and linked to inflammation. Furthermore, histopathological analysis, western blot (WB), enzyme-linked immunosorbent assay (ELISA), and immunofluorescence results showed that exposure to BPS led to testicular damage, inflammation, activation of the p38 and ERK MAPK pathways, and disruption of the blood-testis barrier (BTB). Collectively, these findings indicate that BPS impair the intestinal health, disrupt gut microbiome, and ultimately lead to reproductive dysfunction through the gut-blood-testicular axis.},
}
@article {pmid39765038,
year = {2024},
author = {Wang, C and Peng, M and Gao, Z and Fu, F and Li, G and Su, D and Huang, L and Guo, J and Shan, Y},
title = {Citrus aurantium 'Changshan-huyou' physiological premature fruit drop: A promising prebiotic to tackle obesity.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {136},
number = {},
pages = {156347},
doi = {10.1016/j.phymed.2024.156347},
pmid = {39765038},
issn = {1618-095X},
abstract = {BACKGROUND: Presently, the mitigation and governance of obesity have surfaced as significant public health dilemmas on a global scale. A wealth of studies indicated that the host gut microbiota is instrumental in regulating the interplay between high-fat diet (HFD) intake and the pathogenesis of obesity. Physiological premature fruit drop, a major byproduct of citrus, is rich in a variety of bioactive constituents, yet its potential has remained underutilized for an extended period.<br><br>PURPOSE: The objective of this investigation is to examine the chemical constituents of Citrus aurantium'Changshan-huyou' premature fruit drop (HYFD) and investigate its anti-obesity effects, elucidating its potential pathways.<br><br>METHODS: Volatile compounds and flavonoids in HYFD were analyzed using chromatographic and mass spectrometric techniques. Furthermore, this study utilized biochemical assays and histopathological examinations to evaluate the effects of HYFD on HFD-fed mice. The impact of HYFD on the gut microbiota of the mice was examined through 16S rRNA gene sequencing, and fecal microbiota transplantation was employed to validate the role of the gut microbial community in host obesity prevention. Concurrently, transcriptome was employed to identify differentially expressed genes, providing further insights into the molecular mechanisms through which HYFD manifests its anti-obesity effects.<br><br>RESULTS: Our findings demonstrated that HYFD supplementation significantly alleviated adiposity and ameliorated the dysbiosis of gut microbiota in HFD-induced mice. HYFD rectified the HFD-induced gut microbiota dysregulation, enhanced the presence of beneficial microbial taxa linked to lipid metabolism, including Parabacteroides and Alistipes, and elevated concentrations of the anti-obesity short-chain fatty acids, comprising caproic acid and isocaproic acid. Additionally, transcriptomic analyses confirmed that HYFD prevented obesity in mice by enhancing fatty acid catabolism via the activation of the AMPK/PPAR&#x3b1;/CPT1a signaling pathway.<br><br>CONCLUSION: Our results provided novel insights into the mechanism of citrus physiological premature fruit drop and its potential role in preventing obesity, while sparking greater interest in leveraging more biomass waste.},
}
@article {pmid39765033,
year = {2024},
author = {Xu, M and Guo, Y and Wang, F and Lin, C and Cao, D and Yan, Y and Chai, S and Zhao, Y and Deng, S and Wei, J and Kang, X and Liu, Y and Zhang, Y and Luo, L and Liu, SL and Liu, H},
title = {Enterolactone combined with m6A Reader IGF2BP3 inhibits malignant angiogenesis and disease progression in ovarian cancer.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {136},
number = {},
pages = {156343},
doi = {10.1016/j.phymed.2024.156343},
pmid = {39765033},
issn = {1618-095X},
abstract = {BACKGROUND: Among all gynecological cancers, ovarian cancer is the leading cause of death. Epithelial ovarian cancer (EOC) accounts for over 85 % of ovarian cancer cases and is characterized by insidious onset, early metastasis, and a high recurrence rate. Alterations in gut microbiota, often as a consequence of chemotherapy, can promote cancer development and exacerbate the disease. The m6A reader IGF2BP3 is a regulator in the occurrence and progression of various tumors and is associated with angiogenesis. Enterolactone (ENL) has demonstrated significant anti-tumor activity against various human cancers, including EOC. However, whether ENL could interact with IGF2BP3 to suppress EOC remains unclear.<br><br>PURPOSE: This study aims to investigate suppressive effects of ENL upon combining with IGF2BP3 on EOC and elucidates the underlying mechanism.<br><br>METHODS: The Cell Counting Kit-8 and crystal violet assays were used to assess tumor cell proliferation. Scratch and Transwell assays were employed to evaluate tumor cell migration, while tube formation assays were utilized to examine angiogenesis. Western blotting was used to measure the expression levels of IGF2BP3, VEGF, PI3K, AKT1, p-PI3K, and p-AKT1. An in vivo xenograft nude mouse model was established, fecal samples were collected, and 16S rDNA sequencing was performed to analyze gut microbiota in association with the suppressive effects of ENL and its interactions with IGF2BP3.<br><br>RESULTS: IGF2BP3 is highly expressed in EOC and is positively correlated with poor survival in EOC patients. ENL reduces IGF2BP3 expression in EOC, thereby inhibiting the IGF2BP3-mediated VEGF/PI3K/AKT signaling pathway and suppressing the proliferation, migration, invasion, and angiogenesis of EOC. Additionally, ENL ameliorates gut microbiome, especially in conjunction with shIGF2BP3.<br><br>CONCLUSION: ENL interacts with IGF2BP3 and suppresses its expression in EOC, leading to the deactivation of the IGF2BP3-mediated VEGF/PI3K/AKT signaling pathway and the subsequent inhibition of angiogenesis. The combination of ENL and shIGF2BP3 demonstrates a synergistic effect on EOC. ENL also ameliorates the gut microbiome, especially in conjunction with shIGF2BP3, to suppress EOC.},
}
@article {pmid39764653,
year = {2024},
author = {Mao, Y and Huang, Y and Zhang, W and Liang, H and Liu, F and Luo, Q and Xu, C and Qin, Y and Liu, J and Tang, S and Liu, H and Ge, X},
title = {FMT reduces systemic inflammatory response in severe acute pancreatitis by increasing the abundance of intestinal Bifidobacteria and fecal bacteria.},
journal = {Biomolecules &amp; biomedicine},
volume = {},
number = {},
pages = {},
doi = {10.17305/bb.2024.11445},
pmid = {39764653},
issn = {2831-090X},
abstract = {Severe acute pancreatitis (SAP) is one of the leading causes of hospital admissions for gastrointestinal diseases, with a rising incidence worldwide. Intestinal microbiota dysbiosis caused by SAP exacerbates systemic inflammatory response syndrome and organ dysfunction. Fecal microbiota transplantation (FMT) has emerged as a promising therapeutic option for gastrointestinal diseases. In this study, fecal samples from healthy, control, and FMT-treated groups were analyzed using 16S rRNA sequencing to assess microbiome abundance and diversity. Composition and functional prediction analyses were conducted to explore the mechanisms underlying FMT in SAP. FMT significantly improved clinical parameters in SAP patients, including leukocyte count, C-reactive protein (CRP), neutrophil granulocyte count, lactate dehydrogenase (LDH), and calcitonin (P < 0.05). Organ failure rates significantly increased in the control group but decreased in the FMT group after treatment (P < 0.05). Fecal microbiota sequencing revealed that FMT significantly upregulated the abundance of Bifidobacterium longum among all SAP patients (P < 0.05). Receiver operating characteristic (ROC) curve analysis indicated that Bifidobacterium longum might play a critical role in the efficacy of FMT, with an area under the curve (AUC) value of 0.84. Additionally, there was a negative correlation between Bifidobacterium longum abundance and procalcitonin (PCT) levels, as well as a negative correlation between Escherichia coli abundance and both CT and Ca values (P < 0.05). The relative abundances of Bifidobacterium longum and Escherichia coli were significantly higher in the FMT group compared to the Bifidobacterium triple viable group (P < 0.05). In conclusion, this research supports FMT as a safe and effective intervention for treating SAP patients.},
}
@article {pmid39764615,
year = {2025},
author = {Harris, SC and Bajaj, JS},
title = {Interaction of the Gut-Liver-Brain Axis and the sterolbiome with sexual dysfunction in patients with cirrhosis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2446390},
doi = {10.1080/19490976.2024.2446390},
pmid = {39764615},
issn = {1949-0984},
mesh = {Humans ; *Liver Cirrhosis/complications/metabolism ; *Gastrointestinal Microbiome ; *Brain-Gut Axis/physiology ; *Sexual Dysfunction, Physiological/metabolism/etiology/physiopathology ; *Liver/metabolism ; Sterols/metabolism ; Brain/metabolism ; Gonadal Steroid Hormones/metabolism ; Animals ; Quality of Life ; },
abstract = {There is a complex interplay between the gut microbes, liver, and central nervous system, a gut-liver-brain axis, where the brain impacts intestinal and hepatic function while the gut and liver can impact cognition and mental status. Dysregulation of this axis can be seen in numerous diseases. Hepatic encephalopathy, a consequence of cirrhosis, is perhaps the best studied perturbation of this system. However, patients with cirrhosis have been shown to have increased incidence of other disorders of mental health which may be otherwise less clinically identifiable. Sexual dysfunction affects a large proportion of patients with cirrhosis and is associated with decreased quality of life. Screening for sexual dysfunction in patients with cirrhosis is often overlooked, and even when identified, treatment options are limited, particularly in patients with advanced liver disease. The mechanism by which patients with cirrhosis develop sexual dysfunction is multifactorial, but a key driver of this clinical manifestation is alterations in circulating sex hormones. In patients with cirrhosis, low serum sex hormones have been shown to be associated with higher mortality regardless of MELD score. The gut microbiome has been shown to have an immense metabolic capacity to metabolize steroid hormones. This "sterolbiome" has already been implicated in other disease processes and has been linked to low circulating sex hormones, suggesting a new mechanism by which sex hormones may be altered in disease states where the gut-liver-brain axis is disrupted. The aim of this review is to cover sex hormone changes and sexual dysfunction in cirrhosis, examine the gut microbiome and its metabolic capacity, particularly for steroid hormones, and consider how microbial changes using fecal microbiota transplant could modulate sexual dysfunction.},
}
@article {pmid39764609,
year = {2025},
author = {Wu, X and MacKenzie, MD and Yang, J and Lan, G and Liu, Y},
title = {Climate Change Drives Changes in the Size and Composition of Fungal Communities Along the Soil-Seedling Continuum of Schima superba.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17652},
doi = {10.1111/mec.17652},
pmid = {39764609},
issn = {1365-294X},
support = {2022JBGS04//Research Project of Baishanzu National Park/ ; 2023JBGS06//Research Project of Baishanzu National Park/ ; //Fundamental Research Funds for the Central Universities of China/ ; 32071645//National Natural Science Foundation of China/ ; 32471613//National Natural Science Foundation of China/ ; },
abstract = {Plant microbiomes have a major influence on forest structure and functions, as well as tree fitness and evolution. However, a comprehensive understanding of variations in fungi along the soil-plant continuum, particularly within tree seedlings, under global warming is lacking. Here, we investigated the dynamics of fungal communities across different compartments (including bulk soil and rhizosphere soil) and plant organs (including the endosphere of roots, stems and leaves) of Schima superba seedlings exposed to experimental warming and drought using AccuITS absolute quantitative sequencing. Our results revealed that warming and drought significantly reduced the number of specific fungal amplicon sequence variants (ASVs) in the bulk soil and rhizosphere soil, respectively. Variations in fungal communities were mainly explained by compartments and plant organs, with the composition of endophytic fungal communities within leaves (primarily attributed to species gain or loss) being most influenced by climate change. Moreover, warming significantly reduced the migration of Ascomycota, soil saprotrophs, wood saprotrophs and yeasts from the bulk soil to the rhizosphere soil but increased that of plant pathogens from the roots to the stems. Drought significantly decreased the absolute abundances of Chytridiomycota, Glomeromycota and Rozellomycota, as well as the migration of ectomycorrhizal fungi from the bulk soil to the rhizosphere soil but increased that of plant pathogens. Warming could indirectly reduce leaf area by increasing the diversity of leaf pathogens. These findings have potential implications for enhancing the resilience and functioning of natural forest ecosystems under climate change through the manipulation of plant microbiomes, as demonstrated in agroecosystems.},
}
@article {pmid39764565,
year = {2025},
author = {Wang, T and Zhou, D and Hong, Z},
title = {Sarcopenia and cachexia: molecular mechanisms and therapeutic interventions.},
journal = {MedComm},
volume = {6},
number = {1},
pages = {e70030},
pmid = {39764565},
issn = {2688-2663},
abstract = {Sarcopenia is defined as a muscle-wasting syndrome that occurs with accelerated aging, while cachexia is a severe wasting syndrome associated with conditions such as cancer and immunodeficiency disorders, which cannot be fully addressed through conventional nutritional supplementation. Sarcopenia can be considered a component of cachexia, with the bidirectional interplay between adipose tissue and skeletal muscle potentially serving as a molecular mechanism for both conditions. However, the underlying mechanisms differ. Recognizing the interplay and distinctions between these disorders is essential for advancing both basic and translational research in this area, enhancing diagnostic accuracy and ultimately achieving effective therapeutic solutions for affected patients. This review discusses the muscle microenvironment's changes contributing to these conditions, recent therapeutic approaches like lifestyle modifications, small molecules, and nutritional interventions, and emerging strategies such as gene editing, stem cell therapy, and gut microbiome modulation. We also address the challenges and opportunities of multimodal interventions, aiming to provide insights into the pathogenesis and molecular mechanisms of sarcopenia and cachexia, ultimately aiding in innovative strategy development and improved treatments.},
}
@article {pmid39764490,
year = {2025},
author = {Shinoda, A and Koga, Y and Tsuchiya, R and Tserenpurev, BO and Battsetseg, B and Morinaga, Y and Nakayama, J},
title = {Impact of container type on the microbiome of airag, a Mongolian fermented mare's milk.},
journal = {Bioscience of microbiota, food and health},
volume = {44},
number = {1},
pages = {90-99},
pmid = {39764490},
issn = {2186-6953},
abstract = {Airag, a fermented mare's milk in Mongolia, exhibits diverse flavors and microbiota due to distinct production processes and environments in nomadic households. Recently, there has been a shift from the traditional cow skin container, 'khokhuur', to a plastic container for airag production, potentially impacting the microbiota and quality. To address this notion, we aimed to elucidate the differences in the microbiota between airag samples from a plastic container and those from a khokhuur. We collected airag samples produced using either a plastic container or khokhuur from three houses in Mogod Sum (county) in Bulgan Aimag (province) and analyzed the chemical and microbiome properties of the obtained samples. Compared with the khokhuur, the plastic containers exhibited high heat retention at night and boosted lactate production, which sustained a lower pH level in airag. A series of alpha diversity indices of airag microbiota were significantly higher in airag produced in khokhuurs than in those produced in the plastic containers. In particular, Lactobacillus helveticus was the most dominant species, accounting for more than 90% of the total population in airags produced in the plastic containers and khokhuur, whereas some other lactic acid bacteria species and environmental bacteria more colonized airags produced in khokhuurs. The khokhuur itself is likely a source of these bacterial species and likely provides a niche, and the wider volatility of temperature may allow the growth of this wide range of bacteria while maintaining a lower level of lactic acid fermentation.},
}
@article {pmid39764488,
year = {2025},
author = {Hu, S and Yin, H and Li, X and Fan, M and Li, H},
title = {Effects of moderate beer consumption on immunity and the gut microbiome in immunosuppressed mice.},
journal = {Bioscience of microbiota, food and health},
volume = {44},
number = {1},
pages = {32-42},
pmid = {39764488},
issn = {2186-6953},
abstract = {Beer contains a variety of bioactive ingredients and trace elements that can regulate bodily functions, and moderate consumption of beer can enhance immune responses. This study aimed to investigate the potential benefits of moderate consumption of alcoholic or non-alcoholic beer on the gut microbiome, immunity, and intestinal barrier function in immunosuppressed BALB/c mice induced by cyclophosphamide (CTX). Model mice with CTX-induced immunosuppression were administered alcoholic or non-alcoholic beer or galacto-oligosaccharides (GOS) for 28 consecutive days. The GOS and beer intervention groups all showed alleviation of spleen tissue damage, an increased immune organ index, decreased gut inflammation, and reduced serum concentrations of D-lactic acid, lipopolysaccharide, and tumor necrosis factor α. High-throughput 16S rRNA gene sequencing revealed higher relative abundances of Firmicutes and Actinobacteriota, and lower relative abundances of Bacteroidota, Lactobacillus, and Bifidobacterium, in CTX mice than in normal control mice. In addition, Firmicutes showed lower abundance, while Desulfobacterota showed higher abundance in CTX mice with non-alcoholic beer intake than without it. Spearman correlation analysis indicated that Bacteroidota was negatively correlated with propionic acid and butyric acid, while Desulfobacterota was positively correlated with butyric acid. Proteobacteria was negatively correlated with acetic acid, propionic acid, isobutyric acid, and valeric acid. Helicobacter was positively correlated with valeric acid. In conclusion, this is one of the first studies to examine the modulatory effects of moderate alcohol consumption in immunocompromised mice. Our findings indicate that beer consumption can alter the gut microbiome and metabolites, enhancing immunity in mice.},
}
@article {pmid39764470,
year = {2024},
author = {Tan, T and Chen, Q and Chen, P and Li, S and Hu, W and Yang, T and Jia, Y},
title = {Zhili decoction ameliorates ulcerative colitis by modulating gut microbiota and related metabolite, and inhibiting the TLR4/NF-κB/NLRP3 pathway.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1481273},
pmid = {39764470},
issn = {1663-9812},
abstract = {Zhili decoction (ZLD) is a traditional Chinese medicine prescription for ulcerative colitis (UC). However, the mechanism by which ZLD exerts its therapeutic effects in the context of UC remains unclear.<br><br>AIM OF STUDY: The aim of this study was to investigate the effects of ZLD on the gut microbiota and related fecal metabolite levels using a mouse model of UC. In addition, we examined the underlying molecular mechanisms responsible for these effects.<br><br>MATERIALS AND METHODS: The major components of ZLD were detected by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). An integrated approach employing 16S rRNA and fecal metabolomics was employed to assess the potential impacts of ZLD on gut flora abundance and diversity, fecal metabolite levels, and various metabolic pathways. To further investigate the potential mechanisms of ZLD in treating UC, the expression of genes and proteins were examined by RT-qPCR, immunohistochemical staining and Western blotting.<br><br>RESULTS: ZLD markedly alleviated symptoms and inflammatory injury in mice with UC. DSS induced notable alterations in the gut microbiome, and ZLD enhanced gut microbial diversity in UC mice by augmenting the abundance of Bacteroidota, Christensenella, Lactobacillus, etc., while reducing the Firmicutes/Bacteroidota ratio. ZLD treatment significantly modified the metabolic profile of mice with UC. It significantly suppressed the arachidonic acid metabolic pathway and promoted the butyrate acid metabolic pathway. ZLD reduced inflammatory factors and inhibited TLR4/NF-&#x3ba;B/NLRP3 pathway expression. In addition, correlation analysis demonstrated a close relationship between gut microbes, fecal metabolites, and inflammatory factors.<br><br>CONCLUSION: ZLD alleviated UC by regulating gut flora, modulating related metabolite levels, and inhibiting TLR4/NF-&#x3ba;B/NLRP3 pathway.},
}
@article {pmid39764388,
year = {2024},
author = {Dong, X and Hao, X and Wen, J and Yan, Q and Ma, K and Liu, Q and Li, J and Zhang, L},
title = {Study on the mechanism of acupuncture to improve mild cognitive impairment in hypertension by regulating intestinal microbiome.},
journal = {Frontiers in neuroscience},
volume = {18},
number = {},
pages = {1495384},
pmid = {39764388},
issn = {1662-4548},
abstract = {High blood pressure is a significant risk factor for cardiovascular diseases and is linked to an increased risk of mild cognitive impairment (MCI). The lack of effective treatments for these conditions highlights the urgent need for novel therapeutic approaches. Recent research suggests that the gut microbiota-brain-gut axis plays a crucial role in the pathogenesis of hypertension and MCI by regulating the nervous, endocrine, and immune systems. Acupuncture, an established therapeutic modality, has shown promise in influencing the course of hypertension and MCI by modulating the gut microbiota. This review aims to summarize the mechanistic relationships between the gut microbiome, hypertension, and MCI, and to explore the potential of acupuncture as a treatment strategy for managing Mild cognitive impairment in Hypertension concurrently.},
}
@article {pmid39764236,
year = {2024},
author = {Liu, M and Xue, R and Jin, S and Gu, K and Zhao, J and Guan, S and Xie, X and Su, J and Wang, L},
title = {Metabolomic and metagenomic analyses elucidate the role of intercropping in mitigating continuous cropping challenges in tobacco.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1447225},
pmid = {39764236},
issn = {1664-462X},
abstract = {INTRODUCTION: Crop rotation of tobacco with other crops could effectively break the negative impact of continuous tobacco cropping, but the mechanisms of intercropping system effects on tobacco, especially on the rhizosphere, are not clear.<br><br>METHODS: In this study, we investigated the impact of intercropping system on the diversity and function of tobacco metabolites and microorganisms through metabolomic and metagenomic analyses of the tobacco rhizosphere microenvironment intercropped with maize and soybean.<br><br>RESULTS: The results showed that the contents of huperzine b, chlorobenzene, and P-chlorophenylalanine in tobacco rhizosphere soils differed significantly among soybean-tobacco and maize-tobacco intercropping system. Chlorobenzene and P-chlorophenylalanine had the highest relative abundance under the soybean-tobacco intercropping system, and huperzine b had the highest relative abundance in the maize-tobacco cropping system. At the phylum level, the three most dominant strains were the same across all treatments: Proteobacteria, Actinobacteria, and Acidobacteria, with only minor differences in their abundance, with the fourth most abundant strain in both the tobacco monoculture. KEGG enrichment analysis of the tobacco rhizosphere soil microbiome revealed that intercropping significantly increased the abundance of metabolites in the ABC transporters pathway and up-regulated the LivK, LivH, Livg, LivM, and LivF genes of the branched-chain amino acid pathway.<br><br>DISCUSSION: Collectively, our results indicate that the intercropping could enhance the activity of Livs to enhance the ABC transport pathway, and thus improve the transmembrane transport ability of tobacco roots, thus reducing the negative impact of continuous tobacco cropping. At the same time, the maize-tobacco intercropping could promote the production and transportation of phenolic acids, flavonoids, and other bioactive substances in the tobacco root system, which could enhance tobacco adaptation capacity to abiotic stress.},
}
@article {pmid39764130,
year = {2024},
author = {Prat, A and Muñoz, D and Lizarraga, A and Seifert-Gorzycki, J and Sanchez-Vazquez, E and Johnson, P and Mazzulla, PHS and de Miguel, N},
title = {Chromatin accessibility and gene expression in the parasite Trichomonas vaginalis.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-5455511/v1},
pmid = {39764130},
issn = {2693-5015},
abstract = {Trichomonas vaginalis , the most common non-viral sexually transmitted parasite, causes more than 270 million infections annually. The infection's outcome varies greatly depending on different factors that include variation in human immune responses, the vaginal microbiome, and the inherent virulence of the strain. Although the pathogenicity of the different strains depends, at least partially, on differential gene expression of virulence genes; the regulatory mechanisms governing this transcriptional control remain incompletely understood. While many studies have reported a positive correlation between gene expression and chromatin accessibility in other cells, this relationship has not been analyzed in T. vaginalis . To address these questions, we selected two contrasting T. vaginalis strains based on their interactions with host cells: B7268 strain, a highly adherent one and resistant to metronidazole, and NYH209 strain, a poorly adherent one and sensitive to metronidazole. Next, we combined the assay for transposase-accessible chromatin using sequencing (ATAC-seq) with RNA sequencing (RNA-seq), to delve into the relationship between chromatin accessibility and gene expression in these distinct T. vaginalis strains. Our findings demonstrate a correlation between chromatin accessibility and gene expression across both strains. Moreover, we found that chromatin accessibility plays a pivotal role in modulating mRNA expression levels of several established genes linked to parasite pathogenesis and drug resistance. We also identified several open chromatin peaks residing at intergenic regions, revealing possible distal regulatory elements that may control gene expression. These results highlight the importance of chromatin accessibility in modulating gene expression in the parasite T. vaginalis , with possible consequences in pathogenesis and/or drug treatment.},
}
@article {pmid39763948,
year = {2024},
author = {Perez-Castro, L and Nawas, AF and Kilgore, JA and Garcia, R and Lafita-Navarro, MC and Acosta, PH and Nogueira, PAS and Williams, NS and Conacci-Sorrell, M},
title = {Tryptophan metabolite atlas uncovers organ, age, and sex-specific variations.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39763948},
issn = {2692-8205},
abstract = {UNLABELLED: Although tryptophan (Trp) is the largest and most structurally complex amino acid, it is the least abundant in the proteome. Its distinct indole ring and high carbon content enable it to generate various biologically active metabolites such as serotonin, kynurenine (Kyn), and indole-3-pyruvate (I3P). Dysregulation of Trp metabolism has been implicated in diseases ranging from depression to cancer. Investigating Trp and its metabolites in healthy tissues offers pathways to target disease-associated disruptions selectively, while preserving essential functions. In this study, we comprehensively mapped Trp metabolites across the Kyn, serotonin, and I3P pathways, as well as the microbiome-derived metabolite tryptamine, in C57BL/6 mice. Our comprehensive analysis covered 12 peripheral organs, the central nervous system, and serum in both male and female mice at three life stages: young (3 weeks), adult (54 weeks), and aged (74 weeks). We found significant tissue-, sex-, and age-specific variations in Trp metabolism, with notably higher levels of the oncometabolites I3P and Kyn in aging males. These findings emphasize the value of organ-specific analysis of Trp metabolism for understanding its role in disease progression and identifying targeted therapeutic opportunities.<br><br>AUTHOR SUMMARY: Trp metabolism has primarily been studied in cell lines, often leading to generalized assumptions about its role in health and disease. However, how Trp and its metabolites are allocated across tissues, sexes, and life stages has remained poorly understood. This gap is critical, as Trp is the largest amino acid, minimally used for protein synthesis, and largely metabolized in the liver, yet its distribution and metabolism in other tissues are unknown. Misconceptions, such as the idea that all cancers universally increase Kyn production, have contributed to therapeutic failures, highlighting the need for rigorous, tissue-specific studies. Our study systematically quantifies Trp metabolites across organs and tissues in vivo, revealing significant organ-, sex-, and age-specific variations. These findings provide a foundational resource for understanding Trp metabolism in normal physiology and disease, with potential applications in cancer, neurodegeneration, and other metabolic disorders.},
}
@article {pmid39763947,
year = {2024},
author = {Glowacki, RWP and Till, JM and Brock, OD and Engelhart, MJ and Ahern, PP},
title = {Strain-level antigen variation facilitates immune evasion in Bacteroides thetaiotaomicron.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.20.629425},
pmid = {39763947},
issn = {2692-8205},
abstract = {UNLABELLED: The T cell receptor (TCR) repertoire of intestinal CD4+ T cells is enriched for specificity towards microbiome-encoded epitopes shared among many microbiome members, providing broad microbial reactivity from a limited pool of cells. These cells actively coordinate mutualistic host-microbiome interactions, yet many epitopes are shared between gut symbionts and closely related pathobionts and pathogens. Given the disparate impacts of these agents on host health, intestinal CD4+ T cells must maintain strain-level discriminatory power to ensure protective immunity while preventing inappropriate responses against symbionts. However, to date, the mechanisms by which this occurs have remained enigmatic. To interrogate this, we leveraged BθOM mice that express a transgenic TCR specific for a BT4295 -encoded epitope in B. thetaiotaomicron . While many B. thetaiotaomicron strains potently activated BθOM CD4+ T cells in vitro , strain dnLKV9 escaped recognition. Bioinformatic analyses uncovered two BT4295 homologs in B. thetaiotaomicron -dnLKV9, with each homolog harboring sequence modifications relative to strain VPI-5482, specifically a premature stop codon and a T548S substitution within the epitope. Reconstruction of these variants in B. thetaiotaomicron -VPI-5482 [Δ BT4295] conferred evasion from BθOM CD4+ T cells in vitro to this otherwise permissive strain. Adoptive transfer of BθOM CD4+ T cells to gnotobiotic RAG1-/- colonized with B. thetaiotaomicron harboring these variant BT4295 forms verified the sufficiency of these antigen modifications for evasion of BθOM CD4+ T cells. Collectively, these data uncover the existence of strain-level immune evasion in B. thetaiotaomicron and reveal a mechanism whereby strains evade recognition by CD4+ T cells, facilitating strain-level discrimination in responsiveness to the microbiome.<br><br>KEY POINTS: Select B. theta strains evade recognition by a B. theta -specific CD4+ T cell Strain-specific antigen modifications rather than absence of antigen mediate evasion Evasion strategies limit in vivo accumulation of B. theta -specific CD4+ T cells.},
}
@article {pmid39763928,
year = {2024},
author = {Glowacki, RWP and Engelhart, MJ and Till, JM and Kadam, A and Nemet, I and Sangwan, N and Ahern, PP},
title = {Identification of strain-specific cues that regulate biofilm formation in Bacteroides thetaiotaomicron.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.20.629428},
pmid = {39763928},
issn = {2692-8205},
abstract = {UNLABELLED: Members of the gut microbiome encounter a barrage of host- and microbe-derived microbiocidal factors that must be overcome to maintain fitness in the intestine. The long-term stability of many gut microbiome strains within the microbiome suggests the existence of strain-specific strategies that have evolved to foster resilience to such insults. Despite this, little is known about the mechanisms that mediate this resistance. Biofilm formation represents one commonly employed defense strategy against stressors like those found in the intestine. Here, we demonstrate strain-level variation in the capacity of the gut symbiont Bacteroides thetaiotaomicron to form biofilms. Despite the potent induction of biofilm formation by purified bile in most strains, we show that the specific bile acid species driving biofilm formation differ among strains, and uncover that a secondary bile-acid, lithocholic acid, and its conjugated forms, potently induce biofilm formation in a strain-specific manner. Additionally, we found that the short-chain fatty acid, acetic acid, could suppress biofilm formation. Thus, our data defines the molecular components of bile that promote biofilm formation in B. thetaiotaomicron and reveals that distinct molecular cues trigger the induction or inhibition of this process. Moreover, we uncover strain-level variation in these responses, thus identifying that both shared and strain-specific determinants govern biofilm formation in this species.<br><br>IMPORTANCE: In order to thrive within the intestine, it is imperative that gut microbes resist the multitude of insults derived from the host immune system and other microbiome members. As such, they have evolved strategies that ensure their survival within the intestine. We investigated one such strategy, biofilm formation, in Bacteroides thetaiotaomicron , a common member of the human microbiome. We uncovered significant variation in natural biofilm formation in the absence of an overt stimulus among different Bacteroides thetaiotaomicron strains, and revealed that different strains adopted a biofilm lifestyle in response to distinct molecular stimuli. Thus our studies provide novel insights into factors mediating gut symbiont resiliency, revealing strain-specific and shared strategies in these responses. Collectively, our findings underscore the prevalence of strain-level differences that should be factored into our understanding of gut microbiome functions.},
}
@article {pmid39763902,
year = {2024},
author = {Chege, M and Ferretti, P and Webb, S and Macharia, RW and Obiero, G and Kamau, J and Alberts, SC and Tung, J and Akinyi, MY and Archie, EA},
title = {Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.17.628920},
pmid = {39763902},
issn = {2692-8205},
abstract = {BACKGROUND: Animals coexist with complex microbiota, including bacteria, viruses, and eukaryotes (e.g., fungi, protists, and helminths). While the composition of bacterial and viral components of animal microbiota are increasingly well understood, eukaryotic composition remains neglected. Here we characterized eukaryotic diversity in the microbiomes in wild baboons and tested the degree to which eukaryotic community composition was predicted by host social group membership, sex, age, and season of sample collection.<br><br>RESULTS: We analyzed a total of 75 fecal samples collected between 2012 and 2014 from 73 wild baboons in the Amboseli ecosystem in Kenya. DNA from these samples was subjected to shotgun metagenomic sequencing, revealing members of the kingdoms Protista, Chromista, and Fungi in 90.7%, 46.7%, and 20.3% of samples, respectively. Social group membership explained 11.2% of the global diversity in gut eukaryotic species composition, but we did not detect statistically significant effect of season, host age, and host sex. Across samples, the most prevalent protists were Entamoeba coli (74.66% of samples), Enteromonas hominis (53.33% of samples), and Blastocystis subtype 3 (38.66% of samples), while the most prevalent fungi included Pichia manshurica (14.66% of samples), and Ogataea naganishii (6.66% of samples).<br><br>CONCLUSIONS: Protista, Chromista, and Fungi are common members of the gut microbiome of wild baboons. More work on eukaryotic members of primate gut microbiota is essential for primate health monitoring and management strategies.},
}
@article {pmid39763852,
year = {2024},
author = {Liu, Y and Gates, AD and Liu, Z and Duque, Q and Chen, MY and Hamilton, CD and O'Toole, GA and Haney, CH},
title = {In vitro biofilm formation only partially predicts beneficial Pseudomonas fluorescens protection against rhizosphere pathogens.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.17.628960},
pmid = {39763852},
issn = {2692-8205},
abstract = {Plant roots form associations with both beneficial and pathogenic soil microorganisms. While members of the rhizosphere microbiome can protect against pathogens, the mechanisms are poorly understood. We hypothesized that the ability to form a robust biofilm on the root surface is necessary for the exclusion of pathogens; however, it is not known if the same biofilm formation components required in vitro are necessary in vivo. Pseudomonas fluorescens WCS365 is a beneficial strain that is phylogenetically closely related to an opportunistic pathogen P. fluorescens N2C3 and confers robust protection against P. fluorescens N2C3 in the rhizosphere. We used this plant-mutualist-pathogen model to screen collections of P. fluorescens WCS365 increased a ttachment m utants (iam) and s urface a ttachment d efective (sad) transposon insertion mutants that form increased or decreased levels of biofilm on an abiotic surface, respectively. We found that while the P. fluorescens WCS365 mutants had altered biofilm formation in vitro , only a subset of these mutants, including those involved in large adhesion protein (Lap) biosynthesis, flagellin biosynthesis and O-antigen biosynthesis, lost protection against P. fluorescens N2C3. We found that the inability of P. fluorescens WCS365 mutants to grow in planta , and the inability to suppress pathogen growth, both partially contributed to loss of plant protection. We did not find a correlation between the extent of biofilm formed in vitro and pathogen protection in planta indicating that biofilm formation on abiotic surfaces may not fully predict pathogen exclusion in planta . Collectively, our work provides insights into mechanisms of biofilm formation and host colonization that shape the outcomes of host-microbe-pathogen interactions.},
}
@article {pmid39763787,
year = {2024},
author = {Week, B and Ralph, PL and Tavalire, HF and Cresko, WA and Bohannan, BJM},
title = {Quantitative Genetics of Microbiome Mediated Traits.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.16.628599},
pmid = {39763787},
issn = {2692-8205},
abstract = {Multicellular organisms host a rich assemblage of associated microorganisms, collectively known as their "microbiomes". Microbiomes have the capacity to influence their hosts' fitnesses, but the conditions under which such influences contribute to evolution are not clear. This is due in part to a lack of a comprehensive theoretical framework for describing the combined effects of host and associated microbes on phenotypic variation. Here we begin to address this gap by extending the foundations of quantitative genetic theory to include host-associated microbes, as well as alleles of hosts, as factors that explain quantitative host trait variation. We introduce a way to partition host-associated microbiomes into componenents relevant for predicting a microbiome-mediated response to selection. We then apply our general framework to a simulation model of microbiome inheritance to illustrate principles for predicting host trait dynamics, and to generalize classical narrow and broad sense heritabilities to account for microbial effects. We demonstrate that microbiome-mediated responses to host selection can arise from various transmission modes, not solely vertical, with the contribution of non-vertical modes depending on host life history. Our work lays a foundation for integrating microbiome-mediated host variation and adaptation into our understanding of natural variation.},
}
@article {pmid39763785,
year = {2024},
author = {Shanmugam, NRS and Yin, Y},
title = {CAZyme3D: a database of 3D structures for carbohydrate-active enzymes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.27.630555},
pmid = {39763785},
issn = {2692-8205},
abstract = {CAZymes (C arbohydrate A ctive En Zymes) degrade, synthesize, and modify all complex carbohydrates on Earth. CAZymes are extremely important to research in human health, nutrition, gut microbiome, bioenergy, plant disease, and global carbon recycling. Current CAZyme annotation tools are all based on sequence similarity. A more powerful approach is to detect protein structural similarity between query proteins and known CAZymes indicative of distant homology. Here, we developed CAZyme3D (https://pro.unl.edu/CAZyme3D/) to fill the research gap that no dedicated 3D structure databases are currently available for CAZymes. CAZyme3D contains a total of 870,740 AlphaFold predicted 3D structures (named Whole dataset). A subset of CAZymes 3D structures from 188,574 nonredundant sequences (named ID50 dataset) were subject to structural similarity-based clustering analyses. Such clustering allowed us to organize all CAZyme structures using a hierarchical classification, which includes existing levels defined by the CAZy database (class, clan, family, subfamily) and newly defined levels (subclasses, structural cluster [SC] groups, and SCs). The inter-family structural clustering successfully grouped CAZy families and clans with the same structural folds in the same subclasses. The intra-family structural clustering classified structurally similar CAZymes into SCs, which were further classified into SC groups. SCs and SC groups differed from sequence similarity-based CAZy subfamilies. With CAZyme structures as the search database, we created job submission pages, where users can submit query protein sequences or PDB structures for a structural similarity search. CAZyme3D will be a useful new tool to assist the discovery of novel CAZymes by providing a comprehensive database of CAZyme 3D structures.},
}
@article {pmid39763701,
year = {2025},
author = {Hereira-Pacheco, S and Arias-Del Razo, I and Miranda-Carrazco, A and Dendooven, L and Estrada-Torres, A and Navarro-Noya, YE},
title = {Metagenomic analysis of fungal assemblages at a regional scale in high-altitude temperate forest soils: alternative methods to determine diversity, composition and environmental drivers.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18323},
pmid = {39763701},
issn = {2167-8359},
mesh = {*Soil Microbiology ; *Forests ; *Metagenomics/methods ; *Fungi/genetics/classification/isolation &amp; purification ; *Altitude ; Mexico ; Mycobiome/genetics ; Biodiversity ; },
abstract = {BACKGROUND: Understanding the diversity and distribution of fungal communities at a regional scale is important since fungi play a crucial role in ecosystem functioning. Our study used environmental metagenomics to determine fungal communities in mountainous forest soils in the central highlands of Mexico.<br><br>METHODS: We used four different bioinformatic workflows to profile fungal assemblages, i.e., Geneious+UNITE, single- and paired-end microbial community profiling (MiCoP), and Kraken2.<br><br>RESULTS: The workflows yielded different results; one detected a higher abundance of ectomycorrhizal (EcM) and saprophytic fungi, while the other identified more saprophytic and pathogenic fungi. Environmental, vegetation, and geographical factors determined the spatial distribution of soil fungi at a regional scale. Potential hydrogen (pH), calcium (Ca), magnesium (Mg), and silt content were detected as common drivers of fungal communities across different datasets enriched towards a functional guild. Vegetation traits were found to be more influential in shaping symbiotrophic fungi composition than saprotrophic and pathogenic fungi. This highlights the importance of considering vegetation traits when studying fungal community diversity and distribution. Clustering patterns of sampling points near the volcanoes indicated shared environmental and vegetation characteristics. A weak but significant distance decay in taxonomic similarity revealed that dispersal limitation contributed to fungal community composition, although it was not the primary factor in this study. Overall, this study provides important insights into the challenges and opportunities of studying fungal communities at a regional scale using metagenomic data.},
}
@article {pmid39763640,
year = {2024},
author = {Gao, Y and Wu, J and Zeng, J and Huo, X and Lou, K},
title = {Beyond the desert sands: decoding the relationship between camels, gut microbiota, and antibiotic resistance through metagenomics.},
journal = {Science in One Health},
volume = {3},
number = {},
pages = {100071},
pmid = {39763640},
issn = {2949-7043},
abstract = {BACKGROUND: Camels, known as the enduring "ships of the desert," host a complex gut microbiota that plays a crucial role in their survival in extreme environments. However, amidst the fascinating discoveries about the camel gut microbiota, concerns about antibiotic resistance have emerged as a significant global challenge affecting both human and animal populations. Indeed, the continued use of antibiotics in veterinary medicine has led to the widespread emergence of antibiotic-resistant bacteria, which has worsened through gene transfer.<br><br>METHODS: This study offers a deeper examination of this pressing issue by harnessing the potent tools of metagenomics to explore the intricate interplay between the camel (Camelus ferus) gut microbiota and antibiotic resistance.<br><br>RESULTS: Samples from wild camels yielded varying amounts of raw and clean data, generating scaftigs and open reading frames. The camel fecal microbiome was dominated by bacteria (mainly Bacillota and Bacteriodota), followed by viruses, archaea, and eukaryota. The most abundant genera were the Bacteroides, Ruminococcus, and Clostridium. Functional annotation revealed enriched pathways in metabolism, genetic information processing, and cellular processes, with key pathways involving carbohydrate transport and metabolism, replication, and amino acid transport. CAZy database analysis showed high abundances of glycoside hydrolases and glycosyl transferases. Antibiotic resistance gene (ARG) analysis identified Bacillota and Bacteroidota as the main reservoirs, with vancomycin resistance genes being the most prevalent. This study identified three major resistance mechanisms: antibiotic target alteration, antibiotic target protection, and antibiotic efflux.<br><br>CONCLUSION: These findings contribute to a broader understanding of antibiotic resistance within animal microbiomes and provide a foundation for further investigations of strategies to manage and mitigate antibiotic resistance.},
}
@article {pmid39763574,
year = {2025},
author = {Zhou, T and Wu, YX and Zheng, XH and Li, XZ and Xue, WQ and Wang, TM and He, YQ and Zhou, SH and Du, Y and Xie, JR and Chen, YW and Lu, LX and Liao, Y and Jia, WH},
title = {Longitudinal profiles of oral microbiome in patients with nasopharyngeal carcinoma and their prognostic implications.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2447770},
pmid = {39763574},
issn = {2000-2297},
abstract = {BACKGROUND: Oral microbiome has been associated with various cancers, including nasopharyngeal carcinoma (NPC), but its role in cancer treatment and prognosis remains largely unknown. This study aims to address the dynamic changes in oral microbiome following cancer treatment and their prognostic implications in NPC patients.<br><br>PATIENTS AND METHODS: Unstimulated whole saliva samples were collected from 23 NPC patients before and after treatment, with an average of 2.8 samples per patient, and post-treatment saliva samples were collected from additional 13 NPC patients that enrolled after treatment. Following DNA extraction and purification, the salivary microbiome was assessed by 16S rRNA gene amplicon sequencing targeting the V4&#xa0;hypervariable region.<br><br>RESULTS: Alpha-diversity of oral microbiome decreased progressively after treatment and during follow-up, and the beta-diversity of post-treatment samples differed significantly from the pre-treatment ones (R [2]&#x2009;=&#x2009;0.032, p&#x2009;<&#x2009;0.001). Among patients free of disease progression, 31 oral taxa were identified that changed significantly in abundances after treatment, with 8 increasing and 23 decreasing. The declining taxa included two previously reported NPC-enriched bacteria, Lautropia mirabilis and Capnocytophaga sputigena. In contrast, in the only recurrent case, the abundances of the two bacteria did not decrease, but remained at high levels or even increased until recurrence occurred.<br><br>CONCLUSION: NPC treatment can cause persistent decline in microbial diversity of salivary microbiome and abundances of NPC-associated bacteria, and candidate bacteria could be an explanatory factor for NPC prognosis and deserve intensive research.},
}
@article {pmid39763567,
year = {2024},
author = {Ahmad, S and Wu, T and Arnold, M and Hankemeier, T and Ghanbari, M and Roshchupkin, G and Uitterlinden, AG and Neitzel, J and Kraaij, R and Van Duijn, CM and Arfan Ikram, M and Kaddurah-Daouk, R and Kastenmüller, G and , },
title = {The blood metabolome of cognitive function and brain health in middle-aged adults - influences of genes, gut microbiome, and exposome.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {39763567},
support = {R01 AG046171/AG/NIA NIH HHS/United States ; U01 AG024904/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; RF1 AG059093/AG/NIA NIH HHS/United States ; U01 AG061359/AG/NIA NIH HHS/United States ; RF1 AG058942/AG/NIA NIH HHS/United States ; RF1 AG051550/AG/NIA NIH HHS/United States ; },
abstract = {Increasing evidence suggests the involvement of metabolic alterations in neurological disorders, including Alzheimer's disease (AD), and highlights the significance of the peripheral metabolome, influenced by genetic factors and modifiable environmental exposures, for brain health. In this study, we examined 1,387 metabolites in plasma samples from 1,082 dementia-free middle-aged participants of the population-based Rotterdam Study. We assessed the relation of metabolites with general cognition (G-factor) and magnetic resonance imaging (MRI) markers using linear regression and estimated the variance of these metabolites explained by genes, gut microbiome, lifestyle factors, common clinical comorbidities, and medication using gradient boosting decision tree analysis. Twenty-one metabolites and one metabolite were significantly associated with total brain volume and total white matter lesions, respectively. Fourteen metabolites showed significant associations with G-factor, with ergothioneine exhibiting the largest effect (adjusted mean difference = 0.122, P = 4.65×10[-7]). Associations for nine of the 14 metabolites were replicated in an independent, older cohort. The metabolite signature of incident AD in the replication cohort resembled that of cognition in the discovery cohort, emphasizing the potential relevance of the identified metabolites to disease pathogenesis. Lifestyle, clinical variables, and medication were most important in determining these metabolites' blood levels, with lifestyle, explaining up to 28.6% of the variance. Smoking was associated with ten metabolites linked to G-factor, while diabetes and antidiabetic medication were associated with 13 metabolites linked to MRI markers, including N-lactoyltyrosine. Antacid medication strongly affected ergothioneine levels. Mediation analysis revealed that lower ergothioneine levels may partially mediate negative effects of antacids on cognition (31.5%). Gut microbial factors were more important for the blood levels of metabolites that were more strongly associated with cognition and incident AD in the older replication cohort (beta-cryptoxanthin, imidazole propionate), suggesting they may be involved later in the disease process. The detailed results on how multiple modifiable factors affect blood levels of cognition- and brain imaging-related metabolites in dementia-free participants may help identify new AD prevention strategies.},
}
@article {pmid39763332,
year = {2025},
author = {Leembruggen, AJL and Yildiz, G and Hardee, JP and Stamp, LA and Bornstein, JC and Hao, MM},
title = {Plasticity of enteric neurotransmission varies during day-night cycles and with feeding state.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00286.2024},
pmid = {39763332},
issn = {1522-1547},
support = {2021360//DHAC | National Health and Medical Research Council (NHMRC)/ ; 1158952//DHAC | National Health and Medical Research Council (NHMRC)/ ; DE190101209//Department of Education and Training | Australian Research Council (ARC)/ ; DE220100259//Department of Education and Training | Australian Research Council (ARC)/ ; 2009049//Department of Health, Australian Government | National Health and Medical Research Council (NHMRC)/ ; },
abstract = {The circadian cycle is a fundamental biological rhythm that governs many physiological functions across nearly all living organisms. In the gastrointestinal tract, activities such as gut motility, hormone synthesis, and communication between the gut, central nervous system and microbiome all fluctuate in alignment with the circadian cycle. The enteric nervous system (ENS) is critical for co-ordinating many of these activities, however, how its activity is governed by the circadian cycle remains unknown. In this study, we used live calcium imaging to examine alterations in enteric neurotransmission during the 24-hour day/night cycle in mice. Additionally, given the role of food timing as a potent circadian entrainer, we also investigated the impact of an acute 13-hour fast on ENS activity. Our findings reveal that enteric neuronal activity typically increases during the dark phase but shifts to the light phase following an acute fast. Importantly, these changes in neuronal activity were not accompanied by alterations in the gene expression of associated neurotransmitter receptors.},
}
@article {pmid39763118,
year = {2025},
author = {Hu, H and Wang, Y and Zhao, DG and Lu, X},
title = {Oral Delivery of 5-Demethylnobiletin by Media-Milled Black Rice Particle-Stabilized Pickering Emulsion Alleviates Colitis in Mice: Synergistic Effects of Carrier and Loaded Bioactive.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c08558},
pmid = {39763118},
issn = {1520-5118},
abstract = {Traditional colitis treatment strategies have issues such as side effects and poor lesion targeting. In this study, a milled black rice particle-stabilized Pickering emulsion (BR-5-DMN) has been developed as a delivery vehicle for 5-demethylnobiletin (5-DMN) to treat colitis. The alleviating effects of three 5-DMN delivery systems: BR-5-DMN, Tween 80 emulsion for upper gastrointestinal delivery, and soybean oil with most 5-DMN entering the colon were compared. BR-5-DMN exhibited superior effects, enhancing 5-DMN absorption and metabolic conversion. It also improved intestinal barrier function and microbiome homeostasis, restoring short-chain fatty acid synthesis, especially acetic acid, through releasing dietary fiber, bioactives from black rice, and 5-DMN in the colon. Black rice particles in BR-5-DMN promoted the growth of Bifidobacterium while inhibiting Ruminococcus, and both black rice particles and 5-DMN synergistically increased Akkermansia abundance. This study highlights the potential of milled grain particle-stabilized emulsions as effective vehicles for bioactives to treat colitis by regulating gastrointestinal release and synergistic interactions.},
}
@article {pmid39763052,
year = {2025},
author = {Gruber, T and Lang, C and Fliegerová, K and Terler, G and Zebeli, Q and Hartinger, T},
title = {An In Vitro Nutritional Evaluation of Mixed Silages of Drought-Impaired Grass and Sugar Beet Pulp With or Without Silage Inoculants.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.14092},
pmid = {39763052},
issn = {1439-0396},
support = {//This study was supported by the Austrian Federal Ministry of Agriculture, Forestry, Regions and Water Management (Grant 101623)./ ; },
abstract = {Increasing droughts adversely affect grasslands, diminishing the availability and quality of forages for ruminants. We have recently shown that mixed ensiling of drought-impaired grass (DIG) with sugar beet pulp (SBP) improved the conservation and feed value of silage. The application of silage additives may further improve the ruminal degradability, which may thereby shape the fermentation and microbiome in the rumen when those silages are tested as part of dairy diets. Therefore, we performed a long-term in vitro nutritional evaluation of diets containing 50% (DM basis) of mixed silages from DIG and SBP, ensiled either with no additive (T_CON) or with anaerobic fungi culture supernatant (25% in DM; T_AF), mixed ruminal fluid (10% in DM; T_RF) or lactic acid bacteria (1% in FM; T_LAB). The data showed a high degradability of all diets (e.g., > 70% for organic matter), though without differences in nutrient degradabilities among treatments (p > 0.05). Fermentation characteristics, such as ruminal pH, short-chain fatty acid profile, and gas production were only marginally affected by the treatments. Isobutyric acid proportion was higher in T_CON than in T_AF (p = 0.01), whereas isovaleric acid proportion was lower in T_LAB than in T_RF (p = 0.01). The analysis of the bacterial community revealed similar diversity and structure across all treatments in both the liquid and solid fraction. Noteworthy, Lactobacillus was among the predominant genera in the liquid fraction, which may have derived from the mixed silages. In conclusion, mixed silages from DIG and SBP as part of a 50% concentrate diet showed high ruminal degradability, but no beneficial impact by the tested silage additives was observed. Hence, under these conditions, their application appears not justified. Our results warrant further in vivo verification, whereby it would be of interest to determine the impact of the applied silage additives in forage-based diets (e.g., > 50% silage in diet DM) in future research.},
}
@article {pmid39763003,
year = {2025},
author = {Feng, Y and Lu, X and Zhao, J and Li, H and Xu, J and Li, Z and Wang, M and Peng, Y and Tian, T and Yuan, G and Zhang, Y and Liu, J and Zhang, M and Zhu La, AT and Qu, G and Mu, Y and Guo, W and Wu, Y and Zhang, Y and Wang, D and Hu, Y and Kan, B},
title = {Regional antimicrobial resistance gene flow among the One Health sectors in China.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {3},
pmid = {39763003},
issn = {2049-2618},
support = {2022YFC2303900//National Key Research and Development Program of China/ ; 22193064//major projects of the National Natural Science Foundation of China/ ; },
mesh = {Humans ; China ; *Gene Transfer, Horizontal ; *One Health ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; *Gene Flow ; Feces/microbiology ; Drug Resistance, Bacterial/genetics ; Food Microbiology ; Metagenomics/methods ; Genes, Bacterial/genetics ; },
abstract = {BACKGROUND: Antimicrobial resistance poses a significant threat to global health, with its spread intricately linked across human, animal, and environmental sectors. Revealing the antimicrobial resistance gene (ARG) flow among the One Health sectors is essential for better control of antimicrobial resistance.<br><br>RESULTS: In this study, we investigated regional ARG transmission among humans, food, and the environment in Dengfeng, Henan Province, China by combining large-scale metagenomic sequencing with culturing of resistant bacterial isolates in 592 samples. A total of 40 ARG types and 743 ARG subtypes were identified, with a predominance of multidrug resistance genes. Compared with microbes from human fecal samples, those from food and environmental samples showed a significantly higher load of ARGs. We revealed that dietary habits and occupational exposure significantly affect ARG abundance. Pseudomonadota, particularly Enterobacteriaceae, were identified as the main ARG carriers shaping the resistome. The resistome in food samples was found more affected by mobile genetic elements (MGEs), whereas in environmental samples, it was more associated with the microbial composition. We evidenced that horizontal gene transfer (HGT) mediated by plasmids and phages, together with strain transmission, particularly those associated with the Enterobacteriaceae members, drive regional ARG flow. Lifestyle, dietary habits, and occupational exposure are all correlated with ARG dissemination and flies and food are important potential sources of ARGs to humans. The widespread mobile carbapenemase gene, OXA-347, carried by non-Enterobacteriaceae bacteria in the human gut microbiota, requires particular attention. Finally, we showed that machine learning models based on microbiome profiles were effective in predicting the presence of carbapenem-resistant strains, suggesting a valuable approach for AMR surveillance.<br><br>CONCLUSIONS: Our study provides a full picture of regional ARG transmission among the One Health sectors in a county-level city in China, which facilitates a better understanding of the complex routes of ARG transmission and highlights new points of focus for AMR surveillance and control. Video Abstract.},
}
@article {pmid39762999,
year = {2025},
author = {Liu, Z and Tsai, T and Zuo, B and Howe, S and Farrar, JE and Randolph, CE and Maxwell, CV and Zhao, J},
title = {The sow vaginal and gut microbiota associated with longevity and reproductive performance.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {6},
pmid = {39762999},
issn = {1674-9782},
support = {P20 GM121293/GM/NIGMS NIH HHS/United States ; 2023YFE0124400//National Key Research and Development Program of China/ ; 2023B10564001//Specific university discipline construction project/ ; Arkansas Biosciences Institute//Arkansas Biosciences Institute/ ; },
abstract = {BACKGROUND: Sow longevity and reproductivity are essential in the modern swine industry. Although many studies have focused on the genetic and genomic factors for selection, little is known about the associations between the microbiome and sows with longevity in reproduction.<br><br>RESULTS: In this study, we collected and sequenced rectal and vaginal swabs from 48 sows, nine of which completed up to four parities (U4P group), exhibiting reproductive longevity. We first identified predictors of sow longevity in the rectum (e.g., Akkermansia) and vagina (e.g., Lactobacillus) of the U4P group using RandomForest in the early breeding stage of the first parity. Interestingly, these bacteria in the U4P group showed decreased predicted KEGG gene abundance involved in the biosynthesis of amino acids. Then, we tracked the longitudinal changes of the microbiome over four parities in the U4P sows. LEfSe analysis revealed parity-associated bacteria that existed in both the rectum and vagina (e.g., Streptococcus in Parity 1, Lactobacillus in Parity 2, Veillonella in Parity 4). We also identified patterns of bacterial change between the early breeding stage (d 0) and d 110, such as Streptococcus, which was decreased in all four parties. Furthermore, sows in the U4P group with longevity potential also showed better reproductive performance. Finally, we discovered bacterial predictors (e.g., Prevotellaceae NK3B31 group) for the total number of piglets born throughout the four parities in both the rectum and vagina.<br><br>CONCLUSIONS: This study highlights how the rectal and vaginal microbiome in sows with longevity in reproduction changes within four parities. The identification of parity-associated, pregnancy-related, and reproductive performance-correlated bacteria provides the foundation for targeted microbiome modulation to improve animal production.},
}
@article {pmid39762979,
year = {2025},
author = {Oh, S and Kim, J and Shin, CM and Lee, HJ and Lee, HS and Park, KU},
title = {Metagenomic characterization of oral microbiome signatures to predict upper gastrointestinal and pancreaticobiliary cancers: a case-control study.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {20},
pmid = {39762979},
issn = {1479-5876},
support = {16-2021-0007//Seoul National University Bundang Hospital/ ; },
mesh = {Humans ; Case-Control Studies ; *Metagenomics/methods ; *Pancreatic Neoplasms/microbiology/diagnosis ; Female ; Male ; Middle Aged ; *Microbiota/genetics ; Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Aged ; Metagenome ; Saliva/microbiology ; Biliary Tract Neoplasms/microbiology/diagnosis ; Gastrointestinal Neoplasms/microbiology/diagnosis ; },
abstract = {BACKGROUND: This study investigated the oral microbiome signatures associated with upper gastrointestinal (GI) and pancreaticobiliary cancers.<br><br>METHODS: Saliva samples from cancer patients and age- and sex-matched healthy controls were analyzed using 16S rRNA-targeted sequencing, followed by comprehensive bioinformatics analysis.<br><br>RESULTS: Significant dissimilarities in microbial composition were observed between cancer patients and controls across esophageal cancer (EC), gastric cancer (GC), biliary tract cancer (BC), and pancreatic cancer (PC) groups (R[2]&#x2009;=&#x2009;0.067,&#x2009;=&#x2009;0.075,&#x2009;=&#x2009;0.068, and&#x2009;=&#x2009;0.044; p&#x2009;=&#x2009;0.001,&#x2009;=&#x2009;0.001,&#x2009;=&#x2009;0.002, and&#x2009;=&#x2009;0.004, respectively). Additionally, the oral microbiome composition significantly differed by the four cancer sites (p&#x2009;=&#x2009;0.001 for EC vs. GC, EC vs. BC, EC vs. PC, GC vs. BC, and GC vs. PC; p&#x2009;=&#x2009;0.013 for BC vs. PC). We built oral metagenomic classifiers to predict cancer and selected specific microbial taxa with diagnostic properties. For EC, the classifier differentiated cancer patients and controls with good accuracy (area under the curve [AUC]&#x2009;=&#x2009;0.791) and included three genera: Akkermansia, Escherichia-Shigella, and Subdoligranulum. For GC, the classifier exhibited high discriminative power (AUC&#x2009;=&#x2009;0.961); it included five genera (Escherichia-Shigella, Gemella, Holdemanella, Actinomyces, and Stomatobaculum) and three species (Eubacterium sp. oral clone EI074, Ruminococcus sp. Marseille-P328, and Leptotrichia wadei F0279). However, microbial taxa with diagnostic features for BC and PC were not identified.<br><br>CONCLUSIONS: These findings suggested that the oral microbiome composition may serve as an indicator of tumorigenesis in upper GI and pancreaticobiliary cancers. The development of oral metagenomic classifiers for EC and GC demonstrates the potential value of microbial biomarkers in cancer screening.},
}
@article {pmid39762949,
year = {2025},
author = {Ferreira, C and Burgsdorf, I and Perez, T and Ramírez, G and Lalzar, M and Huchon, D and Steindler, L},
title = {Comparative genomics analyses of Actinobacteriota identify Golgi phosphoprotein 3 (GPP34) as a widespread ancient protein family associated with sponge symbiosis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {4},
pmid = {39762949},
issn = {2049-2618},
support = {GBMF9352//Gordon and Betty Moore Foundation/ ; 933/23//Israel Science Foundation/ ; },
mesh = {*Symbiosis ; *Porifera/microbiology ; *Phylogeny ; Animals ; *Genomics ; Bacterial Proteins/genetics/metabolism ; Phosphoproteins/genetics ; Multigene Family ; Genome, Bacterial ; Actinobacteria/genetics/classification ; },
abstract = {BACKGROUND: Sponges harbor microbial communities that play crucial roles in host health and ecology. However, the genetic adaptations that enable these symbiotic microorganisms to thrive within the sponge environment are still being elucidated. To understand these genetic adaptations, we conducted a comparative genomics analysis on 350 genomes of Actinobacteriota, a phylum commonly associated with sponges.<br><br>RESULTS: Our analysis uncovered several differences between symbiotic and free-living bacteria, including an increased abundance of genes encoding prokaryotic defense systems (PDSs) and eukaryotic-like proteins (ELPs) in symbionts. Furthermore, we identified GPP34 as a novel symbiosis-related gene family, found in two symbiotic Actinobacteriota clades, but not in their closely related free-living relatives. Analyses of a broader set of microbes showed that members of the GPP34 family are also found in sponge symbionts across 16 additional bacterial phyla. While GPP34 proteins were thought to be restricted to eukaryotes, our phylogenetic analysis shows that the GPP34 domain is found in all three domains of life, suggesting its ancient origin. We also show that the GPP34 family includes genes with two main structures: a short form that includes only the GPP34 domain and a long form that encompasses a GPP34 domain coupled with a cytochrome P450 domain, which is exclusive to sponge symbiotic bacteria.<br><br>CONCLUSIONS: Given previous studies showing that GPP34 is a phosphatidylinositol-4-phosphate (PI4P)-binding protein in eukaryotes and that other PI4P-binding proteins from bacterial pathogens can interfere with phagolysosome maturation, we propose that symbionts employ GPP34 to modulate phagocytosis to colonize and persist within sponge hosts. Video Abstract.},
}
@article {pmid39762941,
year = {2025},
author = {Hares, MF and Griffiths, BE and Barningham, L and Vamos, EE and Gregory, R and Duncan, JS and Oikonomou, G and Stewart, CJ and Coombes, JL},
title = {Progression of the faecal microbiome in preweaning dairy calves that develop cryptosporidiosis.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {3},
pmid = {39762941},
issn = {2524-4671},
support = {BB/M011186/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {BACKGROUND: Cryptosporidiosis is a diarrheal disease that commonly affects calves under 6 weeks old. The causative agent, Cryptosporidium parvum, has been associated with the abundance of specific taxa in the faecal microbiome during active infection. However, the long-term impact of these microbiome shifts, and potential effects on calf growth and health have not yet been explored in depth.<br><br>METHODS: Three hundred and forty-six (346) calves from three dairy farms had one faecal swab collected during the first week of life (W1). Thereafter, sampled calves were monitored for diarrhoeal disease and those that suffered a diarrhoea event were tested for C. parvum by lateral flow testing (LFT). Calves that experienced diarrhoea and tested positive for C. parvum by LFT were assigned to the Cryptosporidium-positive (Cp+) group (n&#x2009;=&#x2009;32). Matched healthy (H) controls with no history of diarrhoea were selected from the remaining cohort (n&#x2009;=&#x2009;33). The selected subset of calves (n&#x2009;=&#x2009;65) was observed until weaning, collecting a faecal swab, at approximately Week 5 (W5) and Week 10 (W10) after birth, resulting in a total of 191 samples (W1; n&#x2009;=&#x2009;65, W5; n&#x2009;=&#x2009;64, W10; n&#x2009;=&#x2009;62). 16S rRNA gene amplicon sequencing was performed on all extracted samples.<br><br>RESULTS: Analysis of the longitudinal microbiome showed significant changes in the microbial diversity and composition across all three time-points. Whilst Firmicutes were elevated in the Cp+&#x2009;group at W5 compared to the H group, no other significant differences were detected between H and Cp+&#x2009;groups. Whilst the core microbiota showed some taxa were exclusive to each group, the role of these taxa in health and disease has yet to be determined. Antibiotics were also found to have an impact on the relative abundance of some taxa. Though healthy calves received a significantly higher body condition score than Cp+&#x2009;calves at W5, the difference did not reach significance at W10, suggesting that Cp+&#x2009;calves may catch up to their healthy counterparts once the infection has resolved.<br><br>CONCLUSIONS: The findings of this study illustrated the changes in the microbial diversity and composition during the preweaning period in dairy calves. The results also indicated that the faecal microbiome is not predictive of cryptosporidiosis and implied that cryptosporidiosis doesn't cause long-term gut dysbiosis. This study furthered our understanding of the parasite-microbiome relationship and its impact on the bovine host.},
}
@article {pmid39762879,
year = {2025},
author = {Tidbury, F and Brülhart, G and Müller, G and Pavicic, E and Weidlinger, S and Eichner, G and von Wolff, M and Stute, P},
title = {Effectiveness and tolerability of lactic acid vaginal gel compared to oral metronidazole in the treatment of acute symptomatic bacterial vaginosis: a multicenter, randomized-controlled, head-to-head pilot study.},
journal = {BMC women's health},
volume = {25},
number = {1},
pages = {7},
pmid = {39762879},
issn = {1472-6874},
mesh = {Humans ; Female ; *Vaginosis, Bacterial/drug therapy ; *Metronidazole/therapeutic use/administration &amp; dosage ; Pilot Projects ; Adult ; *Lactic Acid/therapeutic use/administration &amp; dosage ; *Vaginal Creams, Foams, and Jellies/administration &amp; dosage/therapeutic use ; Administration, Oral ; Treatment Outcome ; Young Adult ; Administration, Intravaginal ; Acute Disease ; },
abstract = {BACKGROUND: Bacterial vaginosis (BV) is a prevalent vaginal condition among reproductive-age women, characterized by off-white, thin vaginal discharge with a fishy odor. It increases susceptibility to sexually transmitted diseases (STDs) and pelvic inflammatory disease (PID). BV involves a shift in vaginal microbiota, with reduced lactobacilli and increased anaerobic bacteria. Standard treatment with oral metronidazole has been shown to have a limited long-term efficacy, possibly due to biofilm persistence. Alternative treatments, such as lactic acid vaginal gel, aim to restore vaginal pH and lactobacilli. This pilot study compares the efficacy and tolerability of lactic acid gel to standard oral metronidazole for acute BV treatment in non-pregnant women.<br><br>METHODS: A total of 32 women with acute BV were recruited and assigned to either the treatment group (n&#x2009;=&#x2009;16) where they applied a lactic acid vaginal gel for 12 days, or the control group (n&#x2009;=&#x2009;16) which received 500&#xa0;mg oral metronidazole twice daily for seven days. A number of objective and subjective parameters including the Amsel score, the Nugent score and a subjective symptom score were recorded at day 0, three weeks, three months, and six months after the study start.<br><br>RESULTS: In the short-term, lactic acid vaginal gel showed inferior clinical (Amsel criteria) and microbiological (Nugent score) cure rates compared to metronidazole. However, it performed equally well regarding subjective symptom improvement and BV recurrence prevention after up to six months.<br><br>CONCLUSION: Lactic acid vaginal gel was generally very well tolerated and showed mixed but promising results as a stand-alone treatment for acute BV.<br><br>TRIAL REGISTRATION NUMBER: NCT02042287 (22.01.2014).},
}
@article {pmid39762846,
year = {2025},
author = {Hillmann, J and Maass, N and Bauerschlag, DO and Flörkemeier, I},
title = {Promising new drugs and therapeutic approaches for treatment of ovarian cancer-targeting the hallmarks of cancer.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {10},
pmid = {39762846},
issn = {1741-7015},
mesh = {Humans ; *Ovarian Neoplasms/drug therapy ; Female ; *Antineoplastic Agents/therapeutic use ; Molecular Targeted Therapy/methods ; Tumor Microenvironment/drug effects ; Genomic Instability/drug effects ; },
abstract = {Ovarian cancer remains the most lethal gynecological malignancy. Despite the approval of promising targeted therapy such as bevacizumab and PARP inhibitors, 5-year survival has not improved significantly. Thus, there is an urgent need for new therapeutics. New advancements in therapeutic strategies target the pivotal hallmarks of cancer. This review is giving an updated overview of innovative and upcoming therapies for the treatment of ovarian cancer that focuses specific on the hallmarks of cancer. The hallmarks of cancer constitute a broad concept to reenact complexity of malignancies and furthermore identify possible targets for new treatment strategies. For this purpose, we analyzed approvals and current clinical phase III studies (registered at ClinicalTrials.gov (National Library of Medicine, National Institutes of Health; U.S. Department of Health and Human Services, 2024)) for new drugs on the basis of their mechanisms of action and identified new target approaches. A broad spectrum of new promising drugs is currently under investigation in clinical phase III studies targeting mainly the hallmarks "self-sufficiency in growth signals," "genomic instability," and "angiogenesis." The benefit of immune checkpoint inhibitors in ovarian cancer has been demonstrated for the first time. Besides, targeting the tumor microenvironment is of growing interest. Replicative immortality, energy metabolism, tumor promoting inflammation, and the microbiome of ovarian cancer are still barely targeted by drugs. Nevertheless, precision medicine, which focuses on specific disease characteristics, is becoming increasingly important in cancer treatment.},
}
@article {pmid39762435,
year = {2025},
author = {Fackelmann, G and Manghi, P and Carlino, N and Heidrich, V and Piccinno, G and Ricci, L and Piperni, E and Arrè, A and Bakker, E and Creedon, AC and Francis, L and Capdevila Pujol, J and Davies, R and Wolf, J and Bermingham, KM and Berry, SE and Spector, TD and Asnicar, F and Segata, N},
title = {Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39762435},
issn = {2058-5276},
support = {microTOUCH-101045015)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {As plant-based diets gain traction, interest in their impacts on the gut microbiome is growing. However, little is known about diet-pattern-specific metagenomic profiles across populations. Here we considered 21,561 individuals spanning 5 independent, multinational, human cohorts to map how differences in diet pattern (omnivore, vegetarian and vegan) are reflected in gut microbiomes. Microbial profiles distinguished these common diet patterns well (mean AUC = 0.85). Red meat was a strong driver of omnivore microbiomes, with corresponding signature microbes (for example, Ruminococcus torques, Bilophila wadsworthia and Alistipes putredinis) negatively correlated with host cardiometabolic health. Conversely, vegan signature microbes were correlated with favourable cardiometabolic markers and were enriched in omnivores consuming more plant-based foods. Diet-specific gut microbes partially overlapped with food microbiomes, especially with dairy microbes, for example, Streptococcus thermophilus, and typical soil microbes in vegans. The signatures of common western diet patterns can support future nutritional interventions and epidemiology.},
}
@article {pmid39762344,
year = {2025},
author = {Battistolli, M and Varponi, I and Romoli, O and Sandrelli, F},
title = {The circadian clock gene period regulates the composition and daily bacterial load of the gut microbiome in Drosophila melanogaster.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1016},
pmid = {39762344},
issn = {2045-2322},
support = {765937//European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie/ ; P2022MZAF8//Finanziamento dell'Unione Europea - NextGenerationEU - PNRR Missione 4, Componente 2, Investimento 1.1/ ; },
mesh = {Animals ; *Drosophila melanogaster/microbiology ; *Gastrointestinal Microbiome/genetics ; *Period Circadian Proteins/genetics/metabolism ; *Circadian Clocks/genetics ; Drosophila Proteins/genetics/metabolism ; Bacterial Load ; Circadian Rhythm/physiology ; Bacteria/genetics/classification ; },
abstract = {While Drosophila melanogaster serves as a crucial model for investigating both the circadian clock and gut microbiome, our understanding of their relationship in this organism is still limited. Recent analyses suggested that the Drosophila gut microbiome modulates the host circadian transcriptome to minimize rapid oscillations in response to changing environments. Here, we examined the composition and abundance of the gut microbiota in wild-type and arrhythmic per[01] flies, under 12 h:12 h light: dark (12:12 LD) and constant darkness (DD) conditions. The gut microbiota of wild-type and per[01] flies showed differences in composition, suggesting that the D. melanogaster circadian gene per has a role in shaping the gut microbiome. In 12:12 LD and DD conditions, per[01] mutants showed significant daily variations in gut bacterial quantity, unlike wild-type flies. This suggests that per is involved in maintaining the daily stability of gut microbiome load in D. melanogaster. Expanding these analyses to other fly strains with disrupted circadian clocks will clarify whether these effects originate from a circadian function of per or from its possible pleiotropic effects. Finally, some gut bacteria exhibited significant 24 h fluctuations in their relative abundance, which appeared independent from the fly circadian clock, suggesting that certain gut commensal bacteria in Drosophila may possess a host-independent circadian clock.},
}
@article {pmid39762302,
year = {2025},
author = {Kim, MJ and Song, MH and Ji, YS and Park, JW and Shin, YK and Kim, SC and Kim, G and Cho, B and Park, H and Ku, JL and Jeong, SY},
title = {Cell free supernatants of Bifidobacterium adolescentis and Bifidobacterium longum suppress the tumor growth in colorectal cancer organoid model.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {935},
pmid = {39762302},
issn = {2045-2322},
support = {2021M3H9A1030151//National Research Foundation, South Korea/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/metabolism ; *Bifidobacterium longum/metabolism ; *Organoids/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Bifidobacterium adolescentis/metabolism ; Female ; Male ; Probiotics ; Middle Aged ; Aged ; Cell Proliferation ; Cell Line, Tumor ; },
abstract = {The probiotic gut microbiome and its metabolites are pivotal in regulating host metabolism, inflammation, and immunity. Host genetics, colonization at birth, the host lifestyle, and exposure to diseases and drugs determine microbial composition. Dysbiosis and disruption of homeostasis in the beneficial microbiome have been reported to be involved in the tumorigenesis and progression of colorectal cancer (CRC). However, the influence of bacteria-secreted metabolites on CRC growth is yet to be fully elucidated. In this study, we compared the microbial composition of CRC patients to healthy controls to identify distinct patterns of microbiota-derived metabolites in CRC patients. Metagenomic analysis demonstrated that beneficial bacteria strains; Blautia producta, Bifidobacterium adolescentis, and Bifidobacterium longum decreased, while Parabacteroides distasonis and Bacteroides ovatus were more prevalent in the CRC patient group. Treatment of cancer organoid lines with microbial culture supernatants from Blautia producta, Bifidobacterium adolescentis, and Bifidobacterium longum showed remarkable inhibition of cancer growth. This study demonstrates that the bacterial metabolites depleted in CRC patients may inhibit cancer growth and highlights the effects of microbiome-derived metabolites on CRC growth.},
}
@article {pmid39762283,
year = {2025},
author = {Feng, C and Wu, Y and Zhang, X and Wang, S and Wang, J and Yang, H},
title = {Maternal milk fat globule membrane enriched gut L. murinus and circulating SCFAs to improve placental efficiency and fetal development in intrauterine growth restricted mice model.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2449095},
doi = {10.1080/19490976.2024.2449095},
pmid = {39762283},
issn = {1949-0984},
mesh = {Animals ; Female ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Placenta/metabolism ; *Fetal Growth Retardation/metabolism ; *Glycoproteins/metabolism ; *Fatty Acids, Volatile/metabolism ; *Lipid Droplets/metabolism ; *Glycolipids/metabolism ; *Fetal Development/drug effects ; *Disease Models, Animal ; Lactobacillus ; Mice, Inbred C57BL ; Fecal Microbiota Transplantation ; },
abstract = {Intrauterine growth restriction (IUGR) caused by placental dysfunctions leads to fetal growth defects. Maternal microbiome and its metabolites have been reported to promote placental development. Milk fat globule membrane (MFGM) is known for its diverse bioactive functions, while the effects of gestational MFGM supplementation on the maternal gut microbiota, placental efficiency, and fetal development remained unclear. In this study, low protein diet-induced IUGR decreased the litter birth weight, fetal birth weight, and the fetal/placental ratio in pregnant mice, while gestational MFGM supplementation restored these impairments. Meanwhile, MFGM supplementation during gestation enriched intestinal Lactobacillus murinus (L. murinus) and increased luminal and circulating short chain fatty acids (SCFAs) in IUGR pregnant mice, which improved placental efficiency and fetal development due to an enhanced antioxidant capacity and a decreased inflammation. In addition, fecal microbiota transplantation (FMT) with MFGM-derived microbiota reprinted the promoted phenotypes of maternal litter characteristics, gut L. murinus enrichment, placental efficiency, and fetal gut development in MFGM-fed pregnant mice, which were also recapitulated by exogenous administration with L. murinus or SCFAs cocktail. Mechanically, MFGM, MFGM-derived microbiota, L. murinus, or SCFAs cocktail activated IUGR-induced depressive phosphorylation of PI3K-Akt signaling in the placenta. Moreover, in vitro placental cells cultivation under amino acid shortage model (AAS) or oxygen-glucose shortage model (OGS) was used to validate that MFGM-derived key microbial and circulating SCFAs cocktails can alleviate placental oxidative stress and inflammation via activating PI3K/Akt signaling. Taken together, gestational MFGM supplementation enriched intestinal L. murinus and circulating SCFAs of IUGR pregnant mice, thereby improving placental efficiency, fetal growth, and intestinal functions of IUGR fetus. Our findings will provide theoretical support for the application of MFGM in the maternal-placental-fetal nutrition to address pregnancy malnutrition-induced IUGR.},
}
@article {pmid39762227,
year = {2025},
author = {Ding, J and Liu, F and Zeng, J and Gu, H and Huang, J and Wu, B and Shu, L and Yan, Q and He, Z and Wang, C},
title = {Depth heterogeneity of lignin-degrading microbiome and organic carbon processing in mangrove sediments.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {5},
pmid = {39762227},
issn = {2055-5008},
mesh = {*Geologic Sediments/microbiology ; *Lignin/metabolism ; *Microbiota ; *Carbon/metabolism ; *Wetlands ; *Metagenomics/methods ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Biomass ; Metagenome ; Sequence Analysis, DNA ; },
abstract = {Mangrove ecosystems are globally recognized for their blue carbon (C) sequestration capacity. Lignocellulosic detritus constitutes the primary C input to mangrove sediments, but the microbial processes involved in its bioprocessing remain unclear. Using lignocellulosic analysis and metagenomic sequencing across five 100-cm sediment cores, we found a high proportion of lignin (95.0-97.7%) within sediments' lignocellulosic detritus, with a small fraction of lignin-degrading genes (1.24-1.98%) of lignin-degrading genes within the carbohydrate-active enzyme coding genes. Depth stratification was observed in genes and microbial communities involved in lignin depolymerization and mineralization of lignin monomer derivatives. Further microbe-centered analyses of biomass production rates and adaptive metabolism revealed diminished microbial C use efficiency potential and augmented "enzyme latch" with increasing sediment depths. These findings enhance our understanding of sedimentary organic C cycling and storage in coastal blue C ecosystems.},
}
@article {pmid39762141,
year = {2025},
author = {Nguyen, PN and Rehan, SM},
title = {Supporting wild bee development with a bacterial symbiont.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae317},
pmid = {39762141},
issn = {1365-2672},
abstract = {AIMS: Wild bees foster diverse microbiota that may determine survival success of developing larvae. Here, we compare survivorship and microbial communities of Ceratina calcarata small carpenter bees reared from eggs across three treatments: maternally collected control provisions with diverse microbiota, sterile provisions, and probiotic provisions supplemented with a beneficial symbiont, Apilactobacillus kunkeei.<br><br>METHODS AND RESULTS: Survival probability and adult masses differed across treatments, with the probiotic treatment resulting in highest survivorship and masses. By comparing the bacterial (16S rRNA), fungal (ITS), and plant (rbcL) communities of adults reared across treatments, we characterized distinct microbial communities across each that suggest the microbiome may be sensitive to microbial succession and competition.<br><br>CONCLUSIONS: We describe positive implications for the usage of probiotics on wild bees. Furthermore, the sensitivity of bee microbiota's relationships to their host, floral resources, and the environment suggests that holistic approaches best encapsulate the complex network of interactions between bees and their microbes.},
}
@article {pmid39762111,
year = {2025},
author = {Al-Shakhshir, S and Quraishi, MN and Mullish, B and Patel, A and Vince, A and Rowe, A and Homer, V and Jackson, N and Gyimah, D and Shabir, S and Manzoor, S and Cooney, R and Alrubaiy, L and Quince, C and van Schaik, W and Hares, M and Beggs, AD and Efstathiou, E and Rimmer, P and Weston, C and Iqbal, T and Trivedi, PJ},
title = {FAecal micRobiota transplantation in primary sclerosinG chOlangitis (FARGO): study protocol for a randomised, multicentre, phase IIa, placebo-controlled trial.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e095392},
doi = {10.1136/bmjopen-2024-095392},
pmid = {39762111},
issn = {2044-6055},
mesh = {Adult ; Female ; Humans ; Male ; *Cholangitis, Sclerosing/therapy ; Clinical Trials, Phase II as Topic ; *Fecal Microbiota Transplantation/methods ; Gastrointestinal Microbiome ; Inflammatory Bowel Diseases/therapy/microbiology ; Multicenter Studies as Topic ; Randomized Controlled Trials as Topic ; Treatment Outcome ; },
abstract = {INTRODUCTION: Primary sclerosing cholangitis (PSC) is the classical hepatobiliary manifestation of inflammatory bowel disease (IBD). The strong association between gut and liver inflammation has driven several pathogenic hypotheses to which the intestinal microbiome is proposed to contribute. Pilot studies of faecal microbiota transplantation (FMT) in PSC and IBD are demonstrated to be safe and associated with increased gut bacterial diversity. However, the longevity of such changes and the impact on markers of disease activity and disease progression have not been studied. The aim of this clinical trial is to determine the effects of repeated FMT as a treatment for PSC-IBD.<br><br>METHODS AND ANALYSIS: FAecal micRobiota transplantation in primary sclerosinG chOlangitis (FARGO) is a phase IIa randomised placebo-controlled trial to assess the efficacy and safety of repeated colonic administration of FMT in patients with non-cirrhotic PSC-IBD. Fifty-eight patients will be recruited from six sites across England and randomised in a 1:1 ratio between active FMT or FMT placebo arms. FMT will be manufactured by the University of Birmingham Microbiome Treatment Centre, using stool collected from rigorously screened healthy donors. A total of 8&#x2009;weekly treatments will be delivered; the first through colonoscopic administration (week 1) and the remaining seven via once-weekly enema (up to week 8). Participants will then be followed on a 12-weekly basis until week 48 from the first treatment visit. The primary efficacy outcome will be to determine the effect of FMT on serum alkaline phosphatase values over time (end of study at 48 weeks). Key secondary outcomes will be to evaluate the impact of FMT on other liver biochemical parameters, PSC risk scores, circulating and imaging markers of liver fibrosis, health-related quality of life measures, IBD activity and the incidence of PSC-related clinical events. Key translational objectives will be to identify mucosal metagenomic, metatranscriptomic, metabolomic and immunological pathways associated with the administration of FMT.<br><br>ETHICS AND DISSEMINATION: The protocol was approved by the South Central-Hampshire B Research Ethics Committee (REC 23/SC/0147). Participants will be required to provide written informed consent. The results of this trial will be disseminated through national and international presentations and peer-reviewed publications.<br><br>TRIAL REGISTRATION NUMBER: The trial was registered at ClinicalTrials.gov on 23 February 2024 (NCT06286709). Weblink: Study Details | FAecal Microbiota Transplantation in primaRy sclerosinG chOlangitis | ClinicalTrials.gov.},
}
@article {pmid39762107,
year = {2025},
author = {Weldegebreal, F and Ayana, DA and Wilfong, T and Dheresa, M and Yadeta, TA and Negesa, AS and Demmu, YM and Tesfa, T and Alemu, TN and Eticha, TG and Geremew, A and Roba, KT and Abdissa, A and Assefa, N and Negash, AA and Cools, P and Tura, AK},
title = {Relationship between vaginal and gut microbiome and pregnancy outcomes in eastern Ethiopia: a protocol for a longitudinal maternal-infant cohort study (the EthiOMICS study).},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e092461},
doi = {10.1136/bmjopen-2024-092461},
pmid = {39762107},
issn = {2044-6055},
mesh = {Humans ; Female ; Ethiopia ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; *Vagina/microbiology ; Infant, Newborn ; Longitudinal Studies ; *Pregnancy Outcome ; Infant ; Feces/microbiology ; Research Design ; Milk, Human/microbiology ; Adult ; },
abstract = {INTRODUCTION: Although evidence exists on the impact of microbiota on pregnancy outcomes in many high-resource settings, there is a lack of research in many low-resource settings like Ethiopia. This study aims to fill this gap by studying the gut and vaginal microbiota changes throughout pregnancy and assess how these changes relate to pregnancy outcomes among a cohort of pregnant women in eastern Ethiopia.<br><br>METHODS AND ANALYSIS: Vaginal and stool samples will be collected using DNA/RNA Shield Collection kits three times starting at 12-22 weeks, 28-36 weeks and at birth (within 7&#x2009;days). Postnatally, newborns' skin swabs (at birth) and rectal swabs will be obtained until 2 years of age. Moreover, breast milk samples at birth and 6&#x2009;months and environmental samples (water, indoor air and soil) will be collected at enrolment, birth, 6, 12 and 24 months post partum. DNA will be extracted using Roche kits. Metagenomic sequencing will be performed to identify metataxonomic profiling and assess variations in microbial profiles, and &#x3b1; and &#x3b2; diversity of the microbiota. Information on socioeconomic, behavioural, household and biological factors will be collected at enrolment. The collected data will be coded, entered into EpiData 3.1 and analysed using Stata 17.<br><br>ETHICS AND DISSEMINATION: The Institutional Health Research Ethics Review Committee (Ref No. IHRERC/033/2022) of Haramaya University, Ethiopia has approved this study ethically. Written informed consent regarding the study and sample storage for biobanking will be obtained from all participants. Results will be published in international peer-reviewed journals, and summaries will be provided to the study funders. Clinical study data will be submitted to Data Compass (https://datacompass.lshtm.ac.uk/), and molecular profiles of the microbiome and whole-genome sequences will be submitted to the European Nucleotide Archive (https://www. ebi.ac.uk/ena). Requests for data should be directed to daberaf@gmail.com. The decision to share data will be made by the study steering committee under the College of Health and Medical Sciences, Haramaya University, Ethiopia.},
}
@article {pmid39761730,
year = {2025},
author = {Ren, Y and Liu, C and Luo, J and Deng, X and Zheng, D and Shao, J and Xu, Z and Zhang, N and Xiong, W and Liu, H and Li, R and Miao, Y and Zhang, R and Shen, Q and Xun, W},
title = {Substrate preference triggers metabolic patterns of indigenous microbiome during initial composting stages.},
journal = {Bioresource technology},
volume = {419},
number = {},
pages = {132034},
doi = {10.1016/j.biortech.2024.132034},
pmid = {39761730},
issn = {1873-2976},
abstract = {Composting organic waste is a sustainable recycling method in agricultural systems, yet the microbial preferences for different substrates and their influence on composting efficiency remain underexplored. Here, 210 datasets of published 16S ribosomal DNA amplicon sequences from straw and manure composts worldwide were analyzed, and a database of 278 bacterial isolates was compiled. Substrate-driven microbiome variations were most prominent during the initial composting stages. Indigenous synthetic communities exhibit substrate-specific adaptations, increasing compost temperatures by 2 %-10 %, microbial abundance by 44 %-233 %, and microbial activity by 26 %-60 %. Key dissolved substrates, such as choline and succinic acid in straw compost, and phloretin and uric acid in manure compost, drive these microbial preferences. These findings highlight how substrate-specific microbiomes can be engineered to enhance microbial activity, accelerate temperature rise, and extend the thermophilic phase, providing a targeted framework to improve composting efficiency and tailor strategies to different organic waste types.},
}
@article {pmid39761424,
year = {2025},
author = {Luo, B and An, Q and Lei, J and Tan, D and Liu, X and Li, H and Zhao, Y and Qin, J and Zhang, C and Zhang, Y and Shi, C},
title = {Resveratrol amplifies the anti-tumor effect of α-PD-1 by altering the intestinal microbiome and PGD2 content.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2447821},
doi = {10.1080/19490976.2024.2447821},
pmid = {39761424},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Resveratrol/pharmacology ; *Prostaglandin D2/metabolism ; Animals ; *Programmed Cell Death 1 Receptor/metabolism/antagonists &amp; inhibitors ; Mice ; Humans ; Cell Line, Tumor ; },
abstract = {The anti-PD-1 mAb may be further considered along with PGD2 or active molecules that can promote PGD2 synthesis to enhance the anti-tumor immune response.},
}
@article {pmid39760535,
year = {2025},
author = {Saha, S and Schnabl, B},
title = {Modulating the microbiome in chronic liver diseases- current evidence on the role of fecal microbiota transplantation.},
journal = {Expert review of gastroenterology &amp; hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2025.2450707},
pmid = {39760535},
issn = {1747-4132},
abstract = {INTRODUCTION: The gut microbiota has a complex relationship with the human host and is key to maintaining health. Disruption of the healthy diverse gut microbial milieu plays an important role in the pathogenesis of several diseases including Clostridioides difficile infection (CDI), inflammatory bowel disease, irritable bowel syndrome, alcohol-related liver disease and metabolic-dysfunction associated steatotic liver disease (MASLD). Fecal microbiota transplantation (FMT) is highly effective in treating CDI, though its utility in other diseases is still being explored.<br><br>AREAS COVERED: In this narrative review, we explore the role of gut microbiota in liver diseases, focusing on key changes in the microbial composition and function. We summarize current evidence on the role of FMT, identifying gaps in current research and outlining future directions for investigation. We comprehensively searched PubMed through 15 October 2024 to identify relevant studies.<br><br>EXPERT OPINION: While data from available studies shows promise, more research is necessary before we can use FMT for liver diseases. Key areas that require further study are- determining the optimal FMT regimen for each disease, establishing efficacy and safety with larger clinical trials, ensuring safe and equitable access to the FMT product and mechanistic insights into the reasons for success or failure of FMT.},
}
@article {pmid39760468,
year = {2025},
author = {Sasaki-Higashimoto, I and Fujishima, F and Ishida, H and Taniyama, Y and Ozawa, Y and Nakamura, T and Nakaya, N and Sato, C and Okamoto, H and Tsunokake, J and Kunimitsu, A and Mozumi, T and Kamei, T and Suzuki, T},
title = {Histopathological study of the localization/distribution of Fusobacterium nucleatum in esophageal cancer.},
journal = {Pathology international},
volume = {},
number = {},
pages = {},
doi = {10.1111/pin.13505},
pmid = {39760468},
issn = {1440-1827},
abstract = {Fusobacterium nucleatum is implicated in esophageal cancer; however, its distribution in esophageal cancer tissues remains unknown. This study aimed to clarify the presence and distribution of F. nucleatum in esophageal cancer tissues using fluorescence in situ hybridization (FISH). Tissues collected from 70 patients with esophageal squamous cell carcinoma were examined using FISH. Corresponding normal epithelium and metastatic lymph nodes were assessed. F. nucleatum was identified more frequently in esophageal cancer tissues than in the normal epithelium. F. nucleatum also showed significant correlation with factors associated with tumor progression, such as pT factor and tumor size. As tumor progression advanced, the area occupied by F. nucleatum gradually became larger. F. nucleatum positivity was observed around the deep edge of the tumor nest (border-dense type) or identified diffusely in the tumor nest (diffuse distributed type). Furthermore, F. nucleatum was observed in metastatic lymph nodes, lesions of venous invasion, and walls of veins in normal epithelium. In conclusion, we visualized F. nucleatum using FISH and identified different distribution patterns of F. nucleatum, highlighting the spot density of its presence in tumor tissues. Recognizing this quantitative change is pivotal for establishing F. nucleatum as a reliable biomarker.},
}
@article {pmid39760464,
year = {2025},
author = {Petersen, C and Satheesh Babu, AK and Della Lucia, CM and Paz, HA and Iglesias-Carres, L and Zhong, Y and Jalili, T and Symons, JD and Shankar, K and Neilson, AP and Wankhade, UD and Anandh Babu, PV},
title = {Gut microbes metabolize strawberry phytochemicals and mediate their beneficial effects on vascular inflammation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2446375},
doi = {10.1080/19490976.2024.2446375},
pmid = {39760464},
issn = {1949-0984},
mesh = {*Fragaria/microbiology ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Mice, Inbred C57BL ; Mice ; *Dysbiosis/microbiology ; *Phytochemicals/pharmacology/metabolism ; *Diet, High-Fat/adverse effects ; Male ; Bacteria/classification/metabolism/drug effects ; Inflammation/metabolism/drug therapy ; Propionates/metabolism ; Coumaric Acids/metabolism/pharmacology ; Anti-Bacterial Agents/pharmacology ; Humans ; },
abstract = {Evidence suggests that a healthy gut microbiome is essential for metabolizing dietary phytochemicals. However, the microbiome's role in metabolite production and the influence of gut dysbiosis on this process remain unclear. Further, studies on the relationship among gut microbes, metabolites, and biological activities of phytochemicals are limited. We addressed this knowledge gap using strawberry phytochemicals as a model. C57BL/6J mice were fed a standard diet [C]; strawberry-supplemented diet (~2 human servings) [CS]; strawberry-supplemented diet and treated with antibiotics (to deplete gut microbes) [CSA]; high-fat diet (HFD) [HF]; strawberry-supplemented HFD [HS]; and strawberry-supplemented HFD and treated with antibiotics [HSA] for 12 weeks. First, antibiotic treatment suppressed the production of selected metabolites (CSA vs. CS), and p-coumaric acid was identified as a strawberry-derived microbial metabolite. Second, HFD-induced dysbiosis negatively affected metabolite production (HS vs. HF), and hippuric acid was identified as a microbial metabolite in HFD conditions. Third, dietary strawberries improved HFD-induced vascular inflammation (HS vs. HF). However, antibiotic treatment reduced metabolite production and abolished the vascular effects of strawberries (HSA vs. HS), indicating the importance of gut microbes in mediating the vascular benefits of strawberries via metabolites. Fourth, strawberry supplementation decreased Coprobacillus that was positively associated with vascular inflammation, whereas it increased Lachnospiraceae that was negatively associated with vascular inflammation and positively associated with hippuric acid. Fifth, hippuric acid was negatively associated with vascular inflammation. Our study fills in some pieces of the giant puzzle regarding the influence of gut microbes on the biological activities of phytochemicals. HFD-induced gut dysbiosis negatively impacts metabolite production and a strong association exists among gut microbes, strawberry-derived microbial metabolites, and the vascular benefits of dietary strawberries. Further, our study provides significant proof of concept to warrant future research on the use of strawberries as a nutritional strategy to prevent vascular complications.},
}
@article {pmid39760355,
year = {2024},
author = {Drude, N and Diederich, K and Duerr, CU and Haase, N and Harms, C and Heppner, F and Jendrach, M and Kahnau, P and Kolesnichenko, M and Lewejohann, L and Kurreck, C and Lohan, A and Mall, MA and Müller, D and Nagel-Riedasch, S and Opitz, B and Schaupp, L and Schönfelder, G and Weber, A and Willimsky, G and Zang, Y and Rosshart, SP and Diefenbach, A and Jordan, S},
title = {Operating and Biocontainment Procedures of a Facility for Laboratory Mice with a Natural Microbiome: Immunophenotyping Procedure.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {214},
pages = {},
doi = {10.3791/67100},
pmid = {39760355},
issn = {1940-087X},
mesh = {Animals ; Mice ; *Microbiota/immunology ; *Immunophenotyping/methods ; Containment of Biohazards/methods ; Animal Husbandry/methods ; Housing, Animal ; },
abstract = {The use of laboratory mice with a natural microbiome, such as "Wildling mice", offers a promising research tool for both basic and applied science due to their close resemblance to the human superorganism. However, the breeding and maintenance of these mice, which harbor a diverse microbiome including bacteria, viruses, and parasites, pose significant challenges for animal husbandry facilities at research institutions. To address these challenges, a specialized facility concept was developed for housing "Wildling mice" at Charité - Universitätsmedizin Berlin. This approach involved designing a facility with specific structural features and operational protocols to effectively contain the natural microbiome, thereby protecting areas with higher hygiene standards. A methodology for blood sampling from both specified pathogen-free (SPF) and "Wildling mice" for immunophenotyping is demonstrated, highlighting the workflow and biocontainment measures implemented in the facility. Remarkable results reveal that "Wildling mice" exposed to a natural microbiome develop distinct immune cell populations, which are significantly reduced in mice bred and maintained under stringent hygiene conditions. The significance of this study lies in its potential to provide researchers with access to mice that possess a natural microbiome and a mature immune system similar to that of human adults. This approach could enhance the translatability of preclinical findings into clinical practice, thereby advancing the field of biomedical research.},
}
@article {pmid39760042,
year = {2024},
author = {Jin, Y and Zhu, T and Cai, X and Fu, Z and Pan, Q and Tu, H and Wang, S and Li, Y},
title = {Identification and treatment of Enterococcus avium-induced diabetic foot ulcer: a case report and microbiome analysis.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1502337},
pmid = {39760042},
issn = {2296-858X},
abstract = {ABSTRACT: Diabetic foot ulcer (DFU) is a severe complication of diabetes. Due to conservative or delayed treatment, the majority of DFU patients frequently miss the optimal treatment window, thereby leading to amputation. Despite being a rare pathogen with low virulence, Enterococcus avium (E. avium) exhibits some antibiotic resistance and can be fatal for immunocompromised patients. This report describes a DFU case, caused by E. avium infection due to exposure to poultry. Wound microbiota was dynamically monitored using bacterial culture followed by 16S rRNA gene sequencing throughout the illness. Combination of antibiotics was administered to control the secondary infection.<br><br>CASE REPORT: A 56-year-old man presented with a two-week history of redness, swelling, heat, pain, and pus discharge from a ruptured wound on his left heel. The patient was diagnosed with osteomyelitis and a Wagner grade 3 diabetic foot ulcer infection, complicated by the soft tissue infection in the left heel. Strain identification and antibiotic susceptibility tests were immediately performed after admission. The patient underwent three debridement procedures at the DFU site. However, we observed recurrent bacterial infections, based on the clinical progression. Second-generation sequencing detected various pathogens. After targeted treatment with Vacuum sealing drainage (VSD) combined with antibiotic bone cement, the patient's condition stabilised. A skin graft was subsequently performed. Antibiotics were used to control the infection and blood glucose level was controlled throughout the treatment.<br><br>CONCLUSION: Thus, this report provides a comprehensive description of a DFU case, caused by E. avium. Antibiotics and surgical measures should be adjusted according to the pathogens responsible for wound infections in DFU patients. It is important to reduce the mortality and prevent irreversible amputations.},
}
@article {pmid39760039,
year = {2024},
author = {Qu, J and Zou, J and Zhang, J and Qu, J and Lu, H},
title = {Phage therapy for extensively drug resistant Acinetobacter baumannii infection: case report and in vivo evaluation of the distribution of phage and the impact on gut microbiome.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1432703},
pmid = {39760039},
issn = {2296-858X},
abstract = {Numerous studies have documented successful instances of bacteriophage therapy in treating infections caused by extensively drug-resistant Acinetobacter baumannii (XDRAB). However, the safety profile of phage therapy and its effects on the human gut microbiota remain areas of concern. In this study, we collected blood, sputum, and fecal samples from an elderly female patient during two phases of inhaled bacteriophage therapy targeting extensively drug-resistant Acinetobacter baumannii (XDRAB). We investigated the in vivo distribution of bacteriophages and their impact on the gut microbiome. Bacteriophage DNA was detected in blood samples exclusively during the first 4 days of the second phase of phage therapy, with Ct values ranging from 32.6 to 35.3. In sputum samples, the Ct values of phages demonstrated a decreasing trend from 45 to 14.7 during the first phase of phage therapy, subsequently stabilizing between 28.5 and 26.8 in the second phase. In fecal samples, a significant reduction in the Ct value of phages was observed following both phases of bacteriophage treatment, with values decreasing from 35.5 to 22.5 and from 32.6 to 22.7, respectively. The composition of the gut microbiota was analyzed using Illumina-based 16S rRNA sequencing from fecal samples. Sequencing analysis revealed significant alterations in the microbiota composition at both the phylum and genus levels during phage therapy. These findings suggest that inhaled phages are detectable in human blood and tend to accumulate in the intestines. Furthermore, notable changes in the gut microbiota were observed throughout the duration of the phage treatment.},
}
@article {pmid39759836,
year = {2024},
author = {Nesbø, CL and Kublanov, I and Yang, M and Sharan, AA and Meyer, T and Edwards, EA},
title = {High quality Bathyarchaeia MAGs from lignocellulose-impacted environments elucidate metabolism and evolutionary mechanisms.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae156},
pmid = {39759836},
issn = {2730-6151},
abstract = {The archaeal class Bathyarchaeia is widely and abundantly distributed in anoxic habitats. Metagenomic studies have suggested that they are mixotrophic, capable of CO2 fixation and heterotrophic growth, and involved in acetogenesis and lignin degradation. We analyzed 35 Bathyarchaeia metagenome-assembled genomes (MAGs), including the first complete circularized MAG (cMAG) of the Bathy-6 subgroup, from the metagenomes of three full-scale pulp and paper mill anaerobic digesters and three laboratory methanogenic enrichment cultures maintained on pre-treated poplar. Thirty-three MAGs belong to the Bathy-6, lineage while two are from the Bathy-8 lineage. In our previous analysis of the microbial community in the pulp mill digesters, Bathyarchaeia were abundant and positively correlated to hydrogenotrophic and methylotrophic methanogenesis. Several factors likely contribute to the success of the Bathy-6 lineage compared to Bathy-8 in the reactors. The Bathy-6 genomes are larger than those of Bathy-8 and have more genes involved in lignocellulose degradation, including carbohydrate-active enzymes not present in the Bathy-8. Bathy-6 also shares the Bathyarchaeal O-demethylase system recently identified in Bathy-8. All the Bathy-6 MAGs had numerous membrane-associated pyrroloquinoline quinone-domain proteins that we suggest are involved in lignin modification or degradation, together with Radical-S-adenosylmethionine (SAM) and Rieske domain proteins, and AA2, AA3, and AA6-family oxidoreductases. We also identified a complete B12 synthesis pathway and a complete nitrogenase gene locus. Finally, comparative genomic analyses revealed that Bathyarchaeia genomes are dynamic and have interacted with other organisms in their environments through gene transfer to expand their gene repertoire.},
}
@article {pmid39759271,
year = {2024},
author = {Guizado-Batista, A and Porres-Camacho, A and Vargas-Villalobos, S and Cortez-Martínez, M and Umaña-Castro, R and Sancho-Blanco, C and Solano-Campos, F and Quesada-Alvarado, F and Spínola-Parallada, M and Madrigal-Mora, A and Jiménez-Serrano, A and Vargas-Calvo, J and Villalobos-Sequeira, J and Stoos, KB and Blanco-Peña, K},
title = {Antimicrobial-resistant genes in feces from otters (Lontra longicaudis) within the Peñas Blancas river basin, Costa Rica.},
journal = {Heliyon},
volume = {10},
number = {24},
pages = {e40927},
pmid = {39759271},
issn = {2405-8440},
abstract = {Antimicrobial resistance poses a growing threat to human health, yet its implications for wildlife remain a subject of ongoing research. River otters inhabiting the Peñas Blancas River face exposure to various anthropogenic activities in their habitat, potentially leading to the accumulation of antibiotic-resistant genes (ARGs) with unknown consequences for their health. This study aimed to identify specific ARGs in otter feces from this river basin, employing quantitative polymerase chain reaction (qPCR), DNA sequencing of ARGs, and phylogenetic analysis techniques. Over the period from 2019 to 2022, we collected 102 fecal samples from otters through the Peñas Blancas River watershed, spanning its upper and middle basins. We assessed the bacterial presence via the 16S rRNA gene through qPCR analysis and screened for 12 ARGs. Sequences of 16 ARG-positive samples were subsequently analyzed using Maximum-likelihood-base taxonomic placement. In total, 56 samples tested positive for the 16S rRNA gene, with 24 exhibiting at least one ARG. Notably, three samples showcased a "multi-resistance microbiome". qPCR analyses identified seven distinct ARGs: tetB (in 26.8 % of the samples), sulI (21.4 %), sulII (21.4 %), qnrS (10.7 %), tetQ (8.9 %), tetW (7.1 %), and tetA (3.6 %). Phylogenetic analysis confirmed the taxonomic association of all detected ARGs, which were compared with The Comprehensive Antibiotic Resistance Database. Our findings underscore the importance of comprehending the spread of ARGs in wildlife populations, with river otters serving as potential sentinels for ARG dissemination. Moreover, they highlight the potential impact of anthropogenic activities on the health of aquatic ecosystems, emphasizing the need for proactive measures to mitigate antimicrobial resistance in natural environments.},
}
@article {pmid39759130,
year = {2024},
author = {Braadland, PR and Farnes, I and Kure, EH and Yaqub, S and McCann, A and Ueland, PM and Labori, KJ and Hov, JR},
title = {Indole 3-acetate and response to therapy in borderline resectable or locally advanced pancreatic cancer.},
journal = {Frontiers in oncology},
volume = {14},
number = {},
pages = {1488749},
pmid = {39759130},
issn = {2234-943X},
abstract = {BACKGROUND/AIMS: It was recently reported that a higher concentration of the bacterially produced metabolite indole 3-acetate (3-IAA) in blood was linked to a better response to chemotherapy in patients with metastatic pancreatic ductal adenocarcinoma (PDAC). Here, we aimed to extend these observations to patients diagnosed with non-metastatic PDAC.<br><br>METHOD: We measured circulating 3-IAA in samples from a prospective population-based cohort of 124 patients with borderline resectable or locally advanced PDAC, collected before initiating neoadjuvant chemotherapy. The majority (61%) of the patients were treated with FOLFIRINOX. We used univariable and multivariable Cox proportional hazards regression to estimate the association between pre-treatment 3-IAA and overall survival.<br><br>RESULTS: The median serum 3-IAA concentration before chemotherapy was 290 (interquartile range 203-417) ng/mL. The unadjusted hazard ratio (HR) for pre-treatment log2(3-IAA) was 0.93, 95% confidence interval (CI) [0.74-1.16], p=0.52. When adjusting for age, ECOG, CA19-9 and tumor classification, the HR for log2(3-IAA) was 0.87, 95% CI [0.68-1.12], p=0.28.<br><br>CONCLUSION: Our findings suggest that the potentiating effect of 3-IAA observed in metastatic PDAC undergoing chemotherapy may not translate to borderline resectable or locally advanced PDAC. We recommend additional clinical validation of 3-IAA's predictive value in different categories of PDAC before implementation attempts in human studies are initiated.},
}
@article {pmid39758985,
year = {2024},
author = {Yu, Y and Xia, L and Wang, Z and Zhu, T and Zhao, L and Fan, S},
title = {A cross-cohort study identifies potential oral microbial markers for esophageal squamous cell carcinoma.},
journal = {iScience},
volume = {27},
number = {12},
pages = {111453},
pmid = {39758985},
issn = {2589-0042},
abstract = {Current screening methods for esophageal squamous cell carcinoma (ESCC) face challenges such as low patient compliance and high costs. This study aimed to develop a model based on oral microbiome data for identifying ESCC. By analyzing 249 oral flora samples, we identified microbial markers associated with ESCC and constructed random forest classifiers that distinguished patients with ESCC from controls, achieving an area under the ROC curve (AUC) of 0.87. Key ESCC-associated microbial markers included Neisseria perflava and Haemophilus parainfluenzae. The classifier was validated within the cohort, attaining an AUC of 0.93. For comparison, traditional tumor markers carcinoembryonic antigen (CEA) and squamous cell carcinoma antigen (SCC-Ag) yielded AUCs of 0.84. Functional analysis identified pathways linked to ESCC, such as glycerol degradation and nitrate reduction. This study suggests a potential noninvasive method for detecting ESCC, offering a more accessible and accurate alternative to current screening methods.},
}
@article {pmid39758955,
year = {2024},
author = {Dubois, B and Delitte, M and Lengrand, S and Bragard, C and Legrève, A and Debode, F},
title = {PRONAME: a user-friendly pipeline to process long-read nanopore metabarcoding data by generating high-quality consensus sequences.},
journal = {Frontiers in bioinformatics},
volume = {4},
number = {},
pages = {1483255},
pmid = {39758955},
issn = {2673-7647},
abstract = {BACKGROUND: The study of sample taxonomic composition has evolved from direct observations and labor-intensive morphological studies to different DNA sequencing methodologies. Most of these studies leverage the metabarcoding approach, which involves the amplification of a small taxonomically-informative portion of the genome and its subsequent high-throughput sequencing. Recent advances in sequencing technology brought by Oxford Nanopore Technologies have revolutionized the field, enabling portability, affordable cost and long-read sequencing, therefore leading to a significant increase in taxonomic resolution. However, Nanopore sequencing data exhibit a particular profile, with a higher error rate compared with Illumina sequencing, and existing bioinformatics pipelines for the analysis of such data are scarce and often insufficient, requiring specialized tools to accurately process long-read sequences.<br><br>RESULTS: We present PRONAME (PROcessing NAnopore MEtabarcoding data), an open-source, user-friendly pipeline optimized for processing raw Nanopore sequencing data. PRONAME includes precompiled databases for complete 16S sequences (Silva138 and Greengenes2) and a newly developed and curated database dedicated to bacterial 16S-ITS-23S operon sequences. The user can also provide a custom database if desired, therefore enabling the analysis of metabarcoding data for any domain of life. The pipeline significantly improves sequence accuracy, implementing innovative error-correction strategies and taking advantage of the new sequencing chemistry to produce high-quality duplex reads. Evaluations using a mock community have shown that PRONAME delivers consensus sequences demonstrating at least 99.5% accuracy with standard settings (and up to 99.7%), making it a robust tool for genomic analysis of complex multi-species communities.<br><br>CONCLUSION: PRONAME meets the challenges of long-read Nanopore data processing, offering greater accuracy and versatility than existing pipelines. By integrating Nanopore-specific quality filtering, clustering and error correction, PRONAME produces high-precision consensus sequences. This brings the accuracy of Nanopore sequencing close to that of Illumina sequencing, while taking advantage of the benefits of long-read technologies.},
}
@article {pmid39758884,
year = {2025},
author = {Benson-Davies, S and Frederiksen, K and Patel, R},
title = {Bariatric nutrition and evaluation of the metabolic surgical patient: Update to the 2022 Obesity Medicine Association (OMA) bariatric surgery, gastrointestinal hormones, and the microbiome clinical practice statement (CPS).},
journal = {Obesity pillars},
volume = {13},
number = {},
pages = {100154},
pmid = {39758884},
issn = {2667-3681},
abstract = {BACKGROUND: In 2022, the Obesity Medicine Association (OMA) published a Clinical Practice Statement (CPS) which provided an overview of bariatric surgery and related procedures, a discussion on gastrointestinal hormones and a review of the microbiome as it relates to patients with obesity. This update to the 2022 OMA CPS provides a focus on nutrition as it relates to the adult bariatric surgery patient, incorporating a detailed discussion on how to conduct a bariatric nutrition assessment and manage patients seeking metabolic and bariatric surgery (MBS) and postoperative nutrition care. In particular, the section on macronutrients, micronutrients, and bariatric surgery has been updated, highlighting practical approaches to nutrient deficiencies typically encountered in the bariatric surgery patient. Also included is a section on how to envision and develop an interdisciplinary team of medical providers with evidence-based nutrition knowledge and consistent information that improves the quality of nutrition care provided to MBS patients. This CPS adds to the series of OMA CPSs meant to provide guidance to clinicians in their care of patients with obesity.<br><br>METHODS: The foundation of this paper is supported by scientific evidence in the medical literature and expert opinion derived from several bariatric nutrition resources, as well as from the 2022 OMA CPS focused on bariatric surgery.<br><br>RESULTS: This OMA Clinical Practice Statement provides an overview of the current bariatric nutrition clinical guidelines and nutrition tools adapted for clinicians who may not have access to an MBS team or a registered dietitian knowledgeable about bariatric nutrition.<br><br>CONCLUSIONS: This evidence-based review of the literature includes an overview of current bariatric nutrition recommendations. It is intended to provide clinicians with more advanced knowledge and skills in nutrition assessment and management of the preoperative and post-surgical MBS patients. This CPS also addresses macronutrient and micronutrient deficiencies common in MBS patients, and treatment recommendations designed to help the clinician with clinical decision making.},
}
@article {pmid39758630,
year = {2024},
author = {Ahmed, MMA and Hammers, C and Boudreau, PD},
title = {Dual Screen for Metal-Tolerant Metallophore Producers Evaluated with Soil from the Carpenter Snow Creek Site, a Heavy-Metal-Toxified Site in Montana.},
journal = {ACS omega},
volume = {9},
number = {52},
pages = {51213-51220},
pmid = {39758630},
issn = {2470-1343},
support = {P20 GM130460/GM/NIGMS NIH HHS/United States ; },
abstract = {Bacteria have evolved numerous mechanisms to resist metal toxicity, including small-molecule metal chelators (metallophores). This study presents a dual screening methodology to isolate metallophore-producing bacteria from the Carpenter Snow Creek Mining District for potential use in heavy-metal bioremediation. Soil samples were screened on metal-supplemented plates from which colonies were picked onto chrome azurol S (CAS)-dyed plates. Copper or cerium toxicity was used as the primary selection step, while the CAS assay revealed the excretion of metal-binding compounds. From the pool of bacteria encompassed in the native soil microbiome, fifty-one isolates were picked from metal-toxified media by colony morphology. Out of these colonies, 17 exhibited positive results in the CAS assay. 16S rRNA sequencing identified eight unique species within these CAS-positive hits, the nearest BLAST hits of which were from the genera: Rhodanobacter, Dyella, Bradyrhizobium, Luteibacter, Cupriavidus, Arthrobacter, and Paraburkholderia. To validate our workflow, we profiled our Cupriavidus isolate by LCMS metabolomics and genome mining and purified its metabolites. These efforts led to the reisolation of the known metallophore taiwachelin. In efforts to identify lead strains for heavy-metal bioremediation applications, the present work suggests the utility of our screening method in rapidly targeting the metallophore producers from the soil microbiome.},
}
@article {pmid39758363,
year = {2025},
author = {Marzouk, SH and Kwaslema, DR and Omar, MM and Mohamed, SH},
title = {"Harnessing the power of soil microbes: Their dual impact in integrated nutrient management and mediating climate stress for sustainable rice crop production" A systematic review.},
journal = {Heliyon},
volume = {11},
number = {1},
pages = {e41158},
pmid = {39758363},
issn = {2405-8440},
abstract = {Sustainable agricultural practices are essential to meet food demands for the increased population while minimizing the environmental impact. Considering rice as staple food for most of the world's population, it requires innovative approaches to ensure sustainable production. In this paper, we create a hypothesis that integrated nutrient management (INM) acts as a source of energy for microbes and improves the physical, chemical and biological properties of soils, but the current understanding of how soil microbiomes interact in integrated nutrient management toward mediating climate stress to support sustainable rice crop production is limited. Hence, we develop literature search through Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) to explore the hidden knowledge related to that question. The outcomes of the study are postulated as a viable option to minimize excessive chemical fertilizers and promote organic-based nutrient management that directly impacts microbial consortia. This review uncovered that plant-microbe interactions and nutrient transformation depend heavily on soil microbes while the abundance, diversity, and activity of soil microbiome is enhanced more with integrated nutrient management than with sole synthetic fertilizers. Through their ability to enhance nutrient availability and uptake, improve soil structure, heavy metal detoxification, salinity and drought tolerance, and suppress pathogens, they can alleviate abiotic stress associated with climate change. Therefore, optimization of microbial communities serves as a potential mechanism for INM to enhance rice yield and mitigate climate stress. This would improve soil health and enhance the resilience of the rice plant to climate change. However, despite various benefits obtained through INM and microbes in paddy production systems, the literature indicated that adoption of this technology is limited to smallholder farmers due to lack of knowledge, unavailability of sufficient organic materials and poor understanding of the long-term impacts associated with over-application of chemical fertilizers. Therefore, scientists must translate several research discoveries related to sustainable agriculture into simple language that can be adopted by farmers and future research should be a farmers-participatory approach to generate awareness investments and knowledge of farmers in adopting sustainability measures. Additionally, research could focus on identifying mechanisms by which microbiomes improve nutrient uptake and rice growth and how these mechanisms can be optimized through integrated nutrient management strategies with regard to climate stresses.},
}
@article {pmid39758340,
year = {2024},
author = {Shang, X and Fu, Y and Wang, Y and Yan, S},
title = {Ramulus Mori (Sangzhi) alkaloids ameliorate high-fat diet induced obesity in rats by modulating gut microbiota and bile acid metabolism.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1506430},
pmid = {39758340},
issn = {1664-2392},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diet, High-Fat/adverse effects ; *Obesity/metabolism/drug therapy ; Rats ; Male ; *Bile Acids and Salts/metabolism ; *Rats, Sprague-Dawley ; *Alkaloids/pharmacology ; Lipid Metabolism/drug effects ; Liver/metabolism/drug effects ; Receptors, G-Protein-Coupled/metabolism ; },
abstract = {OBJECTIVE: The objective of this study is to investigate the ability of Ramulus Mori (Sangzhi) alkaloid tablets (SZ-A) to ameliorate obesity and lipid metabolism disorders in rats subjected to a high-fat diet (HFD) through metagenomics, untargeted lipidomics, targeted metabolism of bile acid (BA), and BA pathways, providing a novel perspective on the management of metabolic disorders.<br><br>METHODS: In this research, HFD-fed rats were concurrently administered SZ-A orally. We measured changes in body weight (BW), blood lipid profiles, and liver function to assess therapeutic effects. Liver lipid status was visualized through H&amp;E and Oil Red O. Gut microbiota composition was elucidated using metagenomics. The LC-MS-targeted metabolomics approach was utilized to define the fecal BA profiles. Furthermore, the lipid metabolomics of adipose tissue samples was investigated using an LC-MS analysis platform. The expression levels of the BA receptor were determined by western blotting. Additionally, serum insulin (INS), glucagon-like peptide-1 (GLP-1), and inflammatory cytokines were quantified using an ELISA kit. The integrity of the colonic epithelial barrier was assessed using immunofluorescence.<br><br>RESULTS: SZ-A notably decreased BW and blood lipid levels in obese rats while also alleviating liver injury. Additionally, SZ-A reduced the serum levels of leptin (LEP), INS, and GLP-1, indicating its potential to modulate key metabolic hormones. Most notably, SZ-A substantially improved gut microbiota composition. Specifically, it reshaped the gut microbiota structure in HFD-fed rats by increasing the relative abundance of beneficial bacteria, such as Bacteroides, while decreasing the populations of potentially harmful bacteria, such as Dorea and Blautia. At the BA level, SZ-A decreased the levels of harmful BAs, including hyodeoxycholic acid (HDCA), deoxycholic acid (DCA), 12-keto lithocholic acid (12-KLCA), lithocholic acid (LCA), and muricholic acid (MDCA). Between the model group and SZ-A, 258 differentially abundant metabolites were detected, with 72 upregulated and 186 downregulated. Furthermore, these BAs are implicated in the activation of the FXR-FGF15 and TGR5-GLP-1 pathways in the intestine. This activation helps to alleviate HFD-fed intestinal inflammation and restore intestinal barrier damage by modulating inflammatory cytokines and bolstering the intestinal barrier's capabilities.<br><br>CONCLUSIONS: Our findings indicate that SZ-A effectively modulates BW, serum lipid profiles, and liver function in HFD-fed rats. Moreover, SZ-A exerts a positive influence on inflammatory cytokines, thereby mitigating inflammation and promoting the restoration of the intestinal barrier. Significantly, our research indicates that adjusting the gut microbiome and BA levels could serve as an effective approach for both preventing and treating obesity and related metabolic dyslipidemia.},
}
@article {pmid39758313,
year = {2024},
author = {Liu, B and Zhang, Z and Zhao, J and Li, X and Wang, Y and Liu, L and Qiao, W and Chen, L},
title = {Lactiplantibacillus plantarum HM-P2 influences gestational gut microbiome and microbial metabolism.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1489359},
pmid = {39758313},
issn = {2296-861X},
abstract = {INTRODUCTION: Human milk-derived probiotics are beneficial bacteria that provide gestational health benefits, for both pregnant women and their offspring. The study aims to investigate whether the administration of human milk-derived probiotic L. plantarum HM-P2 could effectively influence gestational health.<br><br>METHODS: The gestational humanized microbiome model was built by fecal microbiome transplant from gestational women into germ-free (GF) mice.<br><br>RESULTS: HM-P2 was successfully planted and increased the top crypt depth of the colon, and microbes such as L. reuteri, Anaerofilum sp. An201, and Gemmiger were up-regulated in the HM-P2 group throughout gestation. HM-P2 significantly promoted the contents of intestinal caproic acid, bile acids, and tryptophan catabolites such as serotonin. Gut microbes were associated with these bile acids and tryptophans.<br><br>DISCUSSION: HM-P2 could modulate the microbial community and microbial metabolites in gestational humanized GF mice. This probiotic strain could be a potential gestational dietary supplement with health benefits.},
}
@article {pmid39758173,
year = {2025},
author = {Ortiz-Alvarez, L and Xu, H and Ruiz-Campos, S and Acosta, FM and Migueles, JH and Vilchez-Vargas, R and Link, A and Plaza-Díaz, J and Gil, A and Labayen, I and Ruiz, JR and Martinez-Tellez, B},
title = {Higher physical activity levels are related to faecal microbiota diversity and composition in young adults.},
journal = {Biology of sport},
volume = {42},
number = {1},
pages = {123-135},
pmid = {39758173},
issn = {0860-021X},
abstract = {Increasing physical activity (PA) is recognised as an efficacious approach for preventing and treating cardiometabolic diseases. Recently, the composition of microorganisms living within the gut has been proposed as an important appropriate target for treating these diseases. Whether PA is related to faecal microbiota diversity and composition in humans remains to be ascertained. Thus, we examined the association of the time spent in objectively measured PA with faecal microbiota diversity and composition in young adults. A cross-sectional study enrolled 88 young adults aged 22.0 ± 2.3 years (72.7% women), whose time spent in PA at different intensities was objectively measured with a wrist-worn accelerometer for 7 consecutive days. Faecal microbiota diversity and composition were analysed with hypervariable tag sequencing of the V3-V4 region of the 16S rRNA gene. The mean Euclidean Norm of the raw accelerations Minus One (mg) during waking time, considered as overall PA, and the time spent in vigorous PA were positively correlated with alpha diversity indexes (all rho ≥ 0.23, P ≤ 0.034). Regarding faecal microbiota composition, participants with low time spent in vigorous PA had higher relative abundance of the Gammaproteobacteria class (q = 0.021, FDR = q-value) compared to the participants with high time spent in vigorous PA, and lower relative abundance of the Porphyromonadaceae family (q = 0.031) and the Alistipes genus (q = 0.015) compared to the individuals with high and intermediate time spent in vigorous PA, respectively. Our results suggest that PA, especially of vigorous intensity, is related to faecal microbiota diversity and the Gammaproteobacteria class and Porphyromonadaceae family in young adults.},
}
@article {pmid39758068,
year = {2025},
author = {Bolino, M and Avcı, &#x130; and Kayili, HM and Duman, H and Salih, B and Karav, S and Frese, SA},
title = {Identification and comparison of N-glycome profiles from common dietary protein sources.},
journal = {Food chemistry: X},
volume = {25},
number = {},
pages = {102025},
pmid = {39758068},
issn = {2590-1575},
abstract = {The N-glycomes of bovine whey, egg white, pea, and soy protein isolates are described here. N-glycans from four protein isolates were analyzed by HILIC high performance liquid chromatography and quadrupole time-of-flight tandem mass spectrometry (HILIC-FLD-QTOF-MS/MS). In total, 33 N-glycans from bovine whey and egg white and 10 N-glycans from soy and pea glycoproteins were identified. The type of N-glycans per glycoprotein source were attributable to differences in biosynthetic glycosylation pathways. Animal glycoprotein sources favored a combination of complex and hybrid glycan configurations, while the plant proteins were dominated by oligomannosidic N-glycans. Bovine whey glycoprotein isolate contained the most diverse N-glycans by monosaccharide composition as well as structure, while plant sources such as pea and soy glycoprotein isolates contained an overlap of oligomannosidic N-glycans. The results suggest N-glycan structure and composition is dependent on the host organism which are driven by the differences in N-glycan biosynthetic pathways.},
}
@article {pmid39758049,
year = {2025},
author = {Bartha, V and Boutin, S and Schüßler, DL and Felten, A and Fazeli, S and Kosely, F and Luft, T and Wolff, D and Frese, C and Schoilew, K},
title = {Exploring the Influence of Oral and Gut Microbiota on Ulcerative Mucositis: A Pilot Cohort Study.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.15246},
pmid = {39758049},
issn = {1601-0825},
support = {//Deutsche Gesellschaft f&#xfc;r Pr&#xe4;ventivzahnmedizin e. V. and CP GABA/ ; },
abstract = {AIM: Comparing oral and gut microbiome profiles between patients with and without ulcerative mucositis during allogeneic stem cell transplantation (aSCT).<br><br>MATERIALS AND METHODS: Specimens from oral mucosa, saliva, and stool were collected pre-(T0) and post- (T0 +28d&#x2009;&#xb1;&#x2009;14d) aSCT (T1). Microbiome structure differences were analyzed by 16S-rRNA-gene sequencing, and associations to patients' clinical characteristics were investigated.<br><br>RESULTS: Ten of 25 included patients developed ulcerations. The &#x3b1;-diversity decreased between T0 and T1, independent of ulcerations. PERMANOVA revealed differences in beta diversity between T1 stool samples from patients with and without ulcerations. At T1, saliva samples of patients with ulcerations showed an increase of Mycoplasma salvarius, while commensals decreased in saliva and mucosal swabs. The gut microbiome of both groups showed an overabundance of Enterococcus spp., associated with inflammatory conditions. Salival &#x3b1;-diversity of older and overweight patients decreased slower, whereas in mucosal swabs mucositis or impaired renal function was associated with a higher decline. Female gender and history of periodontitis were associated with increased stool microbiome changes, while self-reported probiotics intake was related to reduced changes.<br><br>CONCLUSIONS: Ulcerations appeared in 40% of the patients. Distinct microbial changes, including increased abundance of Mycoplasma salivarius in saliva and decreased abundance of commensals, marked those with ulcerations.<br><br>TRIAL REGISTRATION: The study was registered in the German Register for Clinical Studies (DRKS00032882).},
}
@article {pmid39757420,
year = {2024},
author = {Won, S and Jeong, Y and Kim, JE and Kim, JH and Song, HS and Bae, HH and Kwak, MS and Kim, DK and Sung, MH and Kwak, S},
title = {Evaluation of the Safety and Impact of Heat-Treated Lactiplantibacillus plantarum KM2 Fermentation on Gut Microbiome Architecture.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2411069},
doi = {10.4014/jmb.2411.11069},
pmid = {39757420},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics ; *Fermentation ; Aged ; Double-Blind Method ; *Lactobacillus plantarum/metabolism/growth &amp; development ; *Hot Temperature ; Male ; Female ; Feces/microbiology ; Veillonella/metabolism ; Middle Aged ; },
abstract = {Postbiotics, bioactive compounds from the fermentation process by probiotics, are gaining attention for their potential health benefits as safer alternatives to live probiotic microbes. Lactiplantibacillus plantarum is a well-studied probiotic species known for promoting gut health and immune modulation. However, the safety and effects of its postbiotic formulations on the gut microbiome structure remain less explored. This study presents a randomized, double-blind, placebo-controlled human study of KLP-KM2, a postbiotic consisting of heat-treated L. plantarum KM2 fermentation complex, in elderly participants. Over 12 weeks, KLP-KM2 consumption did not result in noticeable adverse reaction cases compared to the placebo. Nevertheless, the gut microbial diversity and taxonomic architecture of the KLP-KM2 recipients were differentiated from those of the placebo recipients after 12 weeks. A notable outcome was the increase in the number of subjects carrying Veillonella spp., which contributed to the distinct gut microbiome profiles observed between the two groups. Interestingly, KLP-KM2 facilitated the de novo colonization of Veillonella spp. in subjects who had not harbored these bacteria at the baseline. These results suggest the potential of KLP-KM2 as a safe and effective postbiotic intervention to enhance energy metabolism and mobility in older adults.},
}
@article {pmid39757098,
year = {2025},
author = {Wang, FY and Liang, ZY and He, WW and Chen, RC},
title = {[Annual research progress in chronic obstructive pulmonary disease 2024].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {48},
number = {1},
pages = {60-65},
doi = {10.3760/cma.j.cn112147-20241011-00598},
pmid = {39757098},
issn = {1001-0939},
support = {2022YFF0710802//National Key R&amp;D Plan/ ; 82200044, 82270044, 82170042//National Natural Science Foundation of China/ ; KCXFZ20200201100 8256//Developing Foundation of Shenzhen Science and Technology Innovation Commission/ ; SKLRD-Z-202317//The Grant of State Key Laboratory of Respiratory Disease/ ; },
mesh = {*Pulmonary Disease, Chronic Obstructive ; Humans ; Biomarkers ; Bronchodilator Agents/therapeutic use ; Prognosis ; },
abstract = {Chronic obstructive pulmonary disease (COPD) is a major global public health problem and the burden of disease is estimated to continue to increase. Since 2023, significant progress has been achieved in the early identification, pathogenesis, biomarkers, and personalized treatment of COPD. Early-stage COPD, as defined by varying criteria, has been shown to have distinct epidemiological features that affect disease prognosis, emphasizing the importance of early monitoring and intervention. In terms of pathogenesis, terminal bronchial alveolar attachments have been identified as the initial sites of tissue destruction in centrilobular emphysema. Some circulating biomarkers have been shown to potentially play a role in multiple lung function trajectories leading to COPD. The discovery of the evolutionary pattern of the airway mucus microbiome provides a new direction for early intervention in COPD. Prognostic factors such as severity classification of COPD exacerbation from the Rome proposal, diffusion capacity, impulse oscillometry (IOS), and bronchodilator responsiveness are providing new insights for disease management. In terms of treatment, prompt initiation of triple inhalation therapy after an exacerbation has been shown to benefit patients who remain symptomatic despite dual therapy. The use of extra-fine particle formulations has been associated with a reduced risk of side effects from inhaled corticosteroids. New drugs, including ensifentrine and dupilumab, have been demonstrated both efficacy and safety. Future research will focus on disease heterogeneity, novel therapeutic targets and drugs to improve outcomes and reduce the burden of disease in COPD.},
}
@article {pmid39757060,
year = {2025},
author = {Rowland, SN and Green, CG and Halliwill, JR and Singanayagam, A and Heaney, LM},
title = {Gut feelings on short-chain fatty acids to regulate respiratory health.},
journal = {Trends in endocrinology and metabolism: TEM},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tem.2024.12.007},
pmid = {39757060},
issn = {1879-3061},
abstract = {Respiratory infections and diseases pose significant challenges to society and healthcare systems, underscoring the need for preventative and therapeutic strategies. Recent research in rodent models indicates that short-chain fatty acids (SCFAs), metabolites produced by gut bacteria, may offer medicinal benefits for respiratory conditions. In this opinion, we summarize the current literature that highlights the potential of SCFAs to enhance immune balance in humans. SCFAs have demonstrated the potential to decrease the risk of primary and secondary respiratory infections, modulate allergic airway exacerbations, and improve overall epithelial pathogen defenses. Therefore, we suggest that systemic SCFA levels could be targeted to support gut and respiratory health in specific groups, such as patients in hospital, women and their offspring, children, older adults, and athletes/military personnel.},
}
@article {pmid39757039,
year = {2025},
author = {Cruz-Lebrón, A and Faiez, TS and Hess, MM and Sfanos, KS},
title = {Diet and the microbiome as mediators of prostate cancer risk, progression, and therapy response.},
journal = {Urologic oncology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.urolonc.2024.12.001},
pmid = {39757039},
issn = {1873-2496},
abstract = {Complex relationships between the human microbiome and cancer are increasingly recognized for cancer sites that harbor commensal microbial communities such as the gut, genitourinary tract, and skin. For organ sites that likely do not contain commensal microbiota, there is still a substantial capacity for the human-associated microbiota to influence disease etiology across the cancer spectrum. We propose such a relationship for prostate cancer, the most commonly diagnosed cancer in males in the United States. This review explores the current evidence for a role for the urinary and gut microbiota in prostate cancer risk, via both direct interactions (prostate infections) and long-distance interactions such as via the metabolism of procarcinogenic or anticarcinogenic dietary metabolites. We further explore a newly recognized role of the gut microbiota in mediating cancer treatment response or resistance either via production of androgens and/or procarcinogenic metabolites or via direct metabolism of anticancer drugs that are used to treat advanced disease. Overall, we present the current state of knowledge relating to how the human microbiome mediates prostate cancer risk, progression, and therapy response, as well as suggest future research directions for the field.},
}
@article {pmid39756663,
year = {2025},
author = {Ovis-Sánchez, JO and Vital-Jácome, M and Buitrón, G and Cervantes-Avilés, P and Carrillo-Reyes, J},
title = {Antibiotic resistance reduction mechanisms during thermophilic anaerobic digestion of microalgae-bacteria aggregates.},
journal = {Bioresource technology},
volume = {419},
number = {},
pages = {132037},
doi = {10.1016/j.biortech.2025.132037},
pmid = {39756663},
issn = {1873-2976},
abstract = {Microalgae-bacteria-based systems are an emerging and promising approach for wastewater treatment plants (WWTP), having nutrient and antibiotic resistance removal comparable to conventional technologies. Still, antibiotic-resistance genes and bacteria (ARG and ARB) can proliferate in microalga-bacteria aggregates (MABA), a concern to control. Different temperature regimes of MABA continuous anaerobic digestion (AD), thermophilic (55 °C), and mesophilic (35 °C) were evaluated in this study as a strategy to eliminate ARB and ARGs. Plate counting techniques and metagenomic-based analysis revealed that thermophilic temperature had a better performance, achieving ARB log reductions of 1.1 to 1.7 for various antibiotics and significantly reduced ARG abundance up to 19.5 ± 0.8 ppm. The microbiome selection, the mobilome restriction, and directed functionality to thermal stress resistance were the main mechanisms responsible for resistome reduction at thermophilic conditions. Thermophilic AD effectively manages antibiotic resistance in microalgae-bacteria aggregates, which has important implications for wastewater treatment and reduces environmental risks.},
}
@article {pmid39756653,
year = {2025},
author = {Crespo, MT and Trebucq, LL and Senna, CA and Hokama, G and Paladino, N and Agostino, PV and Chiesa, JJ},
title = {Circadian disruption of feeding-fasting rhythm and its consequences for metabolic, immune, cancer, and cognitive processes.},
journal = {Biomedical journal},
volume = {},
number = {},
pages = {100827},
doi = {10.1016/j.bj.2025.100827},
pmid = {39756653},
issn = {2320-2890},
abstract = {The circadian system is composed by a central hypothalamic clock at the suprachiasmatic nuclei (SCN) that communicates with peripheral circadian oscillators for daily coordination of behavior and physiology. The SCN entrain to the environmental 24-h light-dark (LD) cycle and drive daily rhythms of internal synchronizers such as core body temperature, hypothalamic-hypophysary hormones, sympathetic/parasympathetic activity, as well as behavioral and feeding-fasting rhythms, which supply signals setting core molecular clocks at central and peripheral tissues. Steady phase relationships between the SCN and peripheral oscillators keep homeostatic processes such as microbiota/microbiome composition/activity, metabolic supply/demand, energy balance, immunoinflammatory process, sleep amount and quality, psychophysiological stress, etc. Indeed, the risk of health alterations increase when these phase relationships are chronically changed prompting circadian disruption (CD), as occurring after sudden LD cycle changes (so-called jet-lag), or due to changes of activity/feeding-rest/fasting rhythm with respect to LD cycles (as humans subjected to nightwork, or restricting food access at rest in mice). Typical pathologies observed in animal models of CD and epidemiological studies include metabolic syndrome, type-2 diabetes, obesity, chronic inflammation, cancer, sleep disruption, decrease in physical and cognitive performance, and mood, among others. The present review discusses different aspects of such physiological dysregulations observed in animal models of CD having altered feeding-fasting rhythms, with potential translation to human health.},
}
@article {pmid39756573,
year = {2025},
author = {Shen, H and Li, Y and Pi, Q and Tian, J and Xu, X and Huang, Z and Huang, J and Pian, C and Mao, S},
title = {Unveiling novel antimicrobial peptides from the ruminant gastrointestinal microbiomes: A deep learning-driven approach yields an anti-MRSA candidate.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.01.005},
pmid = {39756573},
issn = {2090-1224},
abstract = {INTRODUCTION: Antimicrobial peptides (AMPs) present a promising avenue to combat the growing threat of antibiotic resistance. The ruminant gastrointestinal microbiome serves as a unique ecosystem that offers untapped potential for AMP discovery.<br><br>OBJECTIVES: The aims of this study are to develop an effective methodology for the identification of novel AMPs from ruminant gastrointestinal microbiomes, followed by evaluating their antimicrobial efficacy and elucidating the mechanisms underlying their activity.<br><br>METHODS: We developed a deep learning-based model to identify AMP candidates from a dataset comprising 120 metagenomes and 10,373 metagenome-assembled genomes derived from the ruminant gastrointestinal tract. Both in vivo and in vitro experiments were performed to examine and validate the antimicrobial activities of the AMP candidates that were selected through bioinformatic analysis and subsequently synthesized chemically. Additionally, molecular dynamics simulations were conducted to explore the action mechanism of the most potent AMP candidate.<br><br>RESULTS: The deep learning model identified 27,192 potential secretory AMP candidates. Following bioinformatic analysis, 39 candidates were synthesized and tested. Remarkably, all synthesized peptides demonstrated antimicrobial activity against Staphylococcus aureus, with 79.5% showing effectiveness against multiple pathogens. Notably, Peptide 4, which exhibited the highest antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA), confirmed this effect in a mouse model with wound infection, exhibiting a low propensity for resistance development and minimal cytotoxicity and hemolysis towards mammalian cells. Molecular dynamics simulations provided insights into the mechanism of Peptide 4, primarily its ability to disrupt bacterial cell membranes, leading to cell death.<br><br>CONCLUSION: This study highlights the power of combining deep learning with microbiome research to uncover novel therapeutic candidates, paving the way for the development of next-generation antimicrobials like Peptide 4 to combat the growing threat of MRSA would infections. It also underscores the value of utilizing ruminant microbial resources.},
}
@article {pmid39756177,
year = {2025},
author = {Yang, L and Gao, H and Wang, Y and Norbäck, D and Zhao, Z and Fu, X and Sun, Y and Zhang, X},
title = {Environmental impacts on childhood rhinitis: The role of green spaces, air pollutants, and indoor microbial communities in Taiyuan, a city in Northern China.},
journal = {Ecotoxicology and environmental safety},
volume = {289},
number = {},
pages = {117662},
doi = {10.1016/j.ecoenv.2024.117662},
pmid = {39756177},
issn = {1090-2414},
abstract = {Rhinitis is one of the most common respiratory diseases, influenced by various environmental factors such as green space, air pollution and indoor microbiomes. However, their interactions and combined effects have not been reported. We recruited 1121 preschool children from day care centers in a northern city of China. Health and demographic data were collected through questionnaires answered by the children's parents. Surrounding green space was assessed by Normalized Difference Vegetation Index (NDVI), Enhanced Vegetation Index (EVI) and land cover data of grassland proportion within 1500/3000 m. Ambient air pollution was estimated using the inverse distance weighted (IDW), and the indoor microbiome in classroom vacuum dust was profiled by bacterial 16S rRNA and fungal ITS amplicon sequencing. Mixed-effect logistic regression revealed the proportion of natural grassland, grassland leaf-off and total grassland was negatively associated with current rhinitis. Stratified analysis indicated that greater green space exposure was associated with a reduced current rhinitis in children at high levels of air pollution. Additionally, grassland also protects children against environmental tobacco smoke at home. Indoor microbiome analysis showed Haemophilus and Dolosigranulum were enriched in low-rhinitis day care centers, while Amaricoccus, Blautia and Mycosphaerella were enriched in high-rhinitis day care centers. Mediation analysis indicated that the indoor microbiome did not have significant mediating effects on the relationship between green space and children's current rhinitis. This is the first study to reveal interactions of green space, air pollution and indoor microbiome on rhinitis, providing new insights into how environmental factors collectively influence respiratory health in children.},
}
@article {pmid39756140,
year = {2024},
author = {Kumar, C and Esposito, A and Bertani, I and Musonerimana, S and Midekssa, MJ and Tesfaye, K and Derr, DC and Donaldson, L and Piazza, S and Bez, C and Venturi, V},
title = {Sorghum rhizosphere bacteriome studies and generation of multistrain beneficial bacterial consortia.},
journal = {Microbiological research},
volume = {292},
number = {},
pages = {128036},
doi = {10.1016/j.micres.2024.128036},
pmid = {39756140},
issn = {1618-0623},
abstract = {The plant rhizosphere microbiome plays a crucial role in plant growth and health. Within this microbiome, bacteria dominate, exhibiting traits that benefit plants, such as facilitating nutrient acquisition, fixing nitrogen, controlling pathogens, and promoting root growth. This study focuses on designing synthetic bacterial consortia using key bacterial strains which have been mapped and then isolated from the sorghum rhizosphere microbiome. A large set of samples of the rhizosphere bacteriome of Sorghum bicolor was generated and analyzed across various genotypes and geographical locations. We assessed the taxonomic composition and structure of the sorghum root-associated bacterial community identifying the most prevalent and keystone taxa. A set of 321 bacterial strains was then isolated, and three multi-strain consortia were designed making use of the bacteriome data generated using culture independent methodology. Subsequently, co-existence and plant-growth promoting ability of three bacterial consortia were tested both in vitro and in planta. Consortia 3 promoted plant growth in growth-chamber conditions while Consortia 1 and 2 performed better in field-plot experiments. Despite these differences, bacterial community profiling confirmed the colonization of the inoculated consortia in the sorghum rhizosphere without significant alterations to the overall bacterial community compared to the non inoculated ones. In summary, this study focused on a method, using root bacteriome data, to design and test bacterial consortia for plant beneficial effects with the aim of translating microbiome knowledge into applications.},
}
@article {pmid39755646,
year = {2025},
author = {Sola-Leyva, A and Romero, B and Canha-Gouveia, A and Pérez-Prieto, I and Molina, NM and Vargas, E and Mozas-Moreno, J and Chamorro, C and Saare, M and Salumets, A and Altmäe, S},
title = {Uterus didelphys: the first case report on molecular profiling of endometrial tissue from both uterine cavities.},
journal = {Reproductive biology and endocrinology : RB&amp;E},
volume = {23},
number = {1},
pages = {1},
pmid = {39755646},
issn = {1477-7827},
mesh = {Female ; Humans ; *Endometrium/metabolism/abnormalities ; *Uterus/abnormalities ; *Urogenital Abnormalities/genetics ; Adult ; Microbiota ; },
abstract = {BACKGROUND: A didelphic uterus represents a unique and infrequent congenital condition in which a woman possesses two distinct uteri, each with its own cervix. This anomaly arises due to partial or incomplete merging of the Müllerian ducts during the developmental stages in the womb. Accounting for uterine malformations, a didelphic uterus is a relatively rare condition, affecting approximately 0.5-2% of the population and is considered one of the more uncommon types of uterine abnormalities.<br><br>METHODS: This case report aims to study the physical separation in uterine didelphys and its impact on endometrial microbiome and inflammation, and the patterns of endometrial receptivity observed.<br><br>RESULTS: Endometrial receptivity analyses revealed a similar receptive state in both uteri, both in the early receptive phase. Differential markers of chronic endometritis, including CD138, and MUM1-positive cells, were observed when comparing endometrial biopsies from both uteri. The right uterus exhibited a higher prevalence of these positive cells. Regarding the microbiome, significant differences were found between the uteri, notably in the right uterus, a clear non-dominance of lactobacilli and the presence of genera such as Staphylococcus, Streptococcus, and Acinetobacter.&#xa0;Additionally, the right uterus presented a less 'favourable' microenvironment,&#xa0;a characteristic that was also reflected in the right cervix; both sites presenting less lactobacilli than the left side samples. A distinct metabolomic signature associated with the physical separation of the uteri contributed to the differences in endometrial milieu.<br><br>CONCLUSIONS: Our study revealed that physical separation, among other factors in uterus didelphys, affects the endometrial microbiome, metabolome, and inflammatory state, with significant microbiome variation observed between the uteri, although similar endometrial receptivity patterns were noted.},
}
@article {pmid39755582,
year = {2025},
author = {Cheng, M and Jin, M and Yang, S and Zhao, L and Yu, D and Lin, Z and Li, P and Huang, C and Liu, J and Wang, J and Xue, J and Ma, H and Hu, J and Yang, K and Zhang, T and Liu, H},
title = {Effect of radiotherapy exposure on fruquintinib plus sintilimab treatment in refractory microsatellite stable metastatic colorectal cancer: a prospective observation study.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {1},
pages = {},
doi = {10.1136/jitc-2024-009415},
pmid = {39755582},
issn = {2051-1426},
mesh = {Humans ; *Colorectal Neoplasms/drug therapy/pathology ; Male ; Female ; Prospective Studies ; Middle Aged ; Aged ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; Benzofurans/therapeutic use/pharmacology ; Adult ; Microsatellite Instability ; Quinazolines ; },
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) in combination with antiangiogenic drugs have shown promising outcomes in the third-line and subsequent treatments of patients with microsatellite stable metastatic colorectal cancer (MSS-mCRC). Radiotherapy (RT) may enhance the antitumor effect of immunotherapy. However, the effect of RT exposure on patients receiving ICIs and targeted therapy remains unclear. This study aimed to investigate the association between RT exposure and clinical responses to fruquintinib (a highly selective tyrosine kinase inhibitor of vascular endothelial growth factor receptor) plus sintilimab (an anti-programmed death 1 antibody; F&amp;S) in previously treated patients with MSS-mCRC and to explore predictive biomarkers.<br><br>METHODS: In this prospective observational study, patients with mCRC receiving F&amp;S as third-line or subsequent treatment were enrolled. Eligible patients were divided into the RT cohort (RTC) and the non-RT cohort (NRTC) according to their RT history. The primary endpoint was the objective response rate (ORR). Secondary endpoints included disease control rate (DCR), progression-free survival (PFS), overall survival (OS), and safety. Pretreatment fecal and serum samples were collected for microbiome analysis, metabolome analysis, and immune signatures to identify biomarkers for treatment.<br><br>RESULTS: A total of 55 patients were included, of which 25 were in the RTC and 30 in the NRTC. Better ORR (28.0% vs 6.7%, p=0.048), DCR (80.0% vs 36.7%, p=0.002), median PFS (6.2 vs 2.7 months, p<0.001), and median OS (14.8 vs 5.9 months, p=0.019) were noted in patients with RTC than those with NRTC. The enrichment of Lactobacillus, Bifidobacterium, and PC(20:5(5Z,8Z,11Z,14Z,17Z)/20:3(8Z,11Z,14Z)) in RTC significantly predicted better DCR and PFS, whereas guanosine and interleukin-10 predominated in patients with NRTC were negatively correlated with PFS and OS.<br><br>CONCLUSIONS: Patients with RT exposure benefited significantly from F&amp;S in the third-line or subsequent treatment for MSS-mCRC. Gut microbiota, metabolites, and cytokines may help predict F&amp;S outcomes for mCRC, which may be helpful in treatment decision-making.<br><br>TRIAL REGISTRATION NUMBER: ClinicalTrials.gov identifier: NCT05635149.},
}
@article {pmid39755397,
year = {2025},
author = {Kloppenburg, M and Namane, M and Cicuttini, F},
title = {Osteoarthritis.},
journal = {Lancet (London, England)},
volume = {405},
number = {10472},
pages = {71-85},
doi = {10.1016/S0140-6736(24)02322-5},
pmid = {39755397},
issn = {1474-547X},
mesh = {Humans ; *Osteoarthritis/therapy ; Obesity/complications ; Exercise Therapy ; Weight Loss ; },
abstract = {Osteoarthritis is a heterogeneous disorder that is increasingly prevalent largely due to aging and obesity, resulting in a major disease burden worldwide. Knowledge about the underlying aetiology has improved, with increased understanding of the role of genetic factors, the microbiome, and existence of different pain mechanisms. However, this knowledge has not yet been translated into new treatment options. New evidence has questioned the efficacy of recommended treatments, such as therapeutic exercise programmes and the focus on weight loss, but managing obesity and maintaining activity remain important for the prevention and management of osteoarthritis. Approaches should consider individual and cultural preferences and resource availability to increase patient and community engagement, and optimise outcomes worldwide. Most of the focus has been on established osteoarthritis where management is primarily directed at relieving symptoms. The search for the much needed effective treatments that improve both symptoms and structure, often referred to as disease-modifying osteoarthritic drugs, is ongoing. Promising data indicate that targeting inflammation is effective in hand osteoarthritis.},
}
@article {pmid39755264,
year = {2025},
author = {Yang, X and Wei, L},
title = {Analysis of long Non-Coding RNA and mRNA expression in Clostridium butyricum-Induced apoptosis in SW480 colon cancer cells.},
journal = {Gene},
volume = {940},
number = {},
pages = {149208},
doi = {10.1016/j.gene.2024.149208},
pmid = {39755264},
issn = {1879-0038},
abstract = {Colon cancer is a leading cause of cancer-related deaths worldwide and has been increasingly linked to the gut microbiome. Clostridium butyricum (CB), a probiotic, has demonstrated potential in influencing colon cancer cell behavior, particularly through the modulation of long non-coding RNAs (lncRNAs) and mRNAs. This study examines the effects of CB on the expression of lncRNAs and mRNAs in SW480 colon cancer cells and their association with apoptosis. SW480 cells were co-cultured with CB, and total RNA was extracted for microarray analysis to identify differentially expressed lncRNAs and mRNAs. Quantitative real-time PCR and fluorescence staining were utilized to validate the expression changes of selected lncRNAs and to assess markers of apoptosis. Pathway enrichment analysis was performed to explore the biological functions of genes with altered expression. Co-culture with CB resulted in significant changes in lncRNA and mRNA expression, with 50 lncRNAs upregulated and 152 downregulated by more than five-fold. Similarly, 738 mRNAs were upregulated, while 1,088 were downregulated. Apoptosis analysis revealed that CB treatment induced apoptosis in SW480 cells, as evidenced by the upregulation of pro-apoptotic genes such as CASP1, TNF, and BNIP3L, and the downregulation of anti-apoptotic BCL family members. Pathway analysis suggested the involvement of the MAPK signaling pathway, cytokine-cytokine receptor interactions, and other pathways associated with tumor progression. These findings suggest that CB regulates the expression of lncRNAs and mRNAs involved in apoptosis and tumor progression, highlighting their potential as biomarkers and therapeutic targets in colorectal cancer. This study provides a novel therapeutic strategy for colon cancer treatment.},
}
@article {pmid39755199,
year = {2025},
author = {Liu, L and Zhu, G and Hu, J and Chen, H and Zhai, Y},
title = {An unignorable human health risk posed by antibiotic resistome and microbiome in urban rivers: Insights from Beijing, China.},
journal = {Environmental research},
volume = {268},
number = {},
pages = {120752},
doi = {10.1016/j.envres.2025.120752},
pmid = {39755199},
issn = {1096-0953},
abstract = {Urban rivers are the main water bodies humans frequently come into contact with, so the risks posed are closely monitored. Antibiotic resistance genes (ARGs) residues in reclaimed water pose serious risks to human health. There are urgent needs to improve the understanding of distribution of and risks posed by ARGs in urban rivers. In this study, shotgun metagenomic approach was used to characterize ARGs, mobile genetic elements (MGEs), and virulence factors (VFs) in water and sediment from Xinfeng River in Beijing and to identify microbes, potential antibiotic resistant bacteria, and human pathogens (HPs). MGE, microbial community, VF, and ARG co-occurrences were used to assess the environmental risks posed by ARGs. The results indicated that quinolone was the most abundant ARG type and that tufA and fusA were the two dominant ARG subtypes. Wetland effluent increased ARG abundance in the river, and the effect was detected even 50 m downstream. ARG abundances and distribution in the river had difference in different seasons. The dominant bacteria in the river were Proteobacteria, Bacteroidetes, and Actinobacteria, and 59 HPs were detected. In total, 69 MGEs and 19 VFs were found. Co-occurrence networks indicated that potential antibiotic resistant bacteria, MGEs, VFs, and ARGs in the river significantly correlated, indicating the potential risks posed by ARGs. The results improve our understanding of ARG distribution and environmental risks in urban river water. More attention should be paid to controlling environmental risks posed by ARGs in urban river and reclaimed water.},
}
@article {pmid39755051,
year = {2024},
author = {Wang, J and Zhang, Z and Wang, J and Shi, L and Wang, S and Niu, B and Tian, X and Lv, Q and Wei, L and Li, M and Liu, Y},
title = {Bacillus coagulans alleviates intestinal barrier injury induced by Klebsiella pneumoniae in rabbits by regulating the TLR4/MyD88/NF-κB signalling pathway.},
journal = {Veterinary microbiology},
volume = {301},
number = {},
pages = {110364},
doi = {10.1016/j.vetmic.2024.110364},
pmid = {39755051},
issn = {1873-2542},
abstract = {Probiotics effectively alleviate host diarrhoea, but the specific mechanism is not clear. Therefore, we explored the protective mechanism of Bacillus coagulans (BC) on intestinal barrier injury induced by Klebsiella pneumoniae (K. pneumoniae) in rabbits by HE, immunofluorescence and 16S rRNA. The results showed that BC pretreatment alleviated the changes in average daily gain, average daily feed intake and FCR caused by K. pneumoniae in rabbits. Moreover, BC alleviated the inflammatory cell infiltration, intestinal villus reduction, crypt deepening and goblet cell reduction caused by K. pneumoniae in rabbits. Further research revealed that BC improved the intestinal barrier by improving the mechanical barrier, chemical barrier, immune barrier and microbial barrier. Specifically, BC improved the intestinal mechanical barrier by improving the intestinal structure, increasing the protein expression of PCNA, increasing the number of goblet cells, and altering the expression of occludin, claudin-1 and ZO-1. BC improved the intestinal chemical barrier by regulating the expression of MUC1 and MUC2 and inhibited the TLR4/MyD88/NF-κB signalling pathway by altering the expression levels of the inflammatory factors IL-1β, IL-6 and TNF-α, thus optimizing the intestinal immune barrier. In addition, adding BC to the diet improved the intestinal microbial barrier of rabbits by reducing the abundance of harmful bacteria and increasing the abundance of beneficial bacteria. In summary, BC protects against K. pneumoniae-induced intestinal barrier damage by improving intestinal morphology, mitigating the inflammatory response and regulating the microbial composition. Among the pretreatments, the pretreatment effect of 1 × 10[6] CFU/g was the best. This study provides a theoretical basis for the use of BC to prevent and treat diarrhoea caused by K. pneumoniae in rabbits.},
}
@article {pmid39754662,
year = {2025},
author = {Khan, D and Shaw, R and Kabiraj, A and Paul, A and Bandopadhyay, R},
title = {Microbial inheritance through seed: a clouded area needs to be enlightened.},
journal = {Archives of microbiology},
volume = {207},
number = {1},
pages = {23},
pmid = {39754662},
issn = {1432-072X},
mesh = {*Seeds/microbiology/growth &amp; development ; *Endophytes/genetics/physiology ; *Microbiota/physiology ; Symbiosis ; Bacteria/genetics/metabolism ; Plant Dormancy/genetics ; Plants/microbiology ; },
abstract = {Seed endophytes are actively used by the mother plant as both reservoir and vector of beneficial microbes. During seed dormancy endophytes experience significant physiochemical changes and only competent endophytes could colonise successfully in seeds and some of them act as obligate endophyte that are transmitted vertically across generations. The adaptive nature of endophytes allows them to switch lifestyles depending on environment and host conditions. In this review, instead of providing broad discussion on applicability of endophytes in plant growth improvement, the fundamental nature of endophytes, their survival strategies under stress conditions, transmittance, etc. have been broadly highlighted by collaborating recent discoveries and theories. We have also tried to differentiate endophyte with their pathogenic counterpart and their survival mechanism during seed dormancy stages. Critical analyses of physio-biochemical changes in seeds during maturation and parallel modifications of life styles of seed endophytes along with pathogens will enlighten the shaded part of seed-microbiome interactions. The mutualistic interrelations as well as their shipment towards pathogenic behaviour under stress are being discussed acutely. Finally, importances of conservation of seed microbiome to maintain seed quality and vigour have been pointed out. Throughout the manuscript, the knowledge gap on seed-microbiota have been mentioned, thus, in future, studies on these areas could help us to understand properly the actual role of endophytes for the betterment of maintaining seed quality and vigour.},
}
@article {pmid39754646,
year = {2025},
author = {Shaffer, M and North, D and Bibby, K},
title = {Evaluating Nanotrap Microbiome Particles as A Wastewater Viral Concentration Method.},
journal = {Food and environmental virology},
volume = {17},
number = {1},
pages = {10},
pmid = {39754646},
issn = {1867-0342},
support = {1748019//National Science Foundation/ ; },
mesh = {*Wastewater/virology/microbiology ; *Microbiota ; *Viruses/isolation &amp; purification/classification/genetics ; Metagenomics/methods ; Bacteria/isolation &amp; purification/classification/genetics/virology ; Tobamovirus/isolation &amp; purification/genetics/classification ; },
abstract = {Wastewater-based surveillance has emerged as a powerful approach to monitoring infectious diseases within a community. Typically, wastewater samples are concentrated before viral analyses to improve sensitivity. Current concentration methods vary in time requirements, costs, and efficiency. Here, we evaluated the concentration efficiency and bias of a novel viral concentration approach, Nanotrap Microbiome Particles (NMP), in wastewater. NMP concentration efficiency was target-specific, with significantly lower concentrations of the bacterial indicator HF183 and viral indicator Carjivirus (formerly crAssphage) relative to direct extraction (1.2 × 10[5] vs. 3.4 × 10[5] GC/mL and 2.0 × 10[5] vs. 1.2 × 10[5] GC/mL, respectively), but significantly higher concentrations of the viral fecal indicator Pepper Mild Mottle Virus (PMMoV) relative to direct extraction (1.4 × 10[5] vs. 8.4 × 10[3] GC/mL). Targeted metagenomic sequencing showed that NMP resulted in significantly more unique species reads per sample than direct extractions (p < 0.001) by detecting species that went undetected by direct extractions. Key viral families identified with high abundances were Adenoviridae, Caliciviridae, Herpesviridae, Papillomaviridae, and Polyomaviridae. NMP showed differential ability for concentrating clinically relevant viral families, suggesting that the technology should be evaluated and optimized for specific viral targets before implementation.},
}
@article {pmid39754578,
year = {2025},
author = {Bakhsh, A and Joseph, S and Mannocci, F and Proctor, G and Moyes, D and Niazi, SA},
title = {Apical periodontitis microbiome association with salivary and serum inflammatory burden.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.14184},
pmid = {39754578},
issn = {1365-2591},
support = {//British Endodontic Society/ ; //European Society of Endodontology/ ; },
abstract = {AIMS: Apical Periodontitis (AP) involves complex interactions between the root canal microbiome and the host immune response, with potential risk of local and systemic inflammatory burden, however there is no evidence available regarding correlation between microbiome and inflammatory marker levels. This study aims to identify the microbiome of saliva, intracanal and blood samples in AP subjects and investigate the correlation between intracanal and blood microbiomes with serum inflammatory biomarker levels, and salivary microbiomes with salivary inflammatory biomarker levels.<br><br>METHODOLOGY: Saliva, Intracanal and blood samples were collected from AP patients undergoing root canal retreatment. Following DNA extraction, 16SrRNA gene-sequence analysis (V1-V2) was performed using Illumina MiSeq 300 platform. Serum and salivary inflammatory marker levels were measured using the magnetic multiplex-microbead assay. The alpha and beta diversities were tested using the phyloseq package in R (version 4.1). The abundance of the identified phyla and genera were analysed using non-parametric tests. Spearman&#xb4;s correlation coefficient was used for correlation between microbial abundance and biomarker levels.<br><br>RESULTS: Streptococcus and Prevotella were prevalent in saliva; Enterococcus, Streptococcus and Bacteroidaceae_(G-1) in intracanal; and Cutibacterium and Staphylococcus in blood samples. Streptococcus, Prevotella, Actinomyces and Rothia were the most abundant common genera among all three sample sources. In saliva, Haemophilus, Gemella, Prevotella, and Alloprevotella were positively correlated with salivary levels of IL-8, MMP-2, TNF-&#x3b1;, and IL-6, respectively. Intracanal genera, Enterobacter, and Parvinomonas, were positively correlated serum FGF-23. Finally, the abundance of Novosphingobium, Streptococcus, Bosea, and Corynebacterium genus in blood were positively correlated with FGF-23, MMP-9, CRP, IL-8, and ICAM-1.<br><br>CONCLUSION: Microbiome in saliva, blood and intracanal samples were correlated with some of the inflammatory biomarker levels of saliva and serum, suggesting that the effect of AP goes beyond a periapical infection and may pose a potential systemic inflammatory burden risk if left untreated.},
}
@article {pmid39754287,
year = {2025},
author = {Epstein, HE and Brown, T and Akinrinade, AO and McMinds, R and Pollock, FJ and Sonett, D and Smith, S and Bourne, DG and Carpenter, CS and Knight, R and Willis, BL and Medina, M and Lamb, JB and Thurber, RV and Zaneveld, JR},
title = {Evidence for microbially-mediated tradeoffs between growth and defense throughout coral evolution.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {1},
pmid = {39754287},
issn = {2524-4671},
support = {2006244//National Science Foundation/ ; 1442306//National Science Foundation/ ; 1942647//National Science Foundation/ ; },
abstract = {BACKGROUND: Evolutionary tradeoffs between life-history strategies are important in animal evolution. Because microbes can influence multiple aspects of host physiology, including growth rate and susceptibility to disease or stress, changes in animal-microbial symbioses have the potential to mediate life-history tradeoffs. Scleractinian corals provide a biodiverse, data-rich, and ecologically-relevant host system to explore this idea.<br><br>RESULTS: Using a comparative approach, we tested if coral microbiomes correlate with disease susceptibility across 425&#xa0;million years of coral evolution by conducting a cross-species coral microbiome survey (the "Global Coral Microbiome Project") and combining the results with long-term global disease prevalence and coral trait data. Interpreting these data in their phylogenetic context, we show that microbial dominance predicts disease susceptibility, and traced this dominance-disease association to a single putatively beneficial symbiont genus, Endozoicomonas. Endozoicomonas relative abundance in coral tissue explained 30% of variation in disease susceptibility and 60% of variation in microbiome dominance across 40 coral genera, while also correlating strongly with high growth rates.<br><br>CONCLUSIONS: These results demonstrate that the evolution of Endozoicomonas symbiosis in corals correlates with both disease prevalence and growth rate, and suggest a mediating role. Exploration of the mechanistic basis for these findings will be important for our understanding of how microbial symbioses influence animal life-history tradeoffs.},
}
@article {pmid39754220,
year = {2025},
author = {Karwowska, Z and Aasmets, O and , and Kosciolek, T and Org, E},
title = {Effects of data transformation and model selection on feature importance in microbiome classification data.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {2},
pmid = {39754220},
issn = {2049-2618},
mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome/genetics ; *Algorithms ; *Metagenomics/methods ; Microbiota/genetics ; Bacteria/classification/genetics ; Biomarkers ; Metagenome ; },
abstract = {BACKGROUND: Accurate classification of host phenotypes from microbiome data is crucial for advancing microbiome-based therapies, with machine learning offering effective solutions. However, the complexity of the gut microbiome, data sparsity, compositionality, and population-specificity present significant challenges. Microbiome data transformations can alleviate some of the aforementioned challenges, but their usage in machine learning tasks has largely been unexplored.<br><br>RESULTS: Our analysis of over 8500 samples from 24 shotgun metagenomic datasets showed that it is possible to classify healthy and diseased individuals using microbiome data with minimal dependence on the choice of algorithm or transformation. Presence-absence transformations performed comparably to abundance-based transformations, and only a small subset of predictors is necessary for accurate classification. However, while different transformations resulted in comparable classification performance, the most important features varied significantly, which highlights the need to reevaluate machine learning-based biomarker detection.<br><br>CONCLUSIONS: Microbiome data transformations can significantly influence feature selection but have a limited effect on classification accuracy. Our findings suggest that while classification is robust across different transformations, the variation in feature selection necessitates caution when using machine learning for biomarker identification. This research provides valuable insights for applying machine learning to microbiome data and identifies important directions for future work.},
}
@article {pmid39754121,
year = {2025},
author = {Butler, MJ and Muscat, SM and Caetano-Silva, ME and Shrestha, A and Olmo, BMG and Mackey-Alfonso, SE and Massa, N and Alvarez, BD and Blackwell, JA and Bettes, MN and DeMarsh, JW and McCusker, RH and Allen, JM and Barrientos, RM},
title = {Obesity-associated memory impairment and neuroinflammation precede widespread peripheral perturbations in aged rats.},
journal = {Immunity &amp; ageing : I &amp; A},
volume = {22},
number = {1},
pages = {2},
pmid = {39754121},
issn = {1742-4933},
support = {R03 AG067061/AG/NIA NIH HHS/United States ; RF1 AG028271/AG/NIA NIH HHS/United States ; },
abstract = {BACKGROUND: Obesity and metabolic syndrome are major public health concerns linked to cognitive decline with aging. Prior work from our lab has demonstrated that short-term high fat diet (HFD) rapidly impairs memory function via a neuroinflammatory mechanism. However, the degree to which these rapid inflammatory changes are unique to the brain is unknown. Moreover, deviations in gut microbiome composition have been associated with obesity and cognitive impairment, but how diet and aging interact to impact the gut microbiome, or how rapidly these changes occur, is less clear. Thus, our study investigated the impact of HFD after two distinct consumption durations: 3 months (to model diet-induced obesity) or 3 days (to detect the rapid changes occurring with HFD) on memory function, anxiety-like behavior, central and peripheral inflammation, and gut microbiome profile in young and aged rats.<br><br>RESULTS: Our data indicated that both short-term and long-term HFD consumption impaired memory function and increased anxiety-like behavior in aged, but not young adult, rats. These behavioral changes were accompanied by pro- and anti-inflammatory cytokine dysregulation in the hippocampus and amygdala of aged HFD-fed rats at both time points. However, changes to fasting glucose, insulin, and inflammation in peripheral tissues such as the distal colon and visceral adipose tissue were increased in young and aged rats only after long-term, but not short-term, HFD consumption. Furthermore, while subtle HFD-induced changes to the gut microbiome did occur rapidly, robust age-specific effects were only present following long-term HFD consumption.<br><br>CONCLUSIONS: Overall, these data suggest that HFD-evoked neuroinflammation, memory impairment, and anxiety-like behavior in aging develop quicker than, and separately from the peripheral hallmarks of diet-induced obesity.},
}
@article {pmid39754054,
year = {2025},
author = {Azhar Ud Din, M and Lin, Y and Lyu, C and Yi, C and Fang, A and Mao, F},
title = {Advancing therapeutic strategies for graft-versus-host disease by targeting gut microbiome dynamics in allogeneic hematopoietic stem cell transplantation: current evidence and future directions.},
journal = {Molecular medicine (Cambridge, Mass.)},
volume = {31},
number = {1},
pages = {2},
pmid = {39754054},
issn = {1528-3658},
mesh = {*Graft vs Host Disease/etiology/microbiology ; Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Gastrointestinal Microbiome ; *Transplantation, Homologous ; Animals ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; },
abstract = {Hematopoietic stem cell transplantation (HSCT) is a highly effective therapy for malignant blood illnesses that pose a high risk, as well as diseases that are at risk due to other variables, such as genetics. However, the prevalence of graft-versus-host disease (GVHD) has impeded its widespread use. Ensuring the stability of microbial varieties and associated metabolites is crucial for supporting metabolic processes, preventing pathogen intrusion, and modulating the immune system. Consequently, it significantly affects the overall well-being and susceptibility of the host to disease. Patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT) may experience a disruption in the balance between the immune system and gut bacteria when treated with medicines and foreign cells. This can lead to secondary intestinal inflammation and GVHD. Thus, GM is both a reliable indicator of post-transplant mortality and a means of enhancing GVHD prevention and treatment after allo-HSCT. This can be achieved through various strategies, including nutritional support, probiotics, selective use of antibiotics, and fecal microbiota transplantation (FMT) to target gut microbes. This review examines research advancements and the practical use of intestinal bacteria in GVHD following allo-HSCT. These findings may offer novel insights into the prevention and treatment of GVHD after allo-HSCT.},
}
@article {pmid39753816,
year = {2025},
author = {Gamrath, L and Pedersen, TB and Møller, MV and Volmer, LM and Holst-Christensen, L and Vestermark, LW and Donskov, F},
title = {Role of the Microbiome and Diet for Response to Cancer Checkpoint Immunotherapy: A Narrative Review of Clinical Trials.},
journal = {Current oncology reports},
volume = {},
number = {},
pages = {},
pmid = {39753816},
issn = {1534-6269},
abstract = {PURPOSE OF REVIEW: The advent of checkpoint immunotherapy has dramatically changed the outcomes for patients with cancer. However, a considerable number of patients have little or no response to therapy. We review recent findings on the connection between the gut microbiota and the immune system, exploring whether this link could enhance the effectiveness of immunotherapy.<br><br>RECENT FINDINGS: Clinical studies have reported specific types of bacteria in larger quantities at baseline in responders than in non-responders, especially Akkermansia mucinifila, Ruminococcaceae, Faecalibacterium, and Lachnospiraceae. Following the consumption of a high-fiber diet, bacteria in the gut ferment dietary fiber to short-chain fatty acids (SCFAs), like acetate, propionate, and butyrate. Some of the SCFAs nurture intestinal epithelial cells, and some enter the bloodstream. Here SCFAs can activate DC8&#x2009;+&#x2009;cytotoxic T-cells to induce cancer cell death. High fiber intake in the diet was associated with a reduced risk of progression or death during checkpoint immunotherapy. Recent findings demonstrate that high-fiber plant-based diets such as the Mediterranean Diet positively influence the gut microbiota whereas antibiotics and proton pump inhibitors can negatively influence outcomes of cancer immunotherapy by changing the gut microbiota. This narrative review provides evidence of an association between types of bacteria and their metabolites and favorable responses to checkpoint immunotherapy. Prospective clinical trials are needed to determine if diet interventions can improve treatment outcomes.},
}
@article {pmid39753610,
year = {2025},
author = {Cassol, I and Ibañez, M and Bustamante, JP},
title = {Key features and guidelines for the application of microbial alpha diversity metrics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {622},
pmid = {39753610},
issn = {2045-2322},
mesh = {*Microbiota ; *Biodiversity ; *Phylogeny ; Humans ; Bacteria/classification/genetics ; Guidelines as Topic ; },
abstract = {Studies of microbial communities vary widely in terms of analysis methods. In this growing field, the wide variety of diversity measures and lack of consistency make it harder to compare different studies. Most existing alpha diversity metrics are inherited from other disciplines and their assumptions are not always directly meaningful or true for microbiome data. Many existing microbiome studies apply one or some alpha diversity metrics with no fundamentals but also an unclear results interpretation. This work focuses on a theoretical, empirical, and comparative analysis of 19 frequently and less-frequently used microbial alpha diversity metrics grouped into 4 proposed categories, including key features of every analyzed metric with their mathematical assumptions, to provide a deeper understanding of the existing metrics and a practical implementation guide for future studies. Key metrics that should be required in microbiome analysis include richness, phylogenetic diversity, entropy, dominance of a few microbes over others, and an estimate of unobserved microbes. Collectively, these metrics contribute to a comprehensive set of analyses characterizing samples, allowing the determination of key aspects that might be otherwise obscured by partial or biased information. These guidelines enable further detailed analysis by each author according to their specific interests and clinical trials. Several practical examples are provided to illustrate how these recommendations improve the quality and depth of information obtained, facilitating better interpretation when working with microbiome data. These guidelines can be applied to both existing and future research studies, enhancing the standardization, consistency, and robustness of the analyses conducted. This approach aims to improve the capture of biological diversity, leading to better interpretations and insights.},
}
@article {pmid39753565,
year = {2025},
author = {Chen, YC and Su, YY and Chu, TY and Wu, MF and Huang, CC and Lin, CC},
title = {PreLect: Prevalence leveraged consistent feature selection decodes microbial signatures across cohorts.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {3},
pmid = {39753565},
issn = {2055-5008},
support = {NSTC 112-2221-E-A49 -106 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 112-2221-E-A49 -106 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; MOHW112-TDU-B-222-124013//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; MOHW111-TDU-B-221-114007//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; MOHW112-TDU-B-222-124013//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; MOHW111-TDU-B-221-114007//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; Microbiota ; Bacteria/genetics/classification/isolation &amp; purification ; Machine Learning ; Gastrointestinal Microbiome ; Cohort Studies ; Glycerophospholipids ; Computational Biology/methods ; Lipopolysaccharides ; Metagenomics/methods ; },
abstract = {The intricate nature of microbiota sequencing data-high dimensionality and sparsity-presents a challenge in identifying informative and reproducible microbial features for both research and clinical applications. Addressing this, we introduce PreLect, an innovative feature selection framework that harnesses microbes' prevalence to facilitate consistent selection in sparse microbiota data. Upon rigorous benchmarking against established feature selection methodologies across 42 microbiome datasets, PreLect demonstrated superior classification capabilities compared to statistical methods and outperformed machine learning-based methods by selecting features with greater prevalence and abundance. A significant strength of PreLect lies in its ability to reliably identify reproducible microbial features across varied cohorts. Applied to colorectal cancer, PreLect identifies key microbes and highlights crucial pathways, such as lipopolysaccharide and glycerophospholipid biosynthesis, in cancer progression. This case study exemplifies PreLect's utility in discerning clinically relevant microbial signatures. In summary, PreLect's accuracy and robustness make it a significant advancement in the analysis of complex microbiota data.},
}
@article {pmid39753561,
year = {2025},
author = {Sampson, HR and Allcock, N and Mallon, EB and Ketley, JM and Morrissey, JA},
title = {Air pollution modifies colonisation factors in beneficial symbiont Snodgrassella and disrupts the bumblebee gut microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {2},
pmid = {39753561},
issn = {2055-5008},
mesh = {Animals ; Bees/microbiology/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Symbiosis ; Biofilms/drug effects/growth &amp; development ; Air Pollution/adverse effects ; Particulate Matter/adverse effects ; RNA, Ribosomal, 16S/genetics ; Air Pollutants/adverse effects ; Bacterial Adhesion ; },
abstract = {Particulate air pollutants, a major air pollution component, are detrimental to human health and a significant risk to wildlife and ecosystems globally. Here we report the effects of particulate pollutant black carbon on the beneficial gut microbiome of important global insect pollinator, the buff-tailed bumblebee (Bombus terrestris). Our data shows that exposure to black carbon particulates alters biofilm structure, gene expression and initial adhesion of beneficial bee gut coloniser, Snodgrassella alvi. Exposure of adult Bombus terrestris to non-toxic black carbon particulates significantly increased viable bacteria on MRS agar and 16S absolute abundance of beneficial bacteria Bombilactobacillus in Post-treated bumblebees compared to Pre-treated, demonstrating disruption of the bumblebee gut microbiome. These findings show that black carbon exposure has direct, measurable effects on bees' beneficial commensal bacteria and microbiome. Together these data highlight that black carbon, a single type of particulate pollution, is an underexplored risk to insect pollinator health.},
}
@article {pmid39753162,
year = {2025},
author = {Vo, Q and Simon, ZD and Park, G and Nacionales, DC and Gorski, C and Barrios, EL and Casadesus, G and Efron, PA and Moldawer, LL and Nagpal, R and Chakrabarty, P and Febo, M},
title = {Functional connectivity within sensorimotor cortical and striatal regions is regulated by sepsis in a sex-dependent manner.},
journal = {NeuroImage},
volume = {305},
number = {},
pages = {120995},
doi = {10.1016/j.neuroimage.2024.120995},
pmid = {39753162},
issn = {1095-9572},
abstract = {Sepsis is a state of systemic immune dysregulation and organ failure that is frequently associated with severe brain disability. Epidemiological studies have indicated that younger females have better prognosis and clinical outcomes relative to males, though the sex-dependent response of the brain to sepsis during post-sepsis recovery remains largely uncharacterized. Using a modified polymicrobial intra-abdominal murine model of surgical sepsis, we characterized the acute effects of intra-abdominal sepsis on peripheral inflammation, brain inflammation and brain functional connectivity in young adult mice of both sexes. Following sepsis, both male and female mice survived the procedure, regained body weight within 7 days post-sepsis and showed reduced diversity in their gut microbiome. Interestingly, compared to the sepsis-induced changes observed in female mice, the post-septic male mice exhibited a comparatively robust profile of splenic cell expansion and intracerebral glial proliferation relative to their healthy counterparts. Analysis of resting-state functional Magnetic Resonance Imaging (fMRI) data collected from the post-septic mice revealed that while connectivity to the somatosensory cortex were affected equally in both sexes, intra-network connectivity strength in the striatum preferentially increased in post-septic males but remained near baseline in post-septic female mice. Additionally, the female mice showed reduced network connectivity alterations in the projections from periaqueductal gray to the superior colliculus as also between the anterior cingulate cortex and the striatum. Coupled with the sustained intracerebral gliosis response, the intra-striatal fMRI response patterns in males could signify a delayed recovery from sepsis. Together, our study provides evidence that peripheral sepsis influences peripheral immunity, brain immunity and brain connectivity in a sex-dependent manner, with the fMRI response strongly indicating cognitive benefits in young females recovering from sepsis relative to their male counterparts.},
}
@article {pmid39752320,
year = {2025},
author = {Li, J and Wei, W and Ma, X and Ji, J and Ling, X and Xu, Z and Guan, Y and Zhou, L and Wu, Q and Huang, W and Liu, F and Zhao, M},
title = {Antihypertensive effects of rice peptides involve intestinal microbiome alterations and intestinal inflammation alleviation in spontaneously hypertensive rats.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo04251d},
pmid = {39752320},
issn = {2042-650X},
abstract = {Gut dysbiosis serves as an underlying risk factor for the development of hypertension. The resolution of this dysbiosis has emerged as a promising strategy in improving hypertension. Food-derived bioactive protein peptides have become increasingly more attractive in ameliorating hypertension, primarily due to their anti-inflammatory and anti-oxidant activities. However, the regulatory mechanisms linking rice peptides (RP), gut dysbiosis, and hypertension remain to be fully elucidated. In our study, male spontaneously hypertensive rats (SHR) were fed with chow diet and concomitantly treated with ddH2O (Ctrl) or varying doses of rice peptides (20, 100, or 500 mg (kg bw day)[-1] designated as low-dose RP, LRP; medium-dose RP, MRP; high-dose RP, HAP) or captopril (Cap) by intragastric administration. Wistar-Kyoto (WKY) rats served as the normotensive control group and were orally administered with ddH2O. We observed beneficial effects of RP in lowering blood pressure and ameliorating cardiovascular risk profiles, as evidenced by improvements in glucolipid metabolic disorders, hepatic and renal damage, left ventricular hypertrophy and endothelial dysfunction in hypertensive rats. More importantly, we found that RP attenuated intestinal pathological damage, improved impaired intestinal barrier, and reduced intestinal inflammation by inhibiting the HMGB1-TLR4-NF-κB pathway. Notably, multi-omics integrative analyses have revealed that RP altered the composition and function of the gut microbiota. This is exemplified by the observed enrichment of beneficial bacterial constituents, such as g_Lactobacillus, g_Lactococcus, s_Lactobacillus_intestinalis, and Lactococcus lactis, and elevated production of microbiota-derived short-chain fatty acid metabolites. Collectively, these studies suggest that the hypotensive effects of RP may be associated with modulation of the gut microbiota and its short-chain fatty acids metabolites. This implicates the microbiota-gut-HMGB1-TLR4-NF-κB axis as a novel venue for the amelioration of hypertension and its complications.},
}
@article {pmid39751930,
year = {2025},
author = {Chen, L and Xu, Q and Chen, W and Liu, J and Xu, T and Yang, J and Ji, L},
title = {Tumor-colonizing Lachnoclostridium-mediated chemokine expression enhances the immune infiltration of bladder urothelial carcinoma.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {74},
number = {2},
pages = {62},
pmid = {39751930},
issn = {1432-0851},
mesh = {Humans ; *Urinary Bladder Neoplasms/immunology/pathology ; *Chemokines/metabolism ; *Tumor Microenvironment/immunology ; Prognosis ; Immunotherapy/methods ; Lymphocytes, Tumor-Infiltrating/immunology/metabolism ; Female ; Male ; },
abstract = {Limited research into the tumor immune microenvironment (TIME) for bladder urothelial carcinoma (BUC), particularly the neglect of the intratumoral microbiota, has hindered the development of immunotherapies targeting BUC. Here, we collect 401 patients with BUC with host transcriptome samples and matched tumor microbiome samples from The Cancer Genome Atlas database. Besides, two independent BUC cohorts receiving immunotherapy were obtained. First, we find that the TIME profile is closely related to the prognosis of patients with BUC. Additionally, the genus Lachnoclostridium in tumors could regulate the accumulation of chemokines to recruit immune cell populations into bladder tumors. Among them, chemokines include CCL3, CCL4, CXCL9, CXCL10, and CXCL11, and immune cells mainly involve macrophages and CD8[+] T cells. Analyses based on two independent immunotherapy cohorts suggest that these immune-related chemokines strongly influence the immunotherapeutic efficacy of BUC. Furthermore, drug predictive analyses show that immune-related chemokines impact patients' sensitivity to diverse drugs. These results suggest a dual role of immune-related chemokines in combination therapy against BUC. Collectively, our study provides new insights into the regulation of TIME by intratumoral microbiota and provides guidance for improving immunotherapy against BUC.},
}
@article {pmid39751637,
year = {2025},
author = {Sawicka-Gutaj, N and Stańska, A and Stański, M and Gruszczyński, D and Zawalna, N and Pochylski, M and Ruchała, M},
title = {Elimination of oral foci of infection might lead to clinical improvement of Graves' orbitopathy.},
journal = {Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie},
volume = {},
number = {},
pages = {},
pmid = {39751637},
issn = {1435-702X},
abstract = {PURPOSE: Graves' disease (GD) and Graves' orbitopathy (GO) are multifactorial disorders with links to the gut microbiome and autoimmunity. It is observed that patients with GD exhibit altered gut microbiome diversity. However, little is known about the role of oral microbiota in GD and GO. This study aims to investigate the impact of oral health and oral sanitation on the clinical course of GO in patients disqualified from glucocorticoid treatment due to oral infections.<br><br>METHODS: We reviewed 188 admissions of 127 patients with GO, hospitalized in a tertiary university hospital. Clinical, biochemical, imaging, ophthalmological, and oral health assessment data from each admission were analyzed. Patients excluded from the glucocorticoids (GCs) therapy due to oral foci of infection had the clinical activity score (CAS) reassessed after three months, and they were divided into two groups: with and without improvement.<br><br>RESULTS: Finishing dental treatment in the meantime was the only factor significantly correlated with improvement in these patients (p&#x2009;=&#x2009;0.041). The secondary finding was that anti-thyroid peroxidase antibodies titer was significantly higher in the group with oral foci of infection considered as a contraindication for GCs (medians 28.50 vs 128.00; p&#x2009;=&#x2009;0.026), and those patients were more likely to smoke than the group without oral issues (p&#x2009;=&#x2009;0.024).<br><br>CONCLUSIONS: The results of our study suggest that monitoring and treating oral diseases may be pertinent in patients with GO and might serve as a supportive treatment strategy for managing the condition.<br><br>KEY MESSAGES: What is known: There is a recognized link between gut dysbiosis and the autoimmune processes in Graves' Disease (GD) and Graves' Orbitopathy (GO).<br><br>WHAT IS NEW: Elevated levels of TPOAb have been observed in patients with GO who also have oral foci of infection. Dental treatment has been shown to lead to significant clinical improvements in patients with GO. Maintaining oral hygiene might serve as a supportive treatment strategy for managing GO.},
}
@article {pmid39750501,
year = {2024},
author = {van der Meij, B and Parsons, S and Mazurak, V},
title = {The impact of n-3 polyunsaturated fatty acids in patients with cancer: emerging themes.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCO.0000000000001102},
pmid = {39750501},
issn = {1473-6519},
abstract = {PURPOSE OF REVIEW: This review summarizes recent literature falling broadly under the topic of n-3 polyunsaturated fatty acids (PUFAs) in the oncology setting, highlighting emerging themes and emphasizing novel explorations.<br><br>RECENT FINDINGS: Meta-analyses continue to confirm safety and efficacy of n-3 PUFA supplementation on reducing inflammation and improving survival in people with cancer. Common themes in recent studies emphasize improving tumor-directed efficacy and reducing toxicities of common cancer therapies. New areas of interest include the impact of n-3 PUFA when combined with immunotherapies and applications in pediatric acute lymphoid leukemia. Novel assessments include specialized pro-resolving lipid mediators, the intestinal microbiome and psychological well being. A variety of clinically relevant outcomes including nutritional status, toxicities and survival are being explored in ongoing clinical studies.<br><br>SUMMARY: Evidence confirms the safety of n-3 PUFA for patients with cancers, as well as benefits in some, but not all areas of exploration. Larger, well designed trials with biological assessment of compliance compared to the prescribed n-3 PUFA dose would strengthen the evidence needed to integrate n-3 PUFA recommendations into clinical practice for patients with cancer.},
}
@article {pmid39749808,
year = {2025},
author = {Wu, H},
title = {Charting The Microbial Frontier: A Comprehensive Guidebook for Advancing Microbiome Research.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuae033},
pmid = {39749808},
issn = {1574-6976},
}
@article {pmid39749333,
year = {2024},
author = {Nowotny, HF and Zheng, T and Seiter, TM and Ju, J and Schneider, H and Kroiss, M and Sarkis, AL and Sturm, L and Britz, V and Lechner, A and Potzel, AL and Kunz, S and Bidlingmaier, M and Neuhaus, K and Gottschlich, A and Kobold, S and Reisch, N and Schirmer, M and Reincke, M and Adolf, C},
title = {Sex-dependent modulation of T and NK cells and gut microbiome by low sodium diet in patients with primary aldosteronism.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1428054},
pmid = {39749333},
issn = {1664-3224},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/immunology ; Male ; *Hyperaldosteronism/immunology ; Middle Aged ; *Killer Cells, Natural/immunology ; *Diet, Sodium-Restricted ; Prospective Studies ; Adult ; Sex Factors ; T-Lymphocytes/immunology ; },
abstract = {BACKGROUND: High dietary sodium intake is a major cardiovascular risk factor and adversely affects blood pressure control. Patients with primary aldosteronism (PA) are at increased cardiovascular risk, even after medical treatment, and high dietary sodium intake is common in these patients. Here, we analyze the impact of a moderate dietary sodium restriction on microbiome composition and immunophenotype in patients with PA.<br><br>METHODS: Prospective two-stage clinical trial including two subgroups: 15 treatment-naive PA patients compared to matched normotensive controls; and 31 PA patients on mineralocorticoid receptor antagonist treatment before and three months after sodium restriction. Patients underwent blood pressure measurements, laboratory tests, analysis of peripheral blood mononuclear cells via flow cytometry and microbiome analysis.<br><br>RESULTS: We observed a higher percentage of Tregs in treatment-naive PA patients (p = 0.0303), while the abundance of Bacteroides uniformis was higher in PA patients compared to normotensive controls (p = 0.00027) and the abundance of Lactobacillus species however was higher in the subgroup of&#xa0;normotensive controls (p = 0.0290). Sodium restriction was accompanied by a&#xa0;decrease in pro-inflammatory Tc17 cells in male patients (p = 0.0081, females p&#xa0;= 0.3274). Bacteroides uniformis abundance was higher in female patients (0.01230, p = 0.0016) and decreased upon sodium restriction (0.002309, p&#xa0;= 0.0068).<br><br>CONCLUSION: Dietary sodium restriction in patients with PA modulates the peripheral immune cell composition toward a less inflammatory phenotype. This suggests a potential mechanism by which sodium reduction modulates immune cell composition, leading to blood pressure reduction and positively impacting cardiovascular risk.},
}
@article {pmid39749183,
year = {2024},
author = {Indio, V and Gonzales-Barron, U and Oliveri, C and Lucchi, A and Valero, A and Achemchem, F and Manfreda, G and Savini, F and Serraino, A and De Cesare, A},
title = {Comparative analysis of the microbiome composition of artisanal cheeses produced in the Mediterranean area.},
journal = {Italian journal of food safety},
volume = {13},
number = {4},
pages = {12818},
pmid = {39749183},
issn = {2239-7132},
abstract = {In the PRIMA project ArtiSaneFood, the microbiological parameters of several artisanal cheeses produced in the Mediterranean area have been quantified. In this pilot study, we selected four of these artisanal cheese products from Italy, Portugal, Spain, and Morocco to investigate and compare their microbiomes in terms of taxonomic composition, presence of reads of foodborne pathogens, as well as virulence and antimicrobial resistance genes. Lactococcus, Streptococcus and Lactobacillus were the most represented genera in the Portuguese and Spanish cheeses, Streptococcus in the Italian cheese, and Enterococcus, Klebsiella, Escherichia, and Citrobacter in the Moroccan products. The correlation analysis indicated a negative association between the abundance of some lactic acid bacteria (i.e., Lactococcus, Lactobacillus, Streptococcus, and Leuconostoc) and foodborne pathogenic genera, like Escherichia and Salmonella. The analysis of pathogen abundance, virulence factors, and antimicrobial resistance genes showed a strong clusterization based on the cheese type, confirming that the presence of potential human health risk determinants was higher in the artisanal products derived from unpasteurized milk that underwent spontaneous fermentation.},
}
@article {pmid39749035,
year = {2024},
author = {Rother, C and John, T and Wong, A},
title = {Biomarkers for immunotherapy resistance in non-small cell lung cancer.},
journal = {Frontiers in oncology},
volume = {14},
number = {},
pages = {1489977},
pmid = {39749035},
issn = {2234-943X},
abstract = {Immunotherapy has revolutionised the treatment landscape of non-small cell lung cancer (NSCLC), significantly improving survival outcomes and offering renewed hope to patients with advanced disease. However, the majority of patients experience limited long-term benefits from immune checkpoint inhibition (ICI) due to the development of primary or acquired immunotherapy resistance. Accurate predictive biomarkers for immunotherapy resistance are essential for individualising treatment strategies, improving survival outcomes, and minimising potential treatment-related harm. This review discusses the mechanisms underlying resistance to immunotherapy, addressing both cancer cell-intrinsic and cancer cell-extrinsic resistance processes. We summarise the current utility and limitations of two clinically established biomarkers: programmed death ligand 1 (PD-L1) expression and tumour mutational burden (TMB). Following this, we present a comprehensive review of emerging immunotherapy biomarkers in NSCLC, including tumour neoantigens, epigenetic signatures, markers of the tumour microenvironment (TME), genomic alterations, host-microbiome composition, and circulating biomarkers. The potential clinical applications of these biomarkers, along with novel approaches to their biomarker identification and targeting, are discussed. Additionally, we explore current strategies to overcome immunotherapy resistance and propose incorporating predictive biomarkers into an adaptive clinical trial design, where specific immune signatures guide subsequent treatment selection.},
}
@article {pmid39748884,
year = {2024},
author = {Zhou, H and Pei, Y and Xie, Q and Nie, W and Liu, X and Xia, H and Jiang, J},
title = {Diagnosis and insight into the unique lung microbiota of pediatric pulmonary tuberculosis patients by bronchoalveolar lavage using metagenomic next-generation sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1492881},
pmid = {39748884},
issn = {2235-2988},
mesh = {Humans ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing ; Male ; Child ; *Microbiota/genetics ; *Lung/microbiology ; Child, Preschool ; *Metagenomics/methods ; Sensitivity and Specificity ; Adolescent ; Mycobacterium tuberculosis/genetics/isolation &amp; purification ; Infant ; Bronchoalveolar Lavage ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Although previous studies have reported the dysregulation of respiratory tract microbiota in infectious diseases, insufficient data exist regarding respiratory microbiota imbalances in the lower respiratory tracts of children with pulmonary tuberculosis (PTB). In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of PTB patients using bronchoalveolar lavage fluid (BALF) samples.<br><br>METHODS: A total of 64 participants, comprising 43 pediatric PTB and 21 pediatric pneumonia patients were recruited in the present study. BALF samples were collected from the above participants. Parallel comparisons between mNGS and conventional microbial test (CMT) pathogen detection were performed. Moreover, the diversity and structure of all 64 patients' lung BALF microbiomes were explored using the mNGS data.<br><br>RESULTS: Comparing to the final clinical diagnosis, mNGS in BALF samples produced a sensitivity of 46.51%, which was lower than that of TB-PCR (55.00%) and Xpert (55.00%). The diagnostic efficacy of PTB can be highly enhanced by mNGS combined with TB-PCR (AUC=0.8140, P<0.0001). There were no significant differences in the diversity either between patients with TB and pneumonia. Positive mNGS pathogen results in pediatric PTB patients significantly affect the &#x3b2;-diversity of the pulmonary microbiota. In addition, significant taxonomic differences were found in BALF specimens from patients with PTB and pneumonia, both of which have unique bacterial compositions.<br><br>CONCLUSIONS: mNGS is valuable in the etiological diagnosis of PTB, and can reveal pulmonary microecological characteristics. For pediatric PTB patients, the mNGS should be implemented early and complementary to CMTs.},
}
@article {pmid39748840,
year = {2024},
author = {Fongang, B and Ayele, BA and Wadop, YN and Epenge, E and Nkouonlack, CD and Njamnshi, WY and Jian, X and Sargurupremraj, M and Djotsa, ABSN and Seke Etet, PF and Bernal, R and Atangana, A and Cavazos, JE and Himali, JJ and Fonteh, AN and Maestre, G and Njamnshi, AK and Seshadri, S},
title = {The African Initiative for Bioinformatics Online Training in Neurodegenerative Diseases (AI-BOND): Investing in the next generation of African neuroscientists.},
journal = {Alzheimer's &amp; dementia (New York, N. Y.)},
volume = {10},
number = {4},
pages = {e70002},
pmid = {39748840},
issn = {2352-8737},
abstract = {UNLABELLED: Neurodegenerative disorders, including Alzheimer's disease and AD-related dementias (AD/ADRD), pose significant challenges to health care systems globally, particularly in Africa. With the advances in medical technology and research capabilities, especially in next-generation sequencing and imaging, vast amounts of data have been generated from AD/ADRD research. Given that the greatest increase in AD/ADRD prevalence is expected to occur in Africa, it is critical to establish comprehensive bioinformatics training programs to help African scientists leverage existing data and collect additional information to untangle AD/ADRD heterogeneity in African populations. The South Texas Alzheimer's Disease Research Center, with efforts from the National Institutes of Health and the Global Brain Health Institute, has partnered with the Brain Research Africa Initiative to develop the African Initiative on Bioinformatics Online Training in Neurodegenerative Disease (AI-BOND). AI-BOND is a comprehensive and accessible training program, the aim of which is to advance biostatistics and bioinformatics expertise in Africa in studying neurodegenerative diseases. This expertise is essential to enable African scientists to utilize the extensive AD/ADRD data and enhance the continent's ability to contribute to global research efforts in this field. The training addresses the gap in analyzing neurodegenerative disease data by providing skills and knowledge in genetic epidemiology, biostatistics, and bioinformatics to African students and researchers. This innovative online training program will last 6 months and provide training in skill sets R, SAS, and Python programing, genome-wide association studies, genomics, transcriptomics, proteomics, metabolomics, microbiome analysis, and advanced statistical methods. Additional training will include study design and manuscript and grant writing. The first cohort of the AI-BOND program will graduate in June 2024. The AI-BOND program is expected to build research computational capacities in Africa that will improve the ability of graduates to conduct and utilize large-scale studies, with the goal of curbing the growing incidence of neurodegenerative diseases in Africa.<br><br>HIGHLIGHTS: Alzheimer's disease (AD) and AD-related dementias (ADRD) pose significant health challenges globally, particularly in Africa.The most significant AD/ADRD prevalence increase is predicted to occur in Africa.It is crucial to establish a bioinformatics training capacity in Africa to leverage the vast number of multi-omics and imaging biomarkers of AD/ADRD data being generated.The African Initiative on Bioinformatics Online Training in Neurodegenerative Disease (AI-BOND) training addresses the gaps in study design, biostatistics, genetic epidemiology, and bioinformatics related to neurodegenerative diseases in Africa.The success of AI-BOND is anticipated to help build computational research capacities in Africa.},
}
@article {pmid39748805,
year = {2024},
author = {Busch, K and Murillo, FJ and Lirette, C and Wang, Z and Kenchington, E},
title = {Putative past, present, and future spatial distributions of deep-sea coral and sponge microbiomes revealed by predictive models.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae142},
pmid = {39748805},
issn = {2730-6151},
abstract = {Knowledge of spatial distribution patterns of biodiversity is key to evaluate and ensure ocean integrity and resilience. Especially for the deep ocean, where in situ monitoring requires sophisticated instruments and considerable financial investments, modeling approaches are crucial to move from scattered data points to predictive continuous maps. Those modeling approaches are commonly run on the macrobial level, but spatio-temporal predictions of host-associated microbiomes are not being targeted. This is especially problematic as previous research has highlighted that host-associated microbes may display distribution patterns that are not perfectly correlated not only with host biogeographies, but also with other factors, such as prevailing environmental conditions. We here establish a new simulation approach and present predicted spatio-temporal distribution patterns of deep-sea sponge and coral microbiomes, making use of a combination of environmental data, host data, and microbiome data. This approach allows predictions of microbiome spatio-temporal distribution patterns on scales that are currently not covered by classical sampling approaches at sea. In summary, our presented predictions allow (i) identification of microbial biodiversity hotspots in the past, present, and future, (ii) trait-based predictions to link microbial with macrobial biodiversity, and (iii) identification of shifts in microbial community composition (key taxa) across environmental gradients and shifting environmental conditions.},
}
@article {pmid39748720,
year = {2024},
author = {Crispino, A and Varricchio, S and Esposito, A and Marfella, A and Cerbone, D and Perna, A and Petronio Petronio, G and Staibano, S and Merolla, F and Ilardi, G},
title = {The oral microbiome and its role in oral squamous cell carcinoma: a systematic review of microbial alterations and potential biomarkers.},
journal = {Pathologica},
volume = {116},
number = {6},
pages = {338-357},
doi = {10.32074/1591-951X-N867},
pmid = {39748720},
issn = {1591-951X},
mesh = {Humans ; *Mouth Neoplasms/microbiology/diagnosis/pathology ; *Microbiota ; *Mouth/microbiology ; *Carcinoma, Squamous Cell/microbiology/diagnosis/pathology ; Biomarkers, Tumor/analysis ; Squamous Cell Carcinoma of Head and Neck/microbiology/pathology ; },
abstract = {BACKGROUND: Oral squamous cell carcinoma (OSCC) is one of the most common cancers worldwide. Despite advances in diagnosis and treatment, the incidence of OSCC is increasing, and the mortality rate remains high. This systematic review aims to examine the potential association between the composition of the oral microbiota and OSCC.<br><br>MATERIALS AND METHODS: This study's protocol was developed according to the PRISMA guidelines. Several search engines, including Medline-PubMed, Scopus (via Elsevier), and Google Scholar, were used to identify original studies that analyzed differences in the oral microbiome between OSCC patients and controls. Twenty-seven studies were identified that reported significant differences in microbial abundance between OSCC and controls.<br><br>RESULTS: The systematic review highlights a complex relationship between the oral microbiome and the pathogenesis of OSCC. Significant changes in the microbial composition were identified, with a predominance of phyla such as Bacteroidetes and Fusobacteria, which are associated with inflammatory mechanisms facilitating tumor progression. A remarkable variability in microbial profiles emerged based on the different stages of the disease and the types of samples analyzed, demonstrating the complexity of the oral microbial ecosystem.<br><br>CONCLUSION: Although alterations in the oral cavity microbiome composition are evident in patients with OSCC, identifying a specific pattern remains challenging. However, the integration of advanced analytical techniques, such as artificial intelligence, could overcome this problem, allowing the identification of crucial biomarkers and improving the understanding of the role of the microbiome in carcinogenesis. This approach could transform microbiome analysis into a useful tool for screening and monitoring patients with OSCC.},
}
@article {pmid39748613,
year = {2025},
author = {Liu, C and Udawatte, NS and Liaw, A and Staples, R and Salomon, C and Seneviratne, CJ and Ivanovski, S and Han, P},
title = {Microbial DNA Profiles of Bacterial Extracellular Vesicles from 3D Salivary Polymicrobial Biofilms - A Pilot Study.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e2403300},
doi = {10.1002/adhm.202403300},
pmid = {39748613},
issn = {2192-2659},
support = {//UQ Graduate School Scholarships/ ; //University of Queensland/ ; 1&#xa0;195&#xa0;451//National Health and Medical Research Council/ ; 2&#xa0;034&#xa0;591//National Health and Medical Research Council/ ; PJ-0000042//Australian Dental Research Foundation/ ; //Australian Periodontology Research Foundation/ ; 2023//Colgate-Palmolive Student Research/ ; 2&#xa0;023&#xa0;000&#xa0;467//Human Research Ethics Committee of The University of Queensland/ ; },
abstract = {With the advent of multi-layered and 3D scaffolds, the understanding of microbiome composition and pathogenic mechanisms within polymicrobial biofilms is continuously evolving. A fundamental component in mediating the microenvironment and bacterial-host communication within the biofilm are bilayered nanoparticles secreted by bacteria, known as bacterial extracellular vesicles (BEVs), which transport key biomolecules including proteins, nucleic acids, and metabolites. Their characteristics and microbiome profiles are yet to be explored in the context of in vitro salivary polymicrobial biofilm. This pilot study aimed to compare the profiles of BEVs from salivary biofilm cultured on a 2D tissue culture plate and 3D melt electrowritten medical-grade polycaprolactone (MEW mPCL) scaffold. BEVs derived from MEW mPCL biofilm exhibited enhanced purity and yield without altered EV morphology and lipopolysaccharide (LPS) content, with enriched BEVs-associated DNA from Capnocytophaga, porphyromonas, and veillonella genus. Moreover, compared to saliva controls, MEW mPCL BEVs showed comparable DNA expression of Tannerella forsythia, and Treponema denticola and significantly higher expression in Porphyromonas gingivalis, Eikenella corrodens and Lactobacillus acidophilus. Together, these findings highlight a more detailed microbial profile with BEVs derived from salivary biofilms cultured on 3D MEW PCL scaffolds, which facilitates an effective in vitro model with a greater resemblance to naturally occurring biofilms.},
}
@article {pmid39748236,
year = {2025},
author = {Bongiovanni, T and Santiago, M and Zielinska, K and Scheiman, J and Barsa, C and Jäger, R and Pinto, D and Rinaldi, F and Giuliani, G and Senatore, T and Kostic, AD},
title = {A Lactobacillus consortium provides insights into the sleep-exercise-microbiome nexus in proof of concept studies of elite athletes and in the general population.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {1},
pmid = {39748236},
issn = {2049-2618},
mesh = {Humans ; *Probiotics ; *Gastrointestinal Microbiome ; *Sleep/physiology ; *Athletes ; Male ; *Exercise/physiology ; Adult ; *Lactobacillus ; Female ; Longitudinal Studies ; Young Adult ; Proof of Concept Study ; Soccer ; },
abstract = {BACKGROUND: The complex relationship among sleep, exercise, and the gut microbiome presents a unique opportunity to improve health and wellness. Here, we conducted the first large-scale investigation into the influence of a novel elite athlete-derived probiotic, consisting of a multi-strain Lactobacillus consortium, on sleep quality, exercise recovery, and gut microbiome composition in both elite athletes (n = 11) and the general population (n = 257).<br><br>RESULTS: Our two-phase study design, which included an open-label study followed by a controlled longitudinal study in a professional soccer team, allowed us to identify key interactions between probiotics, the gut microbiome, and the host. In the placebo-controlled study, we observed significant improvements in self-reported sleep quality by 69%, energy levels by 31%, and bowel movements by 37% after probiotic intervention relative to after placebo. These improvements were associated with a significant decrease in D-ROMS (a marker of oxidative stress) and a significantly higher free-testosterone/cortisol ratio. Multi-omics analyses revealed specific changes in microbiome composition and function, potentially providing mechanistic insights into these observed effects.<br><br>CONCLUSION: This study provides novel insights into how a multi-strain Lactobacillus probiotic modulates sleep quality, exercise recovery, and gut microbiome composition in both the general population and elite athletes, and introduces potential mechanisms through which this probiotic could be influencing overall health. Our results emphasize the untapped potential of tailored probiotic interventions derived from extremely fit and healthy individuals in improving several aspects of health and performance directly in humans. Video Abstract.},
}
@article {pmid39748068,
year = {2025},
author = {Li, S and Ma, X and Mei, H and Chang, X and He, P and Sun, L and Xiao, H and Wang, S and Li, R},
title = {Association between gut microbiota and short-chain fatty acids in children with obesity.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {483},
pmid = {39748068},
issn = {2045-2322},
support = {2019ZYYD051//the Special Projects for the Central Government to Guide the Development of Local Science and Technology/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Child ; Male ; *Fatty Acids, Volatile/metabolism/blood ; Female ; Adolescent ; *Pediatric Obesity/microbiology/metabolism/blood ; Case-Control Studies ; Feces/microbiology ; Metabolome ; Metagenomics/methods ; Body Mass Index ; },
abstract = {The gut microbiome and its metabolites may be important role in regulating the pathogenesis of obesity. This study aimed to characterize the gut microbiome and short-chain fatty acid (SCFA) metabolome in obese children. This case-control study recruited children aged 7‒14 years and divided them into a normal group (NG) and an obese group (OG) based on their body mass index. Whole-genome shotgun metagenomic analysis was performed on fecal samples from the OG and NG groups to characterize the signatures and functional potential of the gut microbiota. Serum metabolite profiles were analyzed using high-performance liquid chromatography/mass spectrometry (LC/MS). The Statistical Package for the Social Sciences (SPSS, version 26) and R software were used for data analysis. A total of 99 children were recruited, with 49 in the OG and 50 in the NG. At the phylum level, Proteobacteria were significantly more abundant in children in the OG than those in the NG. At the genus level, Oscillibacter and Alistipes were significantly lower in children in the OG than those in the NG. Caproate levels significantly increased, whereas butyrate and isobutyrate levels decreased in children in the OG than those in the NG. Kyoto encyclopedia of genes and genomes (KEGG) functional analysis revealed 28 enriched KEGG pathways, of which/with the phosphotransferase system (PTS) and enhanced biofilm formation by Escherichia coli were particularly significant in the OG. Spearman's correlation analysis indicated that the genus Oscillibacter and species Clostridium_sp._CAG:302 connect serum metabolites and the gut microbiota in childhood obesity. Childhood obesity is correlated with the symbiotic status of the gut microbiota. The microbiota influences human metabolism via specific pathways, particularly butyrate, caproate, and the genus Oscillibacter, all closely associated with obesity.},
}
@article {pmid39747999,
year = {2025},
author = {Díaz-Rullo, J and González-Moreno, L and Del Arco, A and González-Pastor, JE},
title = {Decoding the general role of tRNA queuosine modification in eukaryotes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {345},
pmid = {39747999},
issn = {2045-2322},
support = {PID2021-126114NB-C43//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114499RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; FPU18/03583//Ministerio de Universidades/ ; FPU18/01109//Ministerio de Universidades/ ; },
mesh = {*RNA, Transfer/genetics/metabolism ; Humans ; *Nucleoside Q/metabolism ; *Eukaryota/genetics/metabolism ; Computational Biology/methods ; Protein Biosynthesis ; Codon/genetics ; Animals ; },
abstract = {Transfer RNA (tRNA) contains modified nucleosides essential for modulating protein translation. One of these modifications is queuosine (Q), which affects NAU codons translation rate. For decades, multiple studies have reported a wide variety of species-specific Q-related phenotypes in different eukaryotes, hindering the identification of a general underlying mechanism behind that phenotypic diversity. Here, through bioinformatics analysis of representative eukaryotic genomes we have predicted: i) the genes enriched in NAU codons, whose translation would be affected by tRNA Q-modification (Q-genes); and ii) the specific biological processes of each organism enriched in Q-genes, which generally in eukaryotes would be related to ubiquitination, phosphatidylinositol metabolism, splicing, DNA repair or cell cycle. These bioinformatics results provide evidence to support for the first time in eukaryotes that the wide diversity of phenotypes associated with tRNA Q-modification previously described in various species would directly depend on the control of Q-genes translation, and would allow prediction of unknown Q-dependent processes, such as Akt activation and p53 expression, which we have tested in human cancer cells. Considering the relevance of the Q-related processes, our findings may support further exploration of the role of Q in cancer and other pathologies. Moreover, since eukaryotes must salvage Q from bacteria, we suggest that changes in Q supply by the microbiome would affect the expression of host Q-genes, altering its physiology.},
}
@article {pmid39747960,
year = {2025},
author = {Fang, Q and Qiu, T and Chen, F and Tian, X and Feng, Z and Cao, Y and Bai, J and Huang, J and Liu, Y},
title = {The relationship between prenatal drought exposure and the diversity and composition of gut microbiome in pregnant women and neonates.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {296},
pmid = {39747960},
issn = {2045-2322},
support = {81903334//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Infant, Newborn ; Pregnancy ; *Droughts ; Adult ; *RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Male ; },
abstract = {Drought induced by climate change poses a serious threat to human health. The gut microbiome also plays a critical role in human health. However, no studies have explored the effect of drought on the human gut microbiome. Therefore, our study aimed to investigate the relationship between drought and gut microbiome. Our study included 59 mothers and 38 neonates in our study. 16S rRNA V3-V4 sequencing was used to profile the gut microbiome. The Standardized Precipitation Evapotranspiration Index (SPEI) was used to represent drought characteristics. KEGG pathway level 3 was employed for functional analysis. Generalized linear models were used to explore the effect of drought on the gut microbiome. Mothers and neonates were divided into the LSPEI (Lower SPEI) group or HSPEI (Higher SPEI) group by calculating the average levels of prenatal SPEI levels. The maternal and neonatal gut microbiome exhibited similar diversities in terms of alpha and beta diversity between the LSPEI and HSPEI groups. However, notable differences were observed in their composition. We found that in the neonatal gut microbiome, Sediminibacterium and Thermovirga were positively associated with SPEI after controlling for PM2.5 in linear regression models. Additionally, SPEI was significantly associated with phenylpropanoid biosynthesis and cyanoamino acid metabolism in neonates. This study identified that prenatal SPEI levels were correlated with specific maternal and neonatal gut microbial taxa, as well as neonatal gut microbial functional pathways. Future studies should further investigate the mechanisms by which drought exposure influences maternal and neonatal gut microbial diversities, composition, and functional pathways.},
}
@article {pmid39747694,
year = {2025},
author = {Hsu, TY and Nzabarushimana, E and Wong, D and Luo, C and Beiko, RG and Langille, M and Huttenhower, C and Nguyen, LH and Franzosa, EA},
title = {Profiling lateral gene transfer events in the human microbiome using WAAFLE.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39747694},
issn = {2058-5276},
support = {K23DK125838//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R24DK110499//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; Research Scholars Award//American Gastroenterological Association (AGA)/ ; Career Development Award//Crohn's and Colitis Foundation (Crohn's &amp; Colitis Foundation)/ ; T32CA009001//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; U54DE023798//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
abstract = {Lateral gene transfer (LGT), also known as horizontal gene transfer, facilitates genomic diversification in microbial populations. While previous work has surveyed LGT in human-associated microbial isolate genomes, the landscape of LGT arising in personal microbiomes is not well understood, as there are no widely adopted methods to characterize LGT from complex communities. Here we developed, benchmarked and validated a computational algorithm (WAAFLE or Workflow to Annotate Assemblies and Find LGT Events) to profile LGT from assembled metagenomes. WAAFLE prioritizes specificity while maintaining high sensitivity for intergenus LGT. Applying WAAFLE to >2,000 human metagenomes from diverse body sites, we identified >100,000 high-confidence previously uncharacterized LGT (~2 per microbial genome-equivalent). These were enriched for mobile elements, as well as restriction-modification functions associated with the destruction of foreign DNA. LGT frequency was influenced by biogeography, phylogenetic similarity of involved pairs (for example, Fusobacterium periodonticum and F. nucleatum) and donor abundance. These forces manifest as networks in which hub taxa donate unequally with phylogenetic neighbours. Our findings suggest that human microbiome LGT may be more ubiquitous than previously described.},
}
@article {pmid39747693,
year = {2025},
author = {Michoud, G and Peter, H and Busi, SB and Bourquin, M and Kohler, TJ and Geers, A and Ezzat, L and , and Battin, TJ},
title = {Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39747693},
issn = {2058-5276},
support = {Vanishing Glaciers Project//NOMIS Stiftung (NOMIS Foundation)/ ; },
abstract = {Glacier-fed streams (GFS) feature among Earth's most extreme aquatic ecosystems marked by pronounced oligotrophy and environmental fluctuations. Microorganisms mainly organize in biofilms within them, but how they cope with such conditions is unknown. Here, leveraging 156 metagenomes from the Vanishing Glaciers project obtained from sediment samples in GFS from 9 mountains ranges, we report thousands of metagenome-assembled genomes (MAGs) encompassing prokaryotes, algae, fungi and viruses, that shed light on biotic interactions within glacier-fed stream biofilms. A total of 2,855 bacterial MAGs were characterized by diverse strategies to exploit inorganic and organic energy sources, in part via functional redundancy and mixotrophy. We show that biofilms probably become more complex and switch from chemoautotrophy to heterotrophy as algal biomass increases in GFS owing to glacier shrinkage. Our MAG compendium sheds light on the success of microbial life in GFS and provides a resource for future research on a microbiome potentially impacted by climate change.},
}
@article {pmid39747692,
year = {2025},
author = {Olm, MR and Spencer, SP and Takeuchi, T and Silva, EL and Sonnenburg, JL},
title = {Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39747692},
issn = {2058-5276},
support = {T32DK007056//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; K08DK134856//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; K08 DK134856/DK/NIDDK NIH HHS/United States ; DP1AT009892//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; T32 DK007056/DK/NIDDK NIH HHS/United States ; F32DK128865//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
abstract = {IgA, the primary human antibody secreted from the gut mucosa, shapes the intestinal microbiota. Methodological limitations have hindered defining which microbial strains are targeted by IgA and the implications of binding. Here we develop a technique, metagenomic immunoglobulin sequencing (MIg-seq), that provides strain-level resolution of microbes coated by IgA and use it to determine IgA coating levels for 3,520 gut microbiome strains in healthy human faeces. We find that both health and disease-associated bacteria are targeted by IgA. Microbial genes are highly predictive of IgA binding levels; in particular, mucus degradation genes are correlated with high binding, and replication rates are significantly reduced for microbes bound by IgA. We demonstrate that IgA binding is more correlated with host immune status than traditional relative abundance measures of microbial community composition. This study introduces a powerful technique for assessing strain-level IgA binding in human stool, paving the way for deeper understanding of IgA-based host-microbe interactions.},
}
@article {pmid39747680,
year = {2025},
author = {Menon, R and Bhattarai, SK and Crossette, E and Prince, AL and Olle, B and Silber, JL and Bucci, V and Faith, J and Norman, JM},
title = {Multi-omic profiling a defined bacterial consortium for treatment of recurrent Clostridioides difficile infection.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {39747680},
issn = {1546-170X},
abstract = {Donor-derived fecal microbiota treatments are efficacious in preventing recurrent Clostridioides difficile infection (rCDI), but they have inherently variable quality attributes, are difficult to scale and harbor the risk of pathogen transfer. In contrast, VE303 is a defined consortium of eight purified, clonal bacterial strains developed for prevention of rCDI. In the phase 2 CONSORTIUM study, high-dose VE303 was well tolerated and reduced the odds of rCDI by more than 80% compared to placebo. VE303 organisms robustly colonized the gut in the high-dose group and were among the top taxa associated with non-recurrence. Multi-omic modeling identified antibiotic history, baseline stool metabolites and serum cytokines as predictors of both on-study CDI recurrence and VE303 colonization. VE303 potentiated early recovery of the host microbiome and metabolites with increases in short-chain fatty acids, secondary bile acids and bile salt hydrolase genes after antibiotic treatment for CDI, which is considered important to prevent CDI recurrences. These results support the idea that VE303 promotes efficacy in rCDI through multiple mechanisms.},
}
@article {pmid39747535,
year = {2025},
author = {Wongsamart, R and Somboonna, N and Cheibchalard, T and Klankeo, P and Ruampatana, J and Nuntapaitoon, M},
title = {Probiotic Bacillus licheniformis DSMZ 28710 improves sow milk microbiota and enhances piglet health outcomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {17},
pmid = {39747535},
issn = {2045-2322},
support = {764002-DT//Ratchadapisek Sompoch Endowment Fund 2021/ ; 764002-DT//Ratchadapisek Sompoch Endowment Fund 2021/ ; //the Second Century Fund (C2F)/ ; //the Second Century Fund (C2F)/ ; //the Second Century Fund (C2F)/ ; //the Second Century Fund (C2F)/ ; CU_FRB65_hea(68)_131_23_61//Thailand Research Fund, Thailand Science Research and Innovation Fund Chulalongkorn University/ ; FOOD_FF_68_013_3100_003//Thailand Research Fund, Thailand Science Research and Innovation Fund Chulalongkorn University/ ; },
mesh = {Animals ; *Probiotics/administration &amp; dosage ; Swine ; *Milk/microbiology ; *Microbiota ; *Bacillus licheniformis ; RNA, Ribosomal, 16S/genetics ; Female ; Colostrum/microbiology ; Dietary Supplements ; Animal Feed ; },
abstract = {Maintaining a diverse and balanced sow milk microbiome is essential to piglet development. Thus, this study aimed to examine the effects of probiotic Bacillus licheniformis supplementation on the microbiome composition of sow colostrum and milk, and to review associated health findings in piglets. B. licheniformis DSMZ 28710 was supplemented at 10 g/day as feed additive before predicted farrowing until weaning by top dressing. Colostrum and milk samples were collected for metagenomic DNA extraction, 16s rRNA sequencing, and bioinformatics analyses for bacterial microbiota diversity. Results indicated that the supplementation increased the abundances of beneficial bacteria, such as Lactobacillus, Pediococcus, Bacteroides, and Bifidobacterium, while decreasing the abundances of pathogenic bacteria, such as Staphylococcus aureus, Enterobacteriaceae, and Campylobacter in the colostrum. The supplementation increased diversity while maintaining richness and evenness. Moreover, the rise in predicted microbial community metabolic function in membrane transport pathways provides crucial evidence showing that the supplementation is potentially beneficial to piglets, as these pathways are important for providing nutrients and immunity to offspring. This research highlights the importance of microbiome composition in sow milk and the potential of B. licheniformis supplementation as a means to improve piglet health and development.},
}
@article {pmid39747287,
year = {2025},
author = {Delgadillo, DR and Borelli, JL and Mayer, EA and Labus, JS and Cross, MP and Pressman, SD},
title = {Biological, environmental, and psychological stress and the human gut microbiome in healthy adults.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {362},
pmid = {39747287},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Adult ; *Stress, Psychological/microbiology ; Male ; *RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Phylogeny ; Middle Aged ; Metagenome ; },
abstract = {Emerging research suggests that the gut microbiome plays a crucial role in stress. We assess stress-microbiome associations in two samples of healthy adults across three stress domains (perceived stress, stressful life events, and biological stress /Respiratory Sinus Arrhythmia; RSA). Study 1 (n = 62; mean-age = 37.3 years; 68% female) and Study 2 (n = 74; mean-age = 41.6 years; female only) measured RSA during laboratory stressors and used 16S rRNA pyrosequencing to classify gut microbial composition from fecal samples. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was used to predict functional pathways of metagenomes. Results showed differences in beta diversity between high and low stressful life events groups across both studies. Study 1 revealed differences in beta diversity between high and low RSA groups. In Study 1, the low perceived stress group was higher in alpha diversity than the high perceived stress group. Levels of Clostridium were negatively associated with RSA in Study 1 and levels Escherichia/Shigella were positively associated with perceived stress in Study 2. Associations between microbial functional pathways (L-lysine production and formaldehyde absorption) and RSA are discussed. Findings suggest that certain features of the gut microbiome are differentially associated with each stress domain.},
}
@article {pmid39746875,
year = {2025},
author = {Faith, JJ},
title = {Assessing live microbial therapeutic transmission.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2447836},
doi = {10.1080/19490976.2024.2447836},
pmid = {39746875},
issn = {1949-0984},
mesh = {Humans ; *Fecal Microbiota Transplantation ; *Clostridium Infections/microbiology/therapy/drug therapy ; *Clostridioides difficile/drug effects/physiology/genetics ; *Gastrointestinal Microbiome ; Feces/microbiology ; Animals ; },
abstract = {The development of fecal microbiota transplantation and defined live biotherapeutic products for the treatment of human disease has been an empirically driven process yielding a notable success of approved drugs for the treatment of recurrent Clostridioides difficile infection. Assessing the potential of this therapeutic modality in other indications with mixed clinical results would benefit from consistent quantitative frameworks to characterize drug potency and composition and to assess the impact of dose and composition on the frequency and duration of strain engraftment. Monitoring these drug properties and engraftment outcomes would help identify minimally sufficient sets of microbial strains to treat disease and provide insights into the intersection between microbial function and host physiology. Broad and correct usage of strain detection methods is essential to this advancement. This article describes strain detection approaches, where they are best applied, what data they require, and clinical trial designs that are best suited to their application.},
}
@article {pmid39746827,
year = {2025},
author = {Goldhawk, DE and Al, KF and Donnelly, SC and Varela-Mattatall, GE and Dassanayake, P and Gelman, N and Prato, FS and Burton, JP},
title = {Assessing microbiota in vivo: debugging with medical imaging.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.12.001},
pmid = {39746827},
issn = {1878-4380},
abstract = {The microbiota is integral to human health and has been mostly characterized through various ex vivo 'omic'-based approaches. To better understand the real-time function and impact of the microbiota, in vivo molecular imaging is required. With technologies such as positron emission tomography (PET), magnetic resonance imaging (MRI), and computed tomography (CT), insight into microbiological processes may be coupled to in vivo information. Noninvasive imaging enables longitudinal tracking of microbes and their components in real time; mapping of microbiota biodistribution, persistence and migration; and simultaneous monitoring of host physiological responses. The development of molecular imaging for clinical translation is an interdisciplinary science, with broad implications for deeper understanding of host-microbe interactions and the role(s) of the microbiome in health and disease.},
}
@article {pmid39746606,
year = {2024},
author = {Deslande, M and Puig-Castellvi, F and Castro-Dionicio, I and Pacheco-Tapia, R and Raverdy, V and Caiazzo, R and Lassailly, G and Leloire, A and Andrikopoulos, P and Kahoul, Y and Zaïbi, N and Toussaint, B and Oger, F and Gambardella, N and Lefebvre, P and Derhourhi, M and Amanzougarene, S and Staels, B and Pattou, F and Froguel, P and Bonnefond, A and Dumas, ME},
title = {Intrahepatic levels of microbiome-derived hippurate associates with improved metabolic dysfunction-associated steatotic liver disease.},
journal = {Molecular metabolism},
volume = {},
number = {},
pages = {102090},
doi = {10.1016/j.molmet.2024.102090},
pmid = {39746606},
issn = {2212-8778},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterised by lipid accumulation in the liver and is often associated with obesity and type 2 diabetes. The gut microbiome recently emerged as a significant player of liver metabolism and health through the production of bioactive compounds that are beneficial for its host - "postbiotics". Circulating hippurate, a host-microbial co-metabolite produced by conjugating microbial benzoate with glycine in the host-liver, is associated with human gut microbial gene richness and with metabolic health. Here, we first report significant associations among MASLD/MASH traits, plasma and hepatic hippurate in 318 individuals with obesity. Further analysis of the 318 patient's hepatic transcriptome showed that liver and plasma hippurate are inversely associated with MASLD, implicating lipid metabolism and regulation of inflammatory responses pathways. These observations strongly point towards a direct mechanistic role of hepatic hippurate in MASLD pathophysiology. To test a potential beneficial role for hippurate in hepatic insulin resistance, we profiled the metabolome of immortalised human hepatocytes (IHH) using ultra-high-performance liquid chromatography coupled to high-resolution tandem mass spectrometry (UHPLC-MS/MS), and characterised intracellular triglyceride accumulation and glucose internalisation after a 24 h insulin exposure. Hippurate treatment inhibited lipid accumulation and rescued insulin resistance induced by 24-hour chronic insulin in IHH. Hippurate also improved hepatocyte metabolic profiles by increasing the abundance of metabolites involved in energy homeostasis (that are depleted by chronic insulin treatment) while decreasing those involved in inflammation. Altogether, our results further highlight hippurate as a mechanistic marker of metabolic health, by its ability to improve metabolic homeostasis as a postbiotic candidate.},
}
@article {pmid39746603,
year = {2024},
author = {Wu, C and Wang, Q and Li, W and Han, M and Zhao, H and Xu, Z},
title = {Research progress on pathogenesis and treatment of febrile seizures.},
journal = {Life sciences},
volume = {362},
number = {},
pages = {123360},
doi = {10.1016/j.lfs.2024.123360},
pmid = {39746603},
issn = {1879-0631},
abstract = {Febrile seizures (FSs) are the most common pediatric neurological disorder, affecting approximately 5 % of children aged 6 months to 5 years. While most FSs are self-limiting and benign, about 20-30 % present as complex FSs (CFSs), which pose a risk of acute brain injury and the development of temporal lobe epilepsy. Various factors, including age, geographical distribution, and type of infection influence the occurrence of FS. Infection is the primary external trigger for FS, while the underlying intrinsic factors are linked to the immature and incomplete myelination of the brain during specific developmental stages. Although the precise pathogenesis of FS is not yet fully understood, it is likely caused by the interaction of immature brain development, fever, neuroinflammation, and genetic susceptibility. This review discussed the pathogenesis of febrile seizures, focusing on factors such as age, fever, neuroinflammation, genetics, and intestinal microbiota, and summarized existing therapeutic approaches. Our review may facilitate the identification of new targets for mechanistic studies and clinical treatment of febrile seizures.},
}
@article {pmid39746576,
year = {2024},
author = {Zhang, Z and Liu, C and Zhao, L and Yao, J},
title = {Systems biology of dry eye: Unraveling molecular mechanisms through multi-omics integration.},
journal = {The ocular surface},
volume = {36},
number = {},
pages = {25-40},
doi = {10.1016/j.jtos.2024.12.010},
pmid = {39746576},
issn = {1937-5913},
abstract = {Dry eye disease (DED) is a multifactorial condition with complex and incompletely understood molecular mechanisms. Advances in multi-omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and microbiomics, have provided new insights into the pathophysiology of DED. Genomic analyses have identified key genetic variants linked to immune regulation and lacrimal gland function. Transcriptomic studies reveal upregulated inflammatory pathways in ocular surface tissues, implicating these as core drivers of chronic inflammation. Proteomic research highlights significant alterations in tear protein composition, especially proteins involved in inflammation and tissue repair. Metabolomics studies focus on disrupted lipid metabolism and oxidative stress, which are crucial in maintaining tear film stability. Furthermore, microbiome research has demonstrated reduced microbial diversity and increased pathogenic bacteria, exacerbating inflammatory responses. The integration of multi-omics data allows for the identification of novel biomarkers and therapeutic targets, enabling precision diagnostics and personalized treatments. Therefore, this review highlights the critical importance of multi-omics approaches in deepening our understanding of DED's complex molecular mechanisms and their potential to transform clinical management and therapeutic innovations in this challenging field.},
}
@article {pmid39746569,
year = {2024},
author = {Touni, AA and Muttar, S and Siddiqui, Z and Shivde, RS and Krischke, E and Paul, D and Youssef, MA and Sperling, AI and Abdel-Aziz, R and Abdel-Wahab, H and Knight, KL and Le Poole, IC},
title = {Bacillus subtilis-derived-exopolysaccharide halts depigmentation and autoimmunity in vitiligo.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2024.12.006},
pmid = {39746569},
issn = {1523-1747},
abstract = {Vitiligo has a complex multifactorial etiology involving a T-cell mediated autoimmune response to cutaneous melanocytes. Microbial dysbiosis has been assigned a contributing role in vitiligo etiology. Treating vitiligo can be a challenging task and finding novel treatment approaches is crucial. Here, we tested exopolysaccharides (EPS) isolated from B.subtilis as a microbiome-based therapy. Vitiligo-prone h3TA2 mice were treated by weekly intraperitoneal EPS injection for 18 weeks. Depigmentation was measured over time, measuring immune responses at end point. EPS treatment significantly limited the rate of depigmentation. The abundance of cutaneous T cells, specifically CD8+ cytotoxic T cells was reduced while regulatory T cells were more abundant in the skin of treated mice compared to untreated mice. Moreover, EPS treatment was associated with increased numbers of splenic M2 macrophages, elevated splenic IDO expression and a systemic cytokine shift towards a type 2 pattern of cytokines. Importantly, splenocytes retrieved from EPS-treated mice were less responsive to cognate tyrosinase peptide as demonstrated by limited release of IFN- g and other inflammatory cytokines. In summary, EPS isolated from B. subtilis interfered with T-cell mediated depigmentation in the h3TA2 mouse model of vitiligo suggesting that B. subtilis EPS could serve as a novel treatment entity for vitiligo.},
}
@article {pmid39746555,
year = {2024},
author = {Yoon, Y and Bunyavanich, S},
title = {Multi-omic Approaches for Endotype Discovery in Allergy/Immunology.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2024.12.1083},
pmid = {39746555},
issn = {1097-6825},
}
@article {pmid39746497,
year = {2024},
author = {Zhao, R and Wang, J and Chung, SK and Xu, B},
title = {New insights into anti-depression effects of bioactive phytochemicals.},
journal = {Pharmacological research},
volume = {212},
number = {},
pages = {107566},
doi = {10.1016/j.phrs.2024.107566},
pmid = {39746497},
issn = {1096-1186},
abstract = {Depression is one of the most common psychological disorders, and due to its high prevalence and mortality rates, it imposes a significant disease burden. Contemporary treatments for depression involve various synthetic drugs, which have limitations such as side effects, single targets, and slow onset of action. Unlike synthetic medications, phytochemicals offer the benefits of a multi-target and multi-pathway mode of treatment for depression. In this literature review, we describe the pharmacological actions, experimental models, and clinical trials of the antidepressant effects of various phytochemicals. Additionally, we summarize the potential mechanisms by which these phytochemicals prevent depression, including regulating neurotransmitters and their receptors, the HPA axis, inflammatory responses, managing oxidative stress, neuroplasticity, and the gut microbiome. Phytochemicals exert therapeutic effects through multiple pathways and targets, making traditional Chinese medicine (TCM) a promising adjunctive antidepressant for the prevention, alleviation, and treatment of depression. Therefore, this review aims to provide robust evidence for subsequent research into developing phytochemical resources as effective antidepressant agents.},
}
@article {pmid39746397,
year = {2024},
author = {Du, Z and Liu, X and Xie, Z and Wang, Q and Lv, Z and Li, L and Wang, H and Xue, D and Zhang, Y},
title = {The Relationship Between A High-Fat Diet, Gut Microbiome, and Systemic Chronic Inflammation: Insights from Integrated Multi-Omics Analysis.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2024.12.026},
pmid = {39746397},
issn = {1938-3207},
abstract = {BACKGROUND: The detrimental effects of a high-fat diet (HFD) extend beyond metabolic consequences and include systemic chronic inflammation (SCI), immune dysregulation, and gut health disruption.<br><br>OBJECTIVES: In this study, we used Mendelian randomization (MR) to investigate the relationship between HFD and gut microbiota, and SCI.<br><br>METHODS: Genetic variants associated with dietary fat were utilized to explore causal relationships. GWAS data for the analyses of the gut microbiota, inflammatory cytokines, immune cell characteristics and serum metabolites were obtained from European individuals. Mediation analysis was used to reveal potential mediating factors. The GMrepo database was used to analyze the bacterial composition in different groups. Transcriptomic and single-cell sequencing analyses were used to explore inflammation and barrier function in colonic tissue.<br><br>RESULTS: HFD consumption was linked to changes in the abundance of 3 bacterial families and 11 bacterial genera. Combined with the GMrepo database, the increased abundance of genus.Lachnospiraceae_FCS020group and the decreased abundance of genus.Bacteroides and genus.Barnesiella are consistent with the MR results. Transcriptomic and single-cell sequencing analyses revealed intestinal inflammation and mucosal barrier dysfunction in HFD-fed mice. MR revealed a link between HFD consumption and increased levels of interleukin (IL)-18 (OR=3.64, 95%CI: 1.24-10.69, P=0.02), MIG (OR=3.14, 95%CI: 1.17-8.47, P=0.02), IL-13 (OR=3.21, 95%CI:1.08-9.52, P=0.04), and IL-2RA (OR=2.93, 95%CI: 1.01-8.53, P=0.049). Twenty-nine immune cell signatures, including altered monocyte and T-cell subsets, were affected by HFD consumption. Twenty-six serum metabolites that are linked to HFD consumption, particularly lipid and amino acid metabolites, were identified. The positive gut microbiota exhibits extensive associations with inflammatory cytokines. In particular, Lachnospiraceae_FCS020 group (OR=1.93, 95% CI: 1.11-3.37, P=0.02) may play a mediating role in HFD-induced increases in IL-2RA levels.<br><br>CONCLUSIONS: Microbial dysbiosis appears to be an important mechanism for HFD-induced SCI. The Lachnospiraceae_FCS020 group may act as a key genus in HFD-mediated elevation of IL-2RA.},
}
@article {pmid39746261,
year = {2025},
author = {Asif, A and Koner, S and Hussain, B and Hsu, BM},
title = {Root-associated functional microbiome endemism facilitates heavy metal resilience and nutrient poor adaptation in native plants under serpentine driven edaphic challenges.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123826},
doi = {10.1016/j.jenvman.2024.123826},
pmid = {39746261},
issn = {1095-8630},
abstract = {Serpentine soils are characterized by high concentrations of heavy metals (HMs) and limited essential nutrients with remarkable endemic plant diversity, yet the mechanisms enabling plant adaptation to thrive in such harsh environments remain largely unknown. Full-length 16S rRNA amplicon sequencing, coupled with physiological and functional assays, was used to explore root-associated bacterial community composition and their metabolic and ecological functions. The results revealed that serpentine plant species exhibited significantly higher metal transfer factor values compared to non-serpentine plant species, particularly evident in Bidens pilosa, Miscanthus floridulus, and Leucaena leucocephala. The serpentine root-associated microbes showed a higher utilization of carboxylic acid, whereas carbohydrate utilization was higher in the non-serpentine site. Zymomonas mobilis and Flavabacterium sp. exhibited high resistance to heavy metal concentrations, showing greater adaptability, while, Staphylococcus carnosus showed sensitivity to HMs, showing limited adaptability. Moreover, Ni, Cr, and Co resistance genes were found, while nitrogen and phosphorous metabolism genes were less abundant in the serpentine site compared to the non-serpentine site. Furthermore, Flavobacterium sp. had a strong positive relationship with Cd and Cu, Zymomonas mobilis with Ni, and Cr, Streptomyces sp. with Co, and Staphylococcus carnosus with N and P cycling. These findings underscore critical role of root-associated bacterial communities and distinctive soil conditions of serpentine habitats in fostering ecological adaptation of native plant species to the challenges posed by HMs and nutrient deficiencies.},
}
@article {pmid39745461,
year = {2024},
author = {Filho, RM and Mengoni, C and Bruno, JS and Fregnani, ER and Segata, N and Camargo, AA and Heidrich, V},
title = {Metagenome-assembled genomes from irradiated human dental plaque.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0091724},
doi = {10.1128/mra.00917-24},
pmid = {39745461},
issn = {2576-098X},
abstract = {We provide 309 quality-controlled bacterial metagenome-assembled genomes recovered from supragingival plaque metagenomes. Samples were collected from head and neck cancer patients following radiotherapy, so the recovered genomes can be useful to investigate the effects of oral cavity irradiation on oral microbiome members.},
}
@article {pmid39745426,
year = {2024},
author = {Gulyaeva, A and Liu, L and Garmaeva, S and Kruk, M and Weersma, RK and Harmsen, HJM and Zhernakova, A},
title = {Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0106624},
doi = {10.1128/spectrum.01066-24},
pmid = {39745426},
issn = {2165-0497},
abstract = {Metagenomics has revealed the incredible diversity of phages within the human gut. However, very few of these phages have been subjected to in-depth experimental characterization. One promising method of obtaining novel phages for experimental characterization is through induction of the prophages integrated into the genomes of cultured gut bacteria. Here, we developed a bioinformatic approach to prophage identification that builds on prophage genomic properties, existing prophage-detecting software, and publicly available virome sequencing data. We applied our approach to 22 strains of bacteria belonging to the genus Faecalibacterium, resulting in identification of 15 candidate prophages, and validated the approach by demonstrating the activity of five prophages from four of the strains. The genomes of three active phages were identical or similar to those of known phages, while the other two active phages were not represented in the Viral RefSeq database. Four of the active phages possessed a diversity-generating retroelement (DGR), and one retroelement had two variable regions. DGRs of two phages were active at the time of the induction experiments, as evidenced by nucleotide variation in sequencing reads. We also predicted that the host range of two active phages may include multiple bacterial species. Finally, we noted that four phages were less prevalent in the metagenomes of inflammatory bowel disease patients compared to a general population cohort, a difference mainly explained by differences in the abundance of the host bacteria. Our study highlights the utility of prophage identification and induction for unraveling phage molecular mechanisms and ecological interactions.IMPORTANCEWhile hundreds of thousands of phage genomes have been discovered in metagenomics studies, only a few of these phages have been characterized experimentally. Here, we explore phage characterization through bioinformatic identification of prophages in genomes of cultured bacteria, followed by prophage induction. Using this approach, we detect the activity of five prophages in four strains of commensal gut bacteria Faecalibacterium. We further note that four of the prophages possess diversity-generating retroelements implicated in rapid mutation of phage genome loci associated with phage-host and phage-environment interactions and analyze the intricate patterns of retroelement activity. Our study highlights the potential of prophage characterization for elucidating complex molecular mechanisms employed by the phages.},
}
@article {pmid39745394,
year = {2024},
author = {Geers, AU and Michoud, G and Busi, SB and Peter, H and Kohler, TJ and Ezzat, L and , and Battin, TJ},
title = {Deciphering the biosynthetic landscape of biofilms in glacier-fed streams.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0113724},
doi = {10.1128/msystems.01137-24},
pmid = {39745394},
issn = {2379-5077},
abstract = {UNLABELLED: Glacier-fed streams are permanently cold, ultra-oligotrophic, and physically unstable environments, yet microbial life thrives in benthic biofilm communities. Within biofilms, microorganisms rely on secondary metabolites for communication and competition. However, the diversity and genetic potential of secondary metabolites in glacier-fed stream biofilms remain poorly understood. In this study, we present the first large-scale exploration of biosynthetic gene clusters (BGCs) from benthic glacier-fed stream biofilms sampled by the Vanishing Glaciers project from the world's major mountain ranges. We found a remarkable diversity of BGCs, with more than 8,000 of them identified within 2,868 prokaryotic metagenome-assembled genomes, some of them potentially conferring ecological advantages, such as UV protection and quorum sensing. The BGCs were distinct from those sourced from other aquatic microbiomes, with over 40% of them being novel. The glacier-fed stream BGCs exhibited the highest similarity to BGCs from glacier microbiomes. BGC composition displayed geographic patterns and correlated with prokaryotic alpha diversity. We also found that BGC diversity was positively associated with benthic chlorophyll a and prokaryotic diversity, indicative of more biotic interactions in more extensive biofilms. Our study provides new insights into a hitherto poorly explored microbial ecosystem, which is now changing at a rapid pace as glaciers are shrinking due to climate change.<br><br>IMPORTANCE: Glacier-fed streams are characterized by low temperatures, high turbidity, and high flow. They host a unique microbiome within biofilms, which form the foundation of the food web and contribute significantly to biogeochemical cycles. Our investigation into secondary metabolites, which likely play an important role in these complex ecosystems, found a unique genetic potential distinct from other aquatic environments. We found the potential to synthesize several secondary metabolites, which may confer ecological advantages, such as UV protection and quorum sensing. This biosynthetic diversity was positively associated with the abundance and complexity of the microbial community, as well as concentrations of chlorophyll a. In the face of climate change, our study offers new insights into a vanishing ecosystem.},
}
@article {pmid39745374,
year = {2024},
author = {Jiang, W and Zhai, Y and Chen, D and Yu, Q},
title = {A novel robust network construction and analysis workflow for mining infant microbiota relationships.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0157024},
doi = {10.1128/msystems.01570-24},
pmid = {39745374},
issn = {2379-5077},
abstract = {UNLABELLED: The gut microbiota plays a crucial role in infant health, with its development during the first 1,000 days influencing health outcomes. Understanding the relationships within the microbiota is essential to linking its maturation process to these outcomes. Several network-based methods have been developed to analyze the developing patterns of infant microbiota, but evaluating the reliability and effectiveness of these approaches remains a challenge. In this study, we created a test data pool using public infant microbiome data sets to assess the performance of four different network-based methods, employing repeated sampling strategies. We found that our proposed Probability-Based Co-Detection Model (PBCDM) demonstrated the best stability and robustness, particularly in network attributes such as node counts, average links per node, and the positive-to-negative link (P/N) ratios. Using the PBCDM, we constructed microbial co-existence networks for infants at various ages, identifying core genera networks through a novel network shearing method. Analysis revealed that core genera were more similar between adjacent age ranges, with increasing competitive relationships among microbiota as the infant microbiome matured. In conclusion, the PBCDM-based networks reflect known features of infant microbiota and offer a promising approach for investigating microbial relationships. This methodology could also be applied to future studies of genomic, metabolic, and proteomic data.<br><br>IMPORTANCE: As a research method and strategy, network analysis holds great potential for mining the relationships of bacteria. However, consistency and solid workflows to construct and evaluate the process of network analysis are lacking. Here, we provide a solid workflow to evaluate the performance of different microbial networks, and a novel probability-based co-existence network construction method used to decipher infant microbiota relationships. Besides, a network shearing strategy based on percolation theory is applied to find the core genera and connections in microbial networks at different age ranges. And the PBCDM method and the network shearing workflow hold potential for mining microbiota relationships, even possibly for the future deciphering of genome, metabolite, and protein data.},
}
@article {pmid39744979,
year = {2025},
author = {Qiao, Y and Yu, J and Zhang, Z and Hou, Q and Guo, Z and Wang, Y},
title = {Regulatory effects of Lactobacillus zhachilii HBUAS52074[T] on depression-like behavior induced by chronic social defeat stress in mice: modulation of the gut microbiota.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo04542d},
pmid = {39744979},
issn = {2042-650X},
abstract = {The gut microbiome has emerged as a growing focus of research and public health interest, leading to the frequent exploration of probiotic dietary supplements as potential treatments for various disorders, such as anxiety and depression. In the present report, changes in inflammation and microbiome composition were assessed in model mice exhibiting depressive-like behaviors that were exposed to the probiotic Lactobacillus zhachilii HBUAS52074[T]. It was found that L. zhachilii HBUAS52074[T] alleviated the severity of depressive-like behaviors while increasing serum 5-HT concentrations. Moreover, L. zhachilii HBUAS52074[T] modulated the composition of the gut microbiota, resulting in a decrease in the abundance of Prevotella and an increase in the abundance of Lactobacillus. Additionally, supplementation with L. zhachilii HBUAS52074[T] enhanced intestinal barrier function and reduced inflammation in peripheral blood, as well as in the hippocampal and prefrontal cortical tissues. Correlational analyses indicated that the abundance of Lactobacillus was positively correlated with the social interaction ratio, time spent in the center, entries into the center, as well as serum 5-HT and serum IL-10 levels but negatively correlated with immobility time. Overall, chronic social defeat stress was found to be associated with inflammation and the exacerbation of depressive-like behaviors. The above findings suggested that L. zhachilii HBUAS52074[T] supplementation was sufficient to alter the parameters. Collectively, these data suggest that L. zhachilii HBUAS52074[T], derived from naturally fermented foods, may possess therapeutic potential for the treatment of depression.},
}
@article {pmid39744736,
year = {2024},
author = {Jeyaraman, N and Jeyaraman, M and Dhanpal, P and Ramasubramanian, S and Ragavanandam, L and Muthu, S and Santos, GS and da Fonseca, LF and Lana, JF},
title = {Gut microbiome and orthopaedic health: Bridging the divide between digestion and bone integrity.},
journal = {World journal of orthopedics},
volume = {15},
number = {12},
pages = {1135-1145},
pmid = {39744736},
issn = {2218-5836},
abstract = {The gut microbiome, a complex ecosystem of microorganisms in the digestive tract, has emerged as a critical factor in human health, influencing metabolic, immune, and neurological functions. This review explores the connection between the gut microbiome and orthopedic health, examining how gut microbes impact bone density, joint integrity, and skeletal health. It highlights mechanisms linking gut dysbiosis to inflammation in conditions such as rheumatoid arthritis and osteoarthritis, suggesting microbiome modulation as a potential therapeutic strategy. Key findings include the microbiome's role in bone metabolism through hormone regulation and production of short-chain fatty acids, crucial for mineral absorption. The review also considers the effects of diet, probiotics, and fecal microbiota transplantation on gut microbiome composition and their implications for orthopedic health. While promising, challenges in translating microbiome research into clinical practice persist, necessitating further exploration and ethical consideration of microbiome-based therapies. This interdisciplinary research aims to link digestive health with musculoskeletal integrity, offering new insights into the prevention and management of bone and joint diseases.},
}
@article {pmid39744688,
year = {2025},
author = {Wang, X and Zhou, XJ and Qiao, X and Falchi, M and Liu, J and Zhang, H},
title = {The evolving understanding of systemic mechanisms in organ-specific IgA nephropathy: a focus on gut-kidney crosstalk.},
journal = {Theranostics},
volume = {15},
number = {2},
pages = {656-681},
pmid = {39744688},
issn = {1838-7640},
mesh = {*Glomerulonephritis, IGA/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; *Kidney/metabolism/microbiology ; *Probiotics/therapeutic use ; Animals ; Akkermansia/physiology ; },
abstract = {The interplay between multiple organs, known as inter-organ crosstalk, represents a complex and essential research domain in understanding the mechanisms and therapies for kidney diseases. The kidneys not only interact pathologically with many other organs but also communicate with other systems through various signaling pathways. It is of paramount importance to comprehend these mechanisms for the development of more efficient therapeutic strategies. Despite extensive research in IgA nephropathy (IgAN), the most common kidney disease, the elaboration mechanism of IgAN remains challenging. Numerous studies suggest that alterations in the intestinal microbiome and its metabolites are pivotal in the progression of IgAN, opening new avenues for understanding its mechanisms. Interestingly, certain presumed probiotics, such as Akkermansia muciniphila, have been implicated in the onset of IgAN, making the exploration of gut microbiota in the context of IgAN pathogenesis even more intriguing. In this review, we summarize the status of gut microbiology studies of IgAN and explore the possible mechanisms and intervention prospects. Future research and treatment directions may increasingly emphasize systemic, multi-organ combined interventions to decelerate the advancement of kidney disease and enhance the overall prognosis of patients.},
}
@article {pmid39744404,
year = {2024},
author = {Adjele, JJB and Devi, P and Kumari, P and Yadav, A and Tchuenchieu Kamgain, AD and Mouafo, HT and Medoua, GN and Essia, JJN and Chauhan, NS and Pandey, R},
title = {Exploring the influence of age and diet on gut microbiota development in children during the first 5 years: a study from Yaoundé, Cameroon.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1512111},
pmid = {39744404},
issn = {1664-302X},
abstract = {INTRODUCTION: The development of the human gut microbiota is shaped by factors like delivery mode, infant feeding practices, maternal diet, and environmental conditions. Diet plays a pivotal role in determining the diversity and composition of the gut microbiome, which in turn impacts immune development and overall health during this critical period. The early years, which are vital for microbial shaping, highlight a gap in understanding how the shift from milk-based diets to solid foods influences gut microbiota development in infants and young children, particularly in Yaoundé, Cameroon.<br><br>METHODS: This study involved an analysis of the gut microbiota composition in 70 children aged &#x2264;5&#x202f;years through 16S rDNA gene metagenomic sequencing of fecal metagenomic DNA. The participants were grouped into four age categories: 0-6&#x202f;months, 7-12&#x202f;months, 13-24&#x202f;months, and 25-60&#x202f;months.<br><br>RESULTS: We observed a reduction in microbial diversity in the younger age groups, which increased progressively with age. At the taxonomic level, our analysis identified Firmicutes as the predominant phylum, with its abundance rising in older age groups, suggesting a maturation of the microbiota characterized by distinct genera associations. In the 0-6&#x202f;month age group, we noted an enrichment of Lactobacilli and Bifidobacteria, which may play a crucial role in modulating and supporting immune system development during infancy. After 6&#x202f;months, we found a higher prevalence of Clostridium, Bacillus, Roseburia, and Faecalibacterium, which are associated with fiber fermentation and the production of short-chain fatty acids (SCFAs).<br><br>CONCLUSION: These findings underscore the influence of milk products and complementary diets on gut microbiota across various age groups, promoting increased diversity essential for healthy gut development. More such studies in the LMICs would augment and strengthen understanding towards functional microbiome.},
}
@article {pmid39744400,
year = {2024},
author = {Bradbury, ES and Holland-Moritz, H and Gill, A and Havrilla, CA},
title = {Plant and soil microbial composition legacies following indaziflam herbicide treatment.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1450633},
pmid = {39744400},
issn = {1664-302X},
abstract = {Land stewards in dryland ecosystems across the western U.S. face challenges to manage the exotic grass Bromus tectorum (cheatgrass), which is a poor forage, is difficult to remove, and increases risk of catastrophic fire. Managers may consider using indaziflam (Rejuvra™), a relatively new pre-emergent herbicide, which may reduce cheatgrass cover within drylands. However, few studies have explored the effects of indaziflam on non-target organisms. We tested how indaziflam application impacted cover and biomass of native and exotics within the plant community and composition and diversity of the soil microbiome by comparing untreated and treated arid shrubland sites in Boulder County, Colorado, USA. We found that indaziflam application decreased cheatgrass cover by as much as 80% and increased native plant cover by the same amount. Indaziflam application also was associated with increased soil nitrate (NO3 [-]), decreased soil organic matter, and had a significant effect on the composition of the soil microbiome. Microbial community composition was significantly related to soil NO3 [-], soil organic matter, soil pH, and native species and cheatgrass biomass. An indicator species analysis suggested that indaziflam application shifted microbial communities. In untreated sites, ammonia-oxidizing bacteria Nitrosomonadaceae and nitrogen-digesting Opitutaceae and the fungi Articulospora proliferata were found. While in treated sites, ammonia-oxidizing archaea which are associated with intact drylands, Nitrososphaeraceae and toxin digesters and acidic-soil species Sphingomonas and Acidimicrobiia were significantly associated. Overall, these results demonstrate that indaziflam application can increase native plant recruitment, while also affecting soil properties and the soil microbiome. The findings from this study can be used to inform decision-making during dryland restoration planning process as indaziflam use may have benefits and unknown long-term consequences for the biogeochemistry and microbial ecology of the system.},
}
@article {pmid39744394,
year = {2024},
author = {Mok, N and Knox, NC and Zhu, F and Arnold, DL and Bar-Or, A and Bernstein, CN and Bonner, C and Forbes, JD and Graham, M and Marrie, RA and O'Mahony, J and Yeh, EA and Zhao, Y and Van Domselaar, G and Banwell, B and Waubant, E and Tremlett, HL},
title = {The fungal gut microbiota in pediatric-onset multiple sclerosis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1258978},
pmid = {39744394},
issn = {1664-302X},
abstract = {Evidence suggests that the gut microbiome may play a role in multiple sclerosis (MS). However, the majority of the studies have focused on gut bacterial communities; none have examined the fungal microbiota (mycobiota) in persons with pediatric-onset multiple sclerosis (POMS). We examined the gut mycobiota in persons with and without POMS through a cross-sectional examination of the gut mycobiota from 46 participants' stool samples (three groups: 18 POMS, 13 acquired monophasic demyelinating syndromes [monoADS], and 15 unaffected controls). Using metataxonomic sequencing of the fungal internal transcribed spacer region 2, the fungal profiles were compared between participants using visualizations, statistical tests, and predictive analysis. While the mycobiome α- (Shannon and inverse Simpson indices) and β-diversity differed across the three groups [analysis of variance (ANOVA), p < 0.05], further post-hoc analysis of the β-diversity identified a difference between monoADS vs. POMS participants [p = 0.005 (adjusted)]. At the genus level of taxonomy, 7 out of 10 of the majority of abundant genera were similar among all three groups, with Saccharomyces spp. and Candida spp. being in the highest abundance. The Agaricus genus was especially high in POMS participants, dominated primarily due to the species Agaricus bisporus (widely consumed as white button mushrooms). The commonality of high abundance fungi found in our cohort suggests a possible connection to diet. Predictive modeling of differential abundance associated with Candida albicans, Cyberlindera jadinii, and Fusarium poae revealed that these fungi were strongly associated with the POMS participants. Our study provides novel insight into the fungal gut mycobiota in POMS. While findings indicate that the gut mycobiome of participants with POMS may largely comprise fungi considered transient from the diet, the differential predictive analysis suggested rare or under-detected fungal markers being of potential importance, warranting consideration in future mycobiome-MS-related studies.},
}
@article {pmid39744392,
year = {2024},
author = {Zheng, Q and Zhang, Y and Li, J and Pei, S and Liu, J and Feng, L and Zhang, L and Liu, X and Luo, B and Ruan, Y and Hu, W and Niu, J and Tian, T},
title = {The impact of interactions between heavy metals and smoking exposures on the formation of oral microbial communities.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1502812},
pmid = {39744392},
issn = {1664-302X},
abstract = {INTRODUCTION: The primary objective of our investigation was to assess the repercussions of prolonged exposure to heavy metals and smoking on the microbiome of the oral buccal mucosa. Concurrently, we aimed to elucidate the intricate interplay between external environmental exposures and the composition of the oral microbial ecosystem, thereby discerning its potential implications for human health.<br><br>METHODS: Our study cohort was stratified into four distinct groups: MS (characterized by concurrent exposure to heavy metals and smoking), M (exposed solely to heavy metals), S (exposed solely to smoking), and C (comprising individuals serving as a control group). Specimens of buccal mucosa and blood were systematically acquired from the participants, facilitating subsequent microbial diversity analysis across the four oral buccal mucosa sample cohorts through 16S rRNA gene sequencing techniques. Simultaneously, blood samples were tested for heavy metal concentrations. In addition, we performed topological analyses by constructing microbial networks.<br><br>RESULTS: Our findings notably indicate that co-exposure to heavy metals and smoking yielded a more pronounced alteration in the diversity of oral microflora when compared to singular exposures to either heavy metals or smoking. By comparing the oral bacterial communities and functional pathways between the four groups, we found significant differences in bacterial communities and functional pathways between the groups. Notably, the impact of heavy metal exposure overshadowed that of smoking, with concurrent exposure to heavy metals and smoking eliciting marginally greater effects than exposure to heavy metals alone. In addition, our analysis of the correlation between microbiota and blood heavy metal concentrations showed that the heavy metal cadmium (Cd) had a significantly greater effect on oral microbiota than other heavy metals.<br><br>DISCUSSION: Chronic exposure to heavy metals and smoking disrupts the normal bacterial communities in the oral mucosa of residents of contaminated areas. This exposure reduces the complexity and stability of microbial networks and increases the risk of various diseases reduces the complexity and stability.},
}
@article {pmid39744391,
year = {2024},
author = {Pagan-Rivera, LH and Ocasio-Rivera, SE and Godoy-Vitorino, F and Miranda, JD},
title = {Spinal cord injury: pathophysiology, possible treatments and the role of the gut microbiota.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1490855},
pmid = {39744391},
issn = {1664-302X},
support = {P30 GM149367/GM/NIGMS NIH HHS/United States ; },
abstract = {Spinal cord injury (SCI) is a devastating pathological state causing motor, sensory, and autonomic dysfunction. To date, SCI remains without viable treatment for its patients. After the injury, molecular events centered at the lesion epicenter create a non-permissive environment for cell survival and regeneration. This newly hostile setting is characterized by necrosis, inflammation, demyelination, axotomy, apoptosis, and gliosis, among other events that limit locomotor recovery. This review provides an overview of the pathophysiology of SCI, highlighting the potential role of the gut microbiota in modulating the inflammatory response and influencing neurological recovery following trauma to the spinal cord. Emphasis on the bidirectional communication between the gut and central nervous system, known as the gut-brain axis is given. After trauma, the gut-brain/spinal cord axis promotes the production of pro-inflammatory metabolites that provide a non-permissive environment for cell survival and locomotor recovery. Therefore, any possible pharmacological treatment, including antibiotics and painkillers, must consider their effects on microbiome dysbiosis to promote cell survival, regeneration, and behavioral improvement. Overall, this review provides valuable insights into the pathophysiology of SCI and the evolving understanding of the role of the gut microbiota in SCI, with implications for future research and clinical practice.},
}
@article {pmid39744339,
year = {2024},
author = {Nouraei, H and Gharechahi, F and Zareshahrabadi, Z and Zomorodian, K and Gharavi, A and Khodadadi, H and Ansari, S and Amirzadeh, N and Pakshir, K},
title = {Molecular characterization of non-Cryptococcus yeast communities isolated from Eucalyptus trees.},
journal = {Current medical mycology},
volume = {10},
number = {},
pages = {},
pmid = {39744339},
issn = {2423-3439},
abstract = {BACKGROUND AND PURPOSE: Plants are crucial habitats for fungus communities as they provide an appropriate physical environment for the growth and reproduction of the yeast microbiome. Varieties of pathogenic and non-pathogenic yeast could be found in Eucalyptus trees. Although Cryptococcus species are the most common pathogenic yeasts associated with Eucalyptus trees, other yeasts also grow on trees and are critical to human health. This study aimed to identify the yeast species associated with Eucalyptus trees.<br><br>MATERIALS AND METHODS: In total, 107 yeast species were collected from Eucalyptus trees and subsequently identified through both molecular and traditional techniques. Genomic DNA extraction was performed using the boiling method. The internal transcribed spacer region of the ribosomal DNA was amplified utilizing the polymerase chain reaction (PCR) technique, followed by the purification and sequencing of the PCR products to identify the isolates.<br><br>RESULTS: Yeast strains belonged to 12 genera and 26 species of both the Ascomycete and Basidiomycete phyla. The most frequent species were Rhodotorula mucilaginosa (24.2%), Candida tropicalis (15%), Candida guilliermondii (11.2%), and Aureobasidium pullulans (10.2%).<br><br>CONCLUSION: In this study, most of the yeast isolates, such as Candida and Trichosporon, were important to human health. Eucalyptus trees, as part of the natural flora, could be considered an environmental reservoir for yeasts, in which they can survive, disperse to the surrounding environment, and become a potential infectious source affecting public health.},
}
@article {pmid39744230,
year = {2025},
author = {Singh, A and Chandrasekar, SV and Valappil, VT and Scaria, J and Ranjan, A},
title = {Tumor immunomodulation by nanoparticle and focused ultrasound alters gut microbiome in a sexually dimorphic manner.},
journal = {Theranostics},
volume = {15},
number = {1},
pages = {216-232},
pmid = {39744230},
issn = {1838-7640},
mesh = {Animals ; Female ; Male ; *Gastrointestinal Microbiome/immunology ; Mice ; *Nanoparticles/administration &amp; dosage ; *Immunomodulation ; Calreticulin/metabolism ; Cell Line, Tumor ; Immunogenic Cell Death/drug effects ; Mice, Inbred C57BL ; Mouth Neoplasms/immunology/microbiology/therapy ; Sex Characteristics ; Cytokines/metabolism ; },
abstract = {Background: Local immunomodulation with nanoparticles (NPs) and focused ultrasound (FUS) is recognized for triggering anti-tumor immunity. However, the impact of these tumor immunomodulations on sex-specific microbiome diversity at distant sites and their correlation with therapeutic effectiveness remains unknown. Here, we conducted local intratumoral therapy using immunogenic cell death-enhancing Calreticulin-Nanoparticles (CRT-NPs) and FUS in male and female mice. We identified immune-related microbiome populations, aiming to translate our findings into clinical applications. Methods: CRT-NPs were synthesized by loading CRT-delivering plasmids into cationic liposomes. Local tumor therapy was performed using CRT-NP and FUS-based histotripsy (HT) on poorly immunogenic Mouse Oral Squamous Cell Carcinoma (MOC2) in the flank regions of male and female mice. Fecal samples were collected and analyzed before and three weeks post-treatment. The microbiome features were then correlated with immune cell dynamics within tumors and systemic cytokine responses to identify prognostic biomarkers in both male and female subjects. Results: Intratumorally administered CRT-NP induced tumor remission and immune cell activation in both male and female mice, whereas HT was ineffective in males and showed efficacy only in females. Turicibacter and Peptococcus inversely correlated with tumor growth, while Enterorhabdus, Subdologranulum, Desulfovibrio, and Aldercreutzia-Asaccharobacter showed direct correlations with tumor growth. HT induced higher levels of Turicibacter in MOC2-bearing females, while males displayed increased Enterorhabdus and Streptococcus populations. Independent of sex, treatments promoting CD4+ T helper cells, functional CD8+ T cells, and total macrophage infiltration correlated with higher levels of Gastrophilales, Romboutsia, Turicibacter, and Peptococcus. Alternatively, Enterorhabdus, Desulfovibrio, Streptococcus, and Staphylococcus corresponded to poor treatment outcomes in both sexes. Conclusion: An enhanced abundance of Enterorhabdus, Desulfovibrio, Streptococcus, and Staphylococcus in response to immunomodulatory therapies could serve as predictive biomarkers in a sex-independent manner. These findings could also be potentially extended to the realm of personalized interventions through fecal transplantations to reverse immunosuppressive phenotypes in males and improve patient outcomes.},
}
@article {pmid39744158,
year = {2024},
author = {Jiménez-Arroyo, C and Molinero, N and Sabater, C and Margolles, A and Terrón-Camero, LC and Andrés-León, E and Ramos, M and Del Val, M and Moreno-Arribas, MV},
title = {Gut microbiome and clinical and lifestyle host factors associated with recurrent positive RT-PCR for SARS-CoV-2.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1494193},
pmid = {39744158},
issn = {2235-2988},
mesh = {Humans ; *COVID-19/microbiology/virology/diagnosis ; *Gastrointestinal Microbiome/genetics ; *SARS-CoV-2/genetics/isolation &amp; purification ; Male ; Female ; Middle Aged ; *Feces/microbiology/virology ; Adult ; Metagenomics/methods ; Life Style ; Aged ; },
abstract = {BACKGROUND: SARS-CoV-2 and COVID-19 are still active in the population. Some patients remained PCR-positive for more than 4 weeks, called "persistently PCR-positive". Recent evidence suggests a link between the gut microbiota and susceptibility to COVID-19, although no studies have explored persistent PCR conditions. We aimed to evaluate the relationship between persistent positive SARS-CoV-2 RT-PCR, the gut microbiome, and individual host determinants.<br><br>METHODS: A shotgun metagenomic analysis was conducted on fecal samples from 28 individuals affected by COVID-19. Patients were divided into two groups: those who had cleared the virus within 30 days (designated as the control group) (n = 15), and those who remained PCR-positive beyond 30 days (called the PCR+ group) (n = 13). We also investigated the correlation between prolonged viral clearance and several additional factors, including clinical parameters, immune responses, microbial metabolites, and dietary habits.<br><br>RESULTS: The composition and functionality of the microbiome varied based on the duration of positivity as determined by PCR. Compared to the control group, the persistent PCR+ group exhibited elevated pathogen levels and augmented diversity in functional gene families (p-value < 0.05). A multi-omics analysis integrating metagenomics, metabolites, and metadata also revealed the specific contribution of certain blood markers in this group, including basophils, IgM, IgG (both general and specific for SARS-CoV-2), and markers of liver damage. Unhealthy diet was identified as a significant factor influencing the duration of PCR positivity.<br><br>CONCLUSIONS: These findings indicate that the gut microbiome may play a role in delayed viral clearance and persistent positive RT-PCR results. Our study also contributes to the understanding of the role of host factors as mediators linking the gut microbiota and disease outcomes. Further large-scale studies must confirm these data; however, they suggest the relevance of monitoring microbiome changes in the early post-viral years to control SARS-CoV-2 and providing individual healthcare support.},
}
@article {pmid39744095,
year = {2024},
author = {Aparicio, A and Sun, Z and Gold, DR and Lasky-Su, JA and Litonjua, AA and Weiss, ST and Lee-Sarwar, K and Liu, YY},
title = {Genotype-microbiome-metabolome associations in early childhood and their link to BMI.},
journal = {mLife},
volume = {3},
number = {4},
pages = {573-577},
pmid = {39744095},
issn = {2770-100X},
support = {R01 HL108818/HL/NHLBI NIH HHS/United States ; U01 HL091528/HL/NHLBI NIH HHS/United States ; UG3 OD023268/OD/NIH HHS/United States ; UH3 OD023268/OD/NIH HHS/United States ; },
abstract = {Through the analysis of data from children aged 6 months to 8 years enrolled in the Vitamin D Antenatal Asthma Reduction Trial (VDAART), significant simultaneous associations were identified between variants in the fragile histidine triad (FHIT) gene, children's body mass index, microbiome features related to obesity, and key lipids and amino acids. These patterns represent evidence of the genotype influence in shaping the host microbiome in developing stages and new potential biomarkers for childhood obesity, insulin resistance, and type 2 diabetes.},
}
@article {pmid39744013,
year = {2024},
author = {Dai, H and Chen, X and Yang, J and Loiola, RA and Lu, A and Cheung, KCP},
title = {Insights and therapeutic advances in pancreatic cancer: the role of electron microscopy in decoding the tumor microenvironment.},
journal = {Frontiers in cell and developmental biology},
volume = {12},
number = {},
pages = {1460544},
pmid = {39744013},
issn = {2296-634X},
abstract = {Pancreatic cancer is one of the most lethal cancers, with a 5-year overall survival rate of less than 10%. Despite the development of novel therapies in recent decades, current chemotherapeutic strategies offer limited clinical benefits due to the high heterogeneity and desmoplastic tumor microenvironment (TME) of pancreatic cancer as well as inefficient drug penetration. Antibody- and nucleic acid-based targeting therapies have emerged as strong contenders in pancreatic cancer drug discovery. Numerous studies have shown that these strategies can significantly enhance drug accumulation in tumors while reducing systemic toxicity. Additionally, electron microscopy (EM) has been a critical tool for high-resolution analysis of the TME, providing insights into the ultrastructural changes associated with pancreatic cancer progression and treatment responses. This review traces the current and technological advances in EM, particularly the development of ultramicrotomy and improvements in sample preparation that have facilitated the detailed visualization of cellular and extracellular components of the TME. This review highlights the contribution of EM in assessing the efficacy of therapeutic agents, from revealing apoptotic changes to characterizing the effects of novel compounds like ionophore antibiotic gramicidin A on cellular ultrastructures. Moreover, the review delves into the potential of EM in studying the interactions between the tumor microbiome and cancer cell migration, as well as in aiding the development of targeted therapies like antibody-drug conjugates (ADCs) and aptamer-drug conjugates (ApDCs).},
}
@article {pmid39743988,
year = {2024},
author = {Mathur, A and Taurin, S and Alshammary, S},
title = {New insights into methods to measure biological age: a literature review.},
journal = {Frontiers in aging},
volume = {5},
number = {},
pages = {1395649},
pmid = {39743988},
issn = {2673-6217},
abstract = {Biological age is a concept that reflects the physiological state of an individual rather than the chronological time since birth. It can help assess the risk of age-related diseases and mortality and the effects of interventions to slow down or reverse aging. However, there is no consensus on measuring biological age best, and different methods may yield different results. In this paper, which includes 140 relevant pieces of literature, out of 33,000, we review some new methods to measure biological age based on recent advances in biotechnology and data science. We discussed some novel biomarkers and algorithms that can capture the dynamic and multidimensional aspects of aging at different levels. We evaluate their performance and validity using various datasets and criteria and compare them with existing methods. We also discuss their potential applications and implications for aging research and clinical practice. We conclude that the new methods offer more accurate and reliable estimates of biological age and open new avenues for understanding and modulating the aging process.},
}
@article {pmid39743788,
year = {2025},
author = {Jin, H and Wang, S and Sheng, J and Yang, X and Li, J and Li, B},
title = {Konjac Glucomannan and Its Degradation Products Inhibit Intestinal Lipid Absorption by Regulating Gut Microbiota and the Production of Short-Chain Fatty Acids.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c06280},
pmid = {39743788},
issn = {1520-5118},
abstract = {The effect of konjac glucomannan (KGM) on lipid absorption is related to the viscosity effect and hepatic lipid synthesis. However, the molecular mechanism of regulation of intestinal lipid absorption by KGM and its correlation with gut microbiota have not been studied. This study explored the effects of KGM and degradation products of KGM (DKGM) on intestinal lipid absorption and output in obese mice and their potential mechanisms. The results showed that KGM significantly reduces blood lipids and intestinal lipid accumulation compared to DKGM in obese mice. Moreover, KGM and DKGM downregulated intestinal HDAC3 and NFLI3 expression to suppress CD36, SREBP1, FABP1, and PPARα expression. Notably, KGM more effectively inhibited fatty acid uptake in extraintestinal tissues than DKGM. Importantly, KGM more effectively enhanced the intestinal barrier, altered microbe abundance associated with lipid absorption, and promoted SCFA production than DKGM. Correlation analysis found that KGM and DKGM inhibited intestinal lipid absorption, which were positively correlated with the abundance of Lactobacillus, Desulfovibrio, Allobaculum etc. In conclusion, KGM more effectively inhibits intestinal lipid absorption and output in high-fat diet mice than DKGM, which is related to viscosity, intestinal HDAC3 activity, and differential remodeling of the microbiome. These findings provide insights into how microbe-dietary fiber interactions regulate the host energy balance.},
}
@article {pmid39743584,
year = {2025},
author = {Ezzat, L and Peter, H and Bourquin, M and Busi, SB and Michoud, G and Fodelianakis, S and Kohler, TJ and Lamy, T and Geers, A and Pramateftaki, P and Baier, F and Marasco, R and Daffonchio, D and Deluigi, N and Wilmes, P and Styllas, M and Schön, M and Tolosano, M and De Staercke, V and Battin, TJ},
title = {Diversity and biogeography of the bacterial microbiome in glacier-fed streams.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39743584},
issn = {1476-4687},
abstract = {The rapid melting of mountain glaciers and the vanishing of their streams is emblematic of climate change[1,2]. Glacier-fed streams (GFSs) are cold, oligotrophic and unstable ecosystems in which life is dominated by microbial biofilms[2,3]. However, current knowledge on the GFS microbiome is scarce[4,5], precluding an understanding of its response to glacier shrinkage. Here, by leveraging metabarcoding and metagenomics, we provide a comprehensive survey of bacteria in the benthic microbiome across 152 GFSs draining the Earth's major mountain ranges. We find that the GFS bacterial microbiome is taxonomically and functionally distinct from other cryospheric microbiomes. GFS bacteria are diverse, with more than half being specific to a given mountain range, some unique to single GFSs and a few cosmopolitan and abundant. We show how geographic isolation and environmental selection shape their biogeography, which is characterized by distinct compositional patterns between mountain ranges and hemispheres. Phylogenetic analyses furthermore uncovered microdiverse clades resulting from environmental selection, probably promoting functional resilience and contributing to GFS bacterial biodiversity and biogeography. Climate-induced glacier shrinkage puts this unique microbiome at risk. Our study provides a global reference for future climate-change microbiology studies on the vanishing GFS ecosystem.},
}
@article {pmid39743544,
year = {2025},
author = {Muñoz-Grez, CP and Vidal, MA and Rojas, TB and Ferrada, LE and Zuñiga, FA and Vera, AA and Sanhueza, SA and Quiroga, RA and Cabrera, CD and Antilef, BE and Cartes, RA and Acevedo, MP and Fraga, MA and Alarcón-Zapata, PF and Hernández, MA and Salas-Burgos, AM and Tapia-Belmonte, F and Yáñez, ML and Riquelme, EM and González, WA and Rivera, CA and Oñate, AA and Lamperti, LI and Nova-Lamperti, E},
title = {Host-microbe computational proteomic landscape in oral cancer revealed key functional and metabolic pathways between Fusobacterium nucleatum and cancer progression.},
journal = {International journal of oral science},
volume = {17},
number = {1},
pages = {1},
pmid = {39743544},
issn = {2049-3169},
mesh = {Humans ; *Fusobacterium nucleatum/metabolism ; *Mouth Neoplasms/microbiology/metabolism ; *Disease Progression ; *Proteomics ; *Carcinoma, Squamous Cell/microbiology/metabolism ; Host-Pathogen Interactions ; Metabolic Networks and Pathways ; Case-Control Studies ; Mass Spectrometry ; },
abstract = {Oral squamous cell carcinoma (OSCC) is the most common manifestation of oral cancer. It has been proposed that periodontal pathogens contribute to OSCC progression, mainly by their virulence factors. However, the main periodontal pathogen and its mechanism to modulate OSCC cells remains not fully understood. In this study we investigate the main host-pathogen pathways in OSCC by computational proteomics and the mechanism behind cancer progression by the oral microbiome. The main host-pathogen pathways were analyzed in the secretome of biopsies from patients with OSCC and healthy controls by mass spectrometry. Then, functional assays were performed to evaluate the host-pathogen pathways highlighted in oral cancer. Host proteins associated with LPS response, cell migration/adhesion, and metabolism of amino acids were significantly upregulated in the human cancer proteome, whereas the complement cascade was downregulated in malignant samples. Then, the microbiome analysis revealed large number and variety of peptides from Fusobacterium nucleatum (F. nucleatum) in OSCC samples, from which several enzymes from the L-glutamate degradation pathway were found, indicating that L-glutamate from cancer cells is used as an energy source, and catabolized into butyrate by the bacteria. In fact, we observed that F. nucleatum modulates the cystine/glutamate antiporter in an OSCC cell line by increasing SLC7A11 expression, promoting L-glutamate efflux and favoring bacterial infection. Finally, our results showed that F. nucleatum and its metabolic derivates promote tumor spheroids growth, spheroids-derived cell detachment, epithelial-mesenchymal transition and Galectin-9 upregulation. Altogether, F. nucleatum promotes pro-tumoral mechanism in oral cancer.},
}
@article {pmid39743449,
year = {2024},
author = {Maan, M and U, JP and Mohamed, DA and Jalaleddine, N and Abuzayeda, M and Khamis, AH and Dutta, M and Moharamzadeh, K},
title = {The Effects of Electronic Cigarettes on Oral Microbiome and Metabolome in 3D Tissue-Engineered Models.},
journal = {International dental journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.identj.2024.12.002},
pmid = {39743449},
issn = {1875-595X},
abstract = {BACKGROUND AND AIM: Recent studies have shown that electronic cigarettes (ECs) use disrupts the oral microbiome composition and diversity, impairing the metabolic pathways of the mucosal cells. However, to date, no reports have evaluated the role of EC exposure in the context of oral metabolome. Hence, the aim of this study was to investigate the role of EC aerosol exposure in the dysregulation of the oral microbiome and metabolome profile using in vitro 3D organotypic models of human oral mucosa.<br><br>METHODS: 3D tissue-engineered human oral mucosa models were generated and infected with oral microbes obtained from saliva of a healthy donor. The epithelial surface of the oral mucosal models was exposed directly to the EC aerosol (flavoured; with and without nicotine) as it came out of a simulated activated device that mimicked the clinical situation. A comprehensive assessment of oral microbiome community composition by bacterial 16S rRNA gene sequencing was performed. A gas chromatography-based mass spectrometry analysis was also conducted to identify the effect of vaping on the oral metabolome profile.<br><br>RESULTS: A higher alpha diversity in flavoured EC with nicotine groups was observed compared to controls, with notable differences in bacterial taxa abundance. Metabolomics analysis further demonstrated distinct clustering of control, EC with flavoured nicotine, and flavoured EC groups, confirming 13 metabolites that were statistically higher in levels in flavoured EC with nicotine group, indicating the adverse effects of nicotine on the oral mucosa model. Altered metabolites were mainly enriched in pathways associated with oral cancer progression.<br><br>CONCLUSION: This study underscores the significant impact of EC use on oral health, highlighting alterations in the oral microbiome, bacterial composition, and metabolite profiles via a clinically relevant in vitro 3D organotypic model of human oral mucosa.},
}
@article {pmid39743291,
year = {2024},
author = {Barone, GD and Zhou, Y and Wang, H and Xu, S and Ma, Z and Cernava, T and Chen, Y},
title = {Implications of bacteria‒bacteria interactions within the plant microbiota for plant health and productivity.},
journal = {Journal of Zhejiang University. Science. B},
volume = {25},
number = {12},
pages = {1039-1054},
pmid = {39743291},
issn = {1862-1783},
support = {2022YFD1400100//the National Key Research and Development Program of China/ ; LZ23C140004//the Natural Science Foundation of Zhejiang Province/ ; 32172356//the National Natural Science Foundation of China/ ; CARS-3-1-15//the China Agriculture Research System/ ; },
mesh = {*Microbiota ; *Bacteria/metabolism ; Crops, Agricultural/microbiology ; Plants/microbiology ; Microbial Interactions ; Agriculture ; },
abstract = {Crop production currently relies on the widespread use of agrochemicals to ensure food security. This practice is considered unsustainable, yet has no viable alternative at present. The plant microbiota can fulfil various functions for its host, some of which could be the basis for developing sustainable protection and fertilization strategies for plants without relying on chemicals. To harness such functions, a detailed understanding of plant‒microbe and microbe‒microbe interactions is necessary. Among interactions within the plant microbiota, those between bacteria are the most common ones; they are not only of ecological importance but also essential for maintaining the health and productivity of the host plants. This review focuses on recent literature in this field and highlights various consequences of bacteria‒bacteria interactions under different agricultural settings. In addition, the molecular and genetic backgrounds of bacteria that facilitate such interactions are emphasized. Representative examples of commonly found bacterial metabolites with bioactive properties, as well as their modes of action, are given. Integrating our understanding of various binary interactions into complex models that encompass the entire microbiota will benefit future developments in agriculture and beyond, which could be further facilitated by artificial intelligence-based technologies.},
}
@article {pmid39742975,
year = {2025},
author = {Dougherty, PE and Pedersen, MS and Forero-Junco, LM and Carstens, AB and Raaijmakers, JM and Riber, L and Hansen, LH},
title = {Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks.},
journal = {Virus research},
volume = {352},
number = {},
pages = {199524},
doi = {10.1016/j.virusres.2024.199524},
pmid = {39742975},
issn = {1872-7492},
abstract = {The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.},
}
@article {pmid39742897,
year = {2024},
author = {Jumaylawee, HRH and Komijani, M and Shahrjerdi, S and Sargolzaei, J},
title = {The interplay of gut microbiota and heavy metals in multiple sclerosis patients.},
journal = {Microbial pathogenesis},
volume = {199},
number = {},
pages = {107269},
doi = {10.1016/j.micpath.2024.107269},
pmid = {39742897},
issn = {1096-1208},
abstract = {Multiple Sclerosis (MS) is a chronic inflammatory disease characterized by central nervous system (CNS). In this study, the concentration of heavy metals was measured in stool samples of MS patients by Inductively Coupled Plasma-Mass Spectroscopy (ICP-MS) method and compared with healthy people. Also, another goal of this study is to investigate the alteration of the gut microbiome of MS patients by metagenomics technique based on the 16S rRNA gene sequencing. The IL-10 ELISA assay showed no significant differences between the serum level of the IL-10 in the patients and the control group (p = 0.510). Heavy metal measurement by ICP-MS showed significantly higher levels of arsenic (As, Mean = 32.77 μg/kg), nickel (Ni, Mean = 7.154 μg/kg), manganese (Mn, Mean = 3723 μg/kg), and zinc (Zn, Mean = 5508 μg/kg) in the stool samples of the MS group compared to the control group, while concentrations of iron (Fe, Mean = 9585 μg/kg), lead (Pb, Mean = 18.54 μg/kg), titanium (Ti, Mean = 69.69 μg/kg), and tin (Sn, Mean = 13.92 μg/kg) were significantly lower. The result of gut microbiome analysis showed an increase in the abundance of the Verrumicrobiaceae, Lachnospiraceae and Ruminococcaceae families was considerably increased in MS patients compared to the control group (p < 0.05). This study reports that high levels of heavy metals such as Ars, Ni, Mn, and Zn, deficiency of Fe, Pb, Ti, and Sn, and alteration of the gut microbiome are involved in the pathogenesis of MS. The novelty of this study lies in its multi-faceted approach to understanding MS by integrating the measurement of heavy metals in stool samples with the analysis of gut microbiome alterations, thereby providing comprehensive insights into heavy metals, the gut microbiome, and potential therapeutic avenues. This study suggests several potential applications and practical implications based on its findings regarding heavy metals, gut microbiome alterations, and IL-10 levels in MS. First, the identification of elevated levels of specific heavy metals and deficiencies in others may lead to targeted screening and monitoring, informing preventive strategies for MS patients. Additionally, the observed gut microbiome changes could facilitate the development of microbiome-based therapies, such as probiotics or dietary interventions, aimed at restoring microbial balance. Finally, exploring the interplay between heavy metals, gut microbiome, and immune response may guide the creation of novel therapeutic interventions, ultimately enhancing treatment efficacy and providing new avenues for managing MS, thereby alleviating the burden of this chronic condition.},
}
@article {pmid39742868,
year = {2024},
author = {Arnone, AA and Tsai, YT and Cline, JM and Wilson, AS and Westwood, B and Seger, ME and Chiba, A and Howard-McNatt, M and Levine, EA and Thomas, A and Soto-Pantoja, DR and Cook, KL},
title = {Endocrine-targeting therapies shift the breast microbiome to reduce estrogen receptor-α breast cancer risk.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {101880},
doi = {10.1016/j.xcrm.2024.101880},
pmid = {39742868},
issn = {2666-3791},
abstract = {Studies indicate that breast tissue has a distinct modifiable microbiome population. We demonstrate that endocrine-targeting therapies, such as tamoxifen, reshape the non-cancerous breast microbiome to influence tissue metabolism and reduce tumorigenesis. Using 16S sequencing, we found that tamoxifen alters β-diversity and increases Firmicutes abundance, including Lactobacillus spp., in mammary glands (MGs) of mice and non-human primates. Immunohistochemistry showed that lipoteichoic acid (LTA)-positive bacteria were elevated in tamoxifen-treated breast tissue. In B6.MMTV-PyMT mice, intra-nipple probiotic bacteria injections reduced tumorigenesis, altered metabolic gene expression, and decreased tumor proliferation. Probiotic-conditioned media selectively reduced viability in estrogen receptor-positive (ER+) breast cancer cells and altered mitochondrial metabolism in non-cancerous epithelial cells. Human tumor samples revealed that LTA-positive bacteria negatively correlated with Ki67, suggesting that endocrine therapies influence tumor-associated microbiota to regulate proliferation. Our data indicate that endocrine-targeting therapies modify the breast microbiome, corresponding with a shift in tissue metabolism to potentially reduce ER+ breast cancer risk.},
}
@article {pmid39742816,
year = {2024},
author = {Li, L and Nielsen, J and Chen, Y},
title = {Personalized gut microbial community modeling by leveraging genome-scale metabolic models and metagenomics.},
journal = {Current opinion in biotechnology},
volume = {91},
number = {},
pages = {103248},
doi = {10.1016/j.copbio.2024.103248},
pmid = {39742816},
issn = {1879-0429},
abstract = {The impact of the gut microbiome on human health is increasingly recognized as dysbiosis has been found to be associated with a spectrum of diseases. Here, we review the databases of genome-scale metabolic models (GEMs), which have paved the way for investigations into the metabolic capabilities of gut microbes and their interspecies dynamics. We further discuss the strategies for developing community-level GEMs, which are crucial for understanding the complex interactions within microbial communities and between the microbiome and its host. Such GEMs can guide the design of synthetic microbial communities for disease treatment. Finally, we explore advances in personalized gut microbiome modeling. These advancements broaden our mechanistic understanding and hold promise for applications in precision medicine and therapeutic interventions.},
}
@article {pmid39742562,
year = {2024},
author = {Wyatt, NJ and Watson, H and Young, GR and Doona, M and Tilling, N and Allerton, D and Masi, AC and Ahmad, T and Doyle, JA and Frith, K and Hart, A and Hildreth, V and Irving, PM and Jones, C and Kennedy, NA and Lawrence, S and Lees, CW and Lees, R and Liddle, T and Lindsay, JO and Marchesi, JR and Parkes, M and Powell, N and Prescott, NJ and Raine, T and Satsangi, J and Whelan, K and Wood, R and King, A and Jostins-Dean, L and Speight, RA and McGregor, N and Stewart, CJ and Lamb, CA},
title = {Evaluation of intestinal biopsy tissue preservation methods to facilitate large-scale mucosal microbiota research.},
journal = {EBioMedicine},
volume = {112},
number = {},
pages = {105550},
doi = {10.1016/j.ebiom.2024.105550},
pmid = {39742562},
issn = {2352-3964},
abstract = {BACKGROUND: Large-scale multicentre studies are needed to understand complex relationships between the gut microbiota, health and disease. Interrogating the mucosal microbiota may identify important biology not captured by stool analysis. Gold standard tissue cryopreservation ('flash freezing') limits large-scale study feasibility. We aimed to compare gut microbiota in gold standard and pragmatic mucosal biopsy storage conditions.<br><br>METHODS: We collected endoscopic recto-sigmoid biopsies from 20 adults with inflammatory bowel disease. Biopsies were preserved using three methods: (i) flash freezing (most proximal and distal biopsy sites); (ii) nucleic acid preservative reagents (QIAGEN Allprotect&#xae;, Invitrogen RNAlater&#x2122;, and Zymo DNA/RNA Shield&#x2122;); and (iii) formalin fixation with paraffin embedding (FFPE), which is used to preserve tissue for clinical histopathology within healthcare settings. Microbiota were sequenced on the MiSeq platform (V4 region, 16S rRNA gene).<br><br>FINDINGS: Tissue microbiota were consistent between most proximal and distal tissue suggesting any within-patient variation observed reflected storage condition, not biopsy location. There was no significant difference in alpha-diversity or microbial community profiles of reagent-preserved versus gold standard tissue. FFPE community structure was significantly dissimilar to other tissue samples, driven by differential relative abundance of obligate gut anaerobes; Faecalibacterium, Anaerostipes and Lachnospiraceae. Despite these differences, tissue microbiota grouped by participant regardless of preservation and storage conditions.<br><br>INTERPRETATION: Preservative reagents offer a convenient alternative to flash freezing tissue in prospective large-scale mucosal microbiota studies. Whilst less comparable, FFPE provides potential for retrospective microbiota studies using historical samples.<br><br>FUNDING: Medical Research Council (MR/T032162/1) and The Leona M. and Harry B. Helmsley Charitable Trust (G-2002-04255).},
}
@article {pmid39742427,
year = {2025},
author = {Zhang, J and Sun, Z and Cheng, L and Kang, J and Liu, Y and Zhao, Y and Xiao, M and Liu, H and Zhu, Q and Guo, Q and Lin, C},
title = {Structural Characterization of Water-Soluble Pectin from the Fruit of Diospyros lotus L. and Its Protective Effects against DSS-Induced Colitis in Mice.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c07611},
pmid = {39742427},
issn = {1520-5118},
abstract = {Polysaccharides from Diospyros lotus L. were investigated for their structural characterization and anti-inflammatory activity. Four low polymer dispersity index (PDI) subfractions were obtained: DRP-1 (153.95 kDa), DRP-2 (61.22 kDa), DRP-3 (22.80 kDa), and DRP-4 (8.93 kDa), respectively. DRP-4 contained the highest number of RG-I domains (43.25%), while DRP-1 had the highest degree of methyl esterification (37.5%). Results from the dextran sulfate sodium (DSS) salt-induced ulcerative colitis (UC) mice model indicated that DCP promoted mucosal and tight junction protein (caudin-1 and occludin) expression. Moreover, DCP improved the microbial community composition through selective enrichment of beneficial bacteria such as Lachnospiraceae and Lactobacillaceae. The anti-inflammatory activity of DCP was speculated to be related to its neutral sugar side chain and low esterification degree. These results suggested that DCP could prevent DSS-induced colitis and inhibit colon inflammation by maintaining a balanced gut microbiome and protecting the colon mucosal barrier.},
}
@article {pmid39742347,
year = {2024},
author = {Xie, S and Liu, M and Li, W},
title = {Impact of Radiotherapy on Endocrine Function and Gut Microbiota in Cervical Cancer Patients Undergoing Ovarian Transposition.},
journal = {International journal of women's health},
volume = {16},
number = {},
pages = {2319-2331},
pmid = {39742347},
issn = {1179-1411},
abstract = {OBJECTIVE: This study aims to investigate the effects of radiotherapy on ovarian function, endocrine function, and gut microbiota in cervical cancer patients who underwent ovarian transposition, compared to those who did not.<br><br>METHODS: This study included 100 cervical cancer patients treated from January to June 2024, divided into a control group (50 cases, radical surgery and radiotherapy) and an observation group (50 cases, ovarian transposition surgery plus radiotherapy). Radiotherapy protocols included conventional, intensity-modulated, or conformal radiotherapy, with 6MVX rays delivering 100-200 cGy per session, 5 sessions per week for 6&#xa0;weeks. In the observation group, the ovarian region was shielded with a lead plate. Outcomes measured included ovarian and endocrine function, quality of life, adverse reactions, and gut microbiota composition. DNA was extracted from fecal samples for 16S rRNA sequencing and bioinformatics analysis, including &#x3b1;- and &#x3b2;-diversity, taxonomic composition, and LEfSe analysis.<br><br>RESULTS: Before radiotherapy, no significant differences in serum sex hormone levels were observed between the groups. After radiotherapy, the control group showed greater increases in FSH and LH and a more pronounced decrease in estradiol (E2) levels. Ovarian function preservation was significantly higher in the observation group (28.00% vs 0.00%). The observation group also had a higher Kupperman score 6 months post-surgery (28.01&#xb1;10.22 vs 21.91&#xb1;7.38). Adverse reaction rates were comparable. Gut microbiota analysis revealed differences in taxonomic composition, with higher Firmicutes (66.5% vs 65.56%) and Faecalibacterium (7.0% vs 2.7%) in the observation group, while Proteobacteria (4.1% vs 13.9%) and Shigella (2.7% vs 8.5%) were more abundant in the control group. LEfSe analysis identified notable species differences, including higher Peptoniphilus and Actinomyces in the observation group.<br><br>CONCLUSION: Ovarian transposition surgery effectively preserves ovarian function in cervical cancer patients. Changes in gut microbiota during radiotherapy may influence endocrine outcomes, warranting further research.},
}
@article {pmid39742335,
year = {2024},
author = {Benslimane, FM and Mohammed, LI and Abu-Hijleh, H and Suleiman, S and Boughattas, S and Zakaria, ZZ and Fthenou, E and Al-Asmakh, M},
title = {Metabarcoding analysis of oral microbiome during pregnancy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1477703},
pmid = {39742335},
issn = {2235-2988},
mesh = {Humans ; Female ; Pregnancy ; *Microbiota/genetics ; Adult ; *Saliva/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Mouth/microbiology ; DNA Barcoding, Taxonomic ; Young Adult ; DNA, Bacterial/genetics ; Pregnancy Trimester, Third ; Qatar ; Cohort Studies ; },
abstract = {Pregnancy is a dynamic physiological process involving significant hormonal, immune, and metabolic changes to support fetal growth and development. This study investigates the changes in salivary microbiome and biochemical markers from the second to the third trimester of pregnancy. Saliva samples were collected from 45 pregnant women enrolled in the Qatar Birth Cohort study at two time points (second and third trimesters). DNA was extracted and subjected to 16S rRNA gene sequencing using Oxford Nanopore Technology. Microbial diversity and taxonomic analyses were performed, along with correlation analyses between microbial abundance and clinical parameters. Biochemically, significant increases in BMI, pulse rate, HbA1c, LDL, total cholesterol, and triglycerides were observed in the third trimester compared to the second. Microbial diversity analysis revealed significant changes in microbial richness and composition. Taxonomy analysis showed a significant 3-fold increase in Bacteroidota. Also, a significant decline in Selenomonas and a significant increase in Veillonella, specifically Veillonella dispar and Veillonella atypica, as well as an increase in Granulicatella were observed in the third trimester, along with a significant decrease in Streptococcus sanguinis. Correlation analysis during the second trimester revealed positive associations between BMI, cholesterol, LDL, and Selenomonas, and negative correlations with Streptococcus and Gemella. In the third trimester, BMI was negatively correlated with Campylobacter, glucose levels were negatively correlated with Neisseria, and triglyceride levels were negatively correlated with Prevotella. These findings highlight significant biochemical and microbial shifts during pregnancy, underscoring the importance of monitoring oral health and metabolic changes in pregnant women.},
}
@article {pmid39742310,
year = {2024},
author = {Wang, Y and Hou, H and Luo, H and Xun, J and Ma, C and Yang, H and Bai, D and Yousuf, S and Lyu, H and Zhang, T and Wan, X and Yao, X and Ma, T and Zhou, Y and Zhu, Z and Zeng, M and An, S and Bai, Q and Bai, Y and Cao, G and Cao, T and Cao, Y and Chang, C and Chang, L and Chen, B and Chen, D and Chen, D and Chen, H and Chen, J and Chen, J and Chen, WH and Chen, X and Chen, Y and Chen, Z and Cheng, C and Cheng, Q and Dai, XJ and Deng, C and Deng, F and Deng, J and Dong, CS and Dong, L and Duan, L and Duan, Y and Fan, Q and Fang, C and Fang, T and Fang, W and Fang, Z and Fu, M and Fu, M and Gao, C and Gao, H and Gao, W and Gao, X and Gao, YZ and Geng, Y and Gong, W and Gu, S and Gu, X and Gu, Z and Guo, JW and Guo, J and Guo, Q and Guo, X and Guo, X and Han, D and Han, Z and Hao, Y and He, J and He, J and He, J and He, R and Hou, G and Hu, B and Hu, H and Hu, Y and Hu, Y and Hu, Y and Huang, G and Huang, H and Huang, J and Huang, S and Jia, B and Jian, X and Jiang, C and Jiang, K and Jiang, L and Jiang, S and Jiao, JY and Jin, H and Jin, J and Kong, S and Lai, X and Leng, Y and Li, B and Li, B and Li, F and Li, H and Li, H and Li, J and Li, K and Li, L and Li, L and Li, M and Li, P and Li, W and Li, W and Li, X and Xuemeng, L and Li, Y and Li, Y and Li, Z and Liang, L and Liang, R and Liang, Z and Liu, Q and Liu, D and Liu, H and Liu, J and Liu, L and Liu, L and Liu, M and Liu, R and Liu, S and Liu, T and Liu, W and Liu, W and Liu, X and Liu, Y and Liu, Y and Liu, Y and Liu, Y and Liu, Z and Liu, Z and Liu, Z and Long, C and Long, Y and Lu, C and Lu, C and Lu, C and Lu, Q and Luan, Y and Luo, P and Luo, S and Ma, N and Ma, XY and Ma, Y and Mao, W and Meng, Y and Ni, Y and Ni, Y and Ning, K and Niu, D and Peng, K and Peng, Z and Qian, X and Qiu, Z and Qu, H and Qu, Z and Ren, Y and Ren, Z and Shen, Y and Shi, L and Shi, L and Shi, W and Shi, Y and Song, T and Song, X and Song, X and Song, X and Su, Q and Su, Y and Sun, L and Sun, Q and Sun, T and Sun, Y and Tang, H and Tang, W and Yu, T and Tian, S and Wang, S and Wang, B and Wang, C and Jin, W and Wang, L and Wang, L and Wang, L and Wang, M and Wang, MK and Wang, P and Wang, S and Wang, S and Wang, X and Wang, X and Wei, M and Wei, Y and Wei, Y and Wei, Y and Wen, C and Wen, X and Wu, L and Wu, S and Wu, Y and Xia, S and Xia, X and Xia, Y and Xiang, X and Xiao, C and Xiao, W and Xiao, Y and Xie, R and Xing, R and Xu, H and Xu, W and Xu, Z and Xue, H and Yan, C and Yan, QL and Yan, S and Yan, X and Yang, M and Yang, Y and Yang, Z and Yang, Z and Yao, G and Yao, Y and Yi, X and Yin, C and Yin, M and Yu, S and Yu, Y and Yu, Y and Yuan, F and Zhai, SL and Zhang, B and Zhang, C and Zhang, F and Zhang, FL and Zhang, H and Zhang, J and Zhang, J and Zhang, K and Zhang, L and Zhang, L and Zhang, L and Zhang, M and Zhang, Q and Zhang, R and Zhang, T and Zhang, T and Zhang, W and Zhang, Y and Zhang, Y and Zhang, Y and Zhang, Z and Zhang, Z and Zhang, ZF and Zhao, B and Zhao, Y and Zhao, Y and Zhao, Z and Zheng, D and Zheng, Y and Zhi, W and Zhong, J and Zhong, X and Zhou, W and Zhou, X and Zhou, Z and Zhou, Z and Zhu, C and Zhu, F and Zhu, X and Zou, Y and Zhou, H and Lei, L and Bi, Y and Shi, H and Sun, HZ and Jin, S and Ren, W and Dai, L and Wang, X and Lan, C and Liu, H and Liu, SJ and Yin, Y and Shi, CL and Gan, RY and Zhao, F and Yu, J and Chen, T and Hong, X and Yang, H and Zhang, B and Chen, S and Li, X and Gao, Y and Liu, YX},
title = {iMeta Conference 2024: Building an innovative scientific research ecosystem for microbiome and One Health.},
journal = {iMeta},
volume = {3},
number = {6},
pages = {e251},
pmid = {39742310},
issn = {2770-596X},
abstract = {The iMeta Conference 2024 provides a platform to promote the development of an innovative scientific research ecosystem for microbiome and One Health. The four key components - Technology, Research (Biology), Academic journals, and Social media - form a synergistic ecosystem. Advanced technologies drive biological research, which generates novel insights that are disseminated through academic journals. Social media plays a crucial role in engaging the public and facilitating scientific communication, thus amplifying the impact of research. Together, these elements create a self-sustaining loop that fosters continuous innovation and collaboration in the field of bioinformatics, biotechnology and microbiome research.},
}
@article {pmid39742304,
year = {2024},
author = {Li, J and Huang, F and Zhou, Y and Huang, T and Tong, X and Zhang, M and Chen, J and Zhang, Z and Du, H and Liu, Z and Zhou, M and Xiahou, Y and Ai, H and Chen, C and Huang, L},
title = {Comprehensive lung microbial gene and genome catalogs assist the mechanism survey of Mesomycoplasma hyopneumoniae strains causing pig lung lesions.},
journal = {iMeta},
volume = {3},
number = {6},
pages = {e258},
pmid = {39742304},
issn = {2770-596X},
abstract = {Understanding the community structure of the lower respiratory tract microbiome is crucial for elucidating its roles in respiratory tract diseases. However, there are few studies about this topic due to the difficulty in obtaining microbial samples from both healthy and disease individuals. Here, using 744 high-depth metagenomic sequencing data of lower respiratory tract microbial samples from 675 well-phenotyped pigs, we constructed a lung microbial gene catalog containing the largest scale of 10,031,593 nonredundant genes to date, 44.8% of which are novel. We obtained 356 metagenome-assembled genomes (MAGs) which were further clustered into 256 species-level genome bins with 41.8% being first reported in the current databases. Based on these data sets and through integrated analysis of the isolation of the related bacterial strains, in vitro infection, and RNA sequencing, we identified and confirmed that Mesomycoplasma hyopneumoniae (M. hyopneumoniae) MAG_47 and its adhesion-related virulence factors (VFs) were associated with lung lesions in pigs. Differential expression levels of adhesion- and immunomodulation-related VFs likely determined the heterogenicity of adhesion and pathogenicity among M. hyopneumoniae strains. M. hyopneumoniae adhesion activated several pathways, including nuclear factor kappa-light-chain-enhancer of activated B, mitogen-activated protein kinase, cell apoptosis, T helper 1 and T helper 2 cell differentiation, tumor necrosis factor signaling, interleukin-6/janus kinase 2/signal transducer and activator of transcription signaling, and response to reactive oxygen species, leading to cilium loss, epithelial cell‒cell barrier disruption, and lung tissue lesions. Finally, we observed the similar phylogenetic compositions of the lung microbiome between humans with Mycoplasma pneumoniae and pigs infected with M. hyopneumoniae. The results provided important insights into pig lower respiratory tract microbiome and its relationship with lung health.},
}
@article {pmid39742301,
year = {2024},
author = {Zhou, N and Han, X and Hu, N and Han, S and Yuan, M and Li, Z and Wang, S and Li, Y and Li, H and Rengel, Z and Jiang, Y and Lou, Y},
title = {The crop mined phosphorus nutrition via modifying root traits and rhizosphere micro-food web to meet the increased growth demand under elevated CO2.},
journal = {iMeta},
volume = {3},
number = {6},
pages = {e245},
pmid = {39742301},
issn = {2770-596X},
abstract = {Elevated CO2 (eCO2) stimulates productivity and nutrient demand of crops. Thus, comprehensively understanding the crop phosphorus (P) acquisition strategy is critical for sustaining agriculture to combat climate changes. Here, wheat (Triticum aestivum L) was planted in field in the eCO2 (550 µmol mol[-1]) and ambient CO2 (aCO2, 415 µmol mol[-1]) environments. We assessed the soil P fractions, root morphological and physiological traits and multitrophic microbiota [including arbuscular mycorrhizal fungi (AMF), alkaline phosphomonoesterase (ALP)-producing bacteria, protozoa, and bacterivorous and fungivorous nematodes] in the rhizosphere and their trophic interactions at jointing stage of wheat. Compared with aCO2, significant 20.2% higher shoot biomass and 26.8% total P accumulation of wheat occurred under eCO2. The eCO2 promoted wheat root length and AMF hyphal biomass, and increased the concentration of organic acid anions and the ALP activity, which was accompanied by significant decreases in calcium-bound inorganic P (Ca-Pi) (by 16.7%) and moderately labile organic P (by 26.5%) and an increase in available P (by 14.4%) in the rhizosphere soil. The eCO2 also increased the growth of ALP-producing bacteria, protozoa, and bacterivorous and fungivorous nematodes in the rhizosphere, governed their diversity and community composition. In addition, the eCO2 strengthened the trophic interactions of microbiota in rhizosphere; specifically, the eCO2 promoted the associations between protozoa and ALP-producing bacteria, between protozoa and AMF, whereas decreased the associations between ALP-producing bacteria and nematodes. Our findings highlighted the important role of root traits and multitrophic interactions among microbiota in modulating crop P-acquisition strategies, which could advance our understanding about optimal P management in agriculture systems under global climate changes.},
}
@article {pmid39742299,
year = {2024},
author = {Yu, G and Xu, C and Wang, X and Ju, F and Fu, J and Ni, Y},
title = {MetOrigin 2.0: Advancing the discovery of microbial metabolites and their origins.},
journal = {iMeta},
volume = {3},
number = {6},
pages = {e246},
pmid = {39742299},
issn = {2770-596X},
abstract = {First introduced in 2021, MetOrigin has quickly established itself as a powerful web server to distinguish microbial metabolites and identify the bacteria responsible for specific metabolic processes. Building on the growing understanding of the interplay between the microbiome and metabolome, and in response to user feedback, MetOrigin has undergone a significant upgrade to version 2.0. This enhanced version incorporates three new modules: (1) Quick search module that facilitates the rapid identification of bacteria associated with a particular metabolite; (2) Orthology analysis module that links metabolic enzyme genes with their corresponding bacteria; (3) Mediation analysis module that investigates potential causal relationships among bacteria, metabolites, and phenotypes, highlighting the mediating role of metabolites. Additionally, the backend MetOrigin database has been updated with the latest data from seven public databases (KEGG, HMDB, BIGG, ChEBI, FoodDB, Drugbank, and T3DB), with expanded coverage of 210,732 metabolites, each linked to its source organism. MetOrigin 2.0 is freely accessible at http://metorigin.met-bioinformatics.cn.},
}
@article {pmid39742297,
year = {2024},
author = {Shen, X and Jin, H and Zhao, F and Kwok, LY and Zhao, Z and Sun, Z},
title = {Short-term probiotic supplementation affects the diversity, genetics, growth, and interactions of the native gut microbiome.},
journal = {iMeta},
volume = {3},
number = {6},
pages = {e253},
pmid = {39742297},
issn = {2770-596X},
abstract = {The precise mechanisms through which probiotics interact with and reshape the native gut microbiota, especially at the species and genetic levels, remain underexplored. This study employed a high-dose probiotic regimen of Bifidobacterium animalis subsp. lactis [200 billion colony forming units (CFU)/day] over 7 days among healthy participants. Weekly fecal samples were collected for metagenomic sequencing analysis. We found that probiotic intake can significantly enhance the diversity of the gut microbiome and impact single nucleotide variations, growth rates, and network interactions of the resident intestinal bacteria. These adaptive changes in the gut microbiota indicate the swift evolutionary responses of native bacteria to the ecological disturbance presented by probiotic supplementation. Notably, the microbial community appears to undergo rapid and multifaceted ecological adjustments, potentially preceding longer-term evolutionary changes. This knowledge lays the groundwork for further exploration into the mechanisms underlying probiotic-mediated modulation of the gut microbiome, highlighting the necessity of encompassing ecological and evolutionary perspectives in the design and optimization of probiotic applications.},
}
@article {pmid39742294,
year = {2024},
author = {Zha, A and Qi, M and Deng, Y and Li, H and Wang, N and Wang, C and Liao, S and Wan, D and Xiong, X and Liao, P and Wang, J and Yin, Y and Tan, B},
title = {Gut Bifidobacterium pseudocatenulatum protects against fat deposition by enhancing secondary bile acid biosynthesis.},
journal = {iMeta},
volume = {3},
number = {6},
pages = {e261},
pmid = {39742294},
issn = {2770-596X},
abstract = {Gut microbiome is crucial for lipid metabolism in humans and animals. However, how specific gut microbiota and their associated metabolites impact fat deposition remains unclear. In this study, we demonstrated that the colonic microbiome of lean and obese pigs differentially contributes to fat deposition, as evidenced by colonic microbiota transplantation experiments. Notably, the higher abundance of Bifidobacterium pseudocatenulatum was significantly associated with lower backfat thickness in lean pigs. Microbial-derived lithocholic acid (LCA) species were also significantly enriched in lean pigs and positively correlated with the abundance of B. pseudocatenulatum. In a high-fat diet (HFD)-fed mice model, administration of live B. pseudocatenulatum decreased fat deposition and enhances colonic secondary bile acid biosynthesis. Importantly, pharmacological inhibition of the bile salt hydrolase (BSH), which mediates secondary bile acid biosynthesis, impaired the anti-fat deposition effect of B. pseudocatenulatum in antibiotic-pretreated, HFD-fed mice. Furthermore, dietary LCA also decreased fat deposition in HFD-fed rats and obese pig models. These findings provide mechanistic insights into the anti-fat deposition role of B. pseudocatenulatum and identify BSH as a potential target for preventing excessive fat deposition in humans and animals.},
}
@article {pmid39741955,
year = {2024},
author = {Newman, NK and Monnier, PM and Rodrigues, RR and Gurung, M and Vasquez-Perez, S and Hioki, KA and Greer, RL and Brown, K and Morgun, A and Shulzhenko, N},
title = {Host response to cholestyramine can be mediated by the gut microbiota.},
journal = {Microbiome research reports},
volume = {3},
number = {4},
pages = {40},
pmid = {39741955},
issn = {2771-5965},
abstract = {Background: The gut microbiota has been implicated as a major factor contributing to metabolic diseases and the response to drugs used for the treatment of such diseases. In this study, we tested the effect of cholestyramine, a bile acid sequestrant that reduces blood cholesterol, on the murine gut microbiota and metabolism. We also explored the hypothesis that some effects of this drug on systemic metabolism can be attributed to alterations in the gut microbiota. Methods: We used a Western diet (WD) for 8 weeks to induce metabolic disease in mice, then treated some mice with cholestyramine added to WD. Metabolic phenotyping, gene expression in liver and ileum, and microbiota 16S rRNA genes were analyzed. Then, transkingdom network analysis was used to find candidate microbes for the cholestyramine effect. Results: We observed that cholestyramine decreased glucose and epididymal fat levels and detected dysregulation of genes known to be regulated by cholestyramine in the liver and ileum. Analysis of gut microbiota showed increased alpha diversity in cholestyramine-treated mice, with fourteen taxa showing restoration of relative abundance to levels resembling those in mice fed a control diet. Using transkingdom network analysis, we inferred two amplicon sequence variants (ASVs), one from the Lachnospiraceae family (ASV49) and the other from the Muribaculaceae family (ASV1), as potential regulators of cholestyramine effects. ASV49 was also negatively linked with glucose levels, further indicating its beneficial role. Conclusion: Our results indicate that the gut microbiota has a role in the beneficial effects of cholestyramine and suggest specific microbes as targets of future investigations.},
}
@article {pmid39741954,
year = {2024},
author = {Delanghe, L and De Boeck, I and Van Malderen, J and Gehrmann, T and Allonsius, CN and Bron, PA and Claes, I and Hagendorens, M and Leysen, J and Wittouck, S and Lebeer, S},
title = {The inner elbow skin microbiome contains Lactobacillus among its core taxa and varies with age, season and lifestyle.},
journal = {Microbiome research reports},
volume = {3},
number = {4},
pages = {43},
pmid = {39741954},
issn = {2771-5965},
abstract = {Background: The human skin microbiome plays an essential role in protecting against pathogens and other external substances. This open ecosystem is also influenced by personal and environmental factors, but the precise impact of these factors, such as lifestyle and season, is understudied. We focused here on the inner elbow, a skin site prone to inflammatory conditions like atopic dermatitis and psoriasis. Methods: We collected skin swabs from the inner elbow of 52 children and adults, with no signs of skin disorders, in the winter and summer seasons. Samples were analyzed using metagenomic shallow shotgun sequencing. In addition, metadata were collected using questionnaires on health, lifestyle, and environmental factors. Results: The core inner elbow community, taxa with a prevalence of 95% or higher, consisted of several well-known skin taxa, such as Staphylococcus hominis, Staphylococcus capitis, Staphylococcus epidermidis, and Cutibacterium acnes. In addition, Streptococcus and Lactobacillus species were also found to be highly prevalent members of the skin microbiota, especially in the age group up to 3 years old. Of all investigated factors, age appeared to be the major driver defining the skin microbiome composition and longitudinal stability over the seasons. Differential abundance analysis using three statistical tests also pointed out that specific skin species were significantly associated with sampling season, age, hygiene practices, vitamin D supplements, probiotics, and the number of household members. Conclusion: This study identifies novel factors influencing the inner elbow skin microbiome composition and paves the way for future comparative and intervention studies in skin disorders such as atopic dermatitis.},
}
@article {pmid39741952,
year = {2024},
author = {Shen, X and Leng, B and Zhang, S and Kwok, LY and Zhao, F and Zhao, J and Sun, Z and Zhang, J},
title = {Secondary analysis reveals gut microbiota differences in patients with Parkinson's disease and/or cognitive impairment.},
journal = {Microbiome research reports},
volume = {3},
number = {4},
pages = {42},
pmid = {39741952},
issn = {2771-5965},
abstract = {Background: Parkinson's disease (PD) is a neurodegenerative disorder, and the main clinical characteristics are bradykinesia and muscle stiffness. Cognitive impairment (CI) is a prevalent non-motor manifestation observed in individuals with PD. According to disease severity, it can be divided into PD with mild cognitive impairment (MCI) and PD dementia. CI in PD patients may precede motor symptoms, and the gut microbiota plays an important role in PD pathogenesis. Therefore, gut microbiota may be one of the diagnostic targets for PD-CI. Methods: This study compared the gut microbiota of 43 PD-CI patients [Montreal Cognitive Assessment (MoCA) score < 26] and 38 PD patients without CI (MoCA ≥ 26). Patients' neuropsychological conditions, depression scale, and brain structure scanned by magnetic resonance imaging (MRI) were also recorded. The fecal metagenomic datasets of patients with PD, PD-CI, and CI only were retrieved from public databases for reanalysis to explore the relationship between PD, CI, and gut microbiota. Results: We found that the cortical thickness and the volume of the hippocampus, gray matter, and thalamus were significantly reduced among patients with PD-CI compared to PD without CI (P < 0.05). Moreover, the gut microbiome in patients with PD-CI had fewer short-chain fatty acid (SCFA) producing bacteria and more pathogenic bacteria. There were also alterations in patterns of metabolic pathway-encoding genes. Additionally, PD affected gut microbiota more than CI. Conclusion: CI may aggravate the severity of PD, but it did not drastically alter subjects' gut microbiota. This study reveals the relationship between gut microbiota, PD, and CI.},
}
@article {pmid39741951,
year = {2024},
author = {Kleerebezem, M and Führen, J},
title = {Synergistic vs. complementary synbiotics: the complexity of discriminating synbiotic concepts using a Lactiplantibacillus plantarum exemplary study.},
journal = {Microbiome research reports},
volume = {3},
number = {4},
pages = {46},
pmid = {39741951},
issn = {2771-5965},
abstract = {Synbiotics are defined as "a mixture comprising live microorganisms and substrate(s) selectively utilized by host microorganisms that confers a health benefit on the host". The definition discriminates between synergistic and complementary synbiotics. Synergistic synbiotics involve a direct interaction between the substrate and co-administered microbe(s), while complementary synbiotics act through independent mechanisms. Here, we evaluate the complexity of discrimination between these two synbiotic concepts using an exemplary study performed with a panel of Lactiplantibacillus plantarum (L. plantarum) strains to identify strain-specific synergistic synbiotics that eventually turned out to work via a complementary synbiotic mechanism. This study highlights that assessing the in situ selectivity of synergistic synbiotics in the intestinal tract is challenging due to the confounding effects of the substrate ingredient on the endogenous microbiome, thereby raising doubts about the added value of distinguishing between synergistic and complementary concepts in synbiotics.},
}
@article {pmid39741946,
year = {2024},
author = {Wosinska, L and Walsh, LH and Walsh, CJ and Cotter, PD and Guinane, CM and O'Sullivan, O},
title = {Cataloging metagenome-assembled genomes and microbial genes from the athlete gut microbiome.},
journal = {Microbiome research reports},
volume = {3},
number = {4},
pages = {41},
pmid = {39741946},
issn = {2771-5965},
abstract = {Aim: Exercise has been increasingly recognized as a potential influencer of the gut microbiome. Nevertheless, findings remain incongruous, particularly in relation to sport-specific patterns. Methods: In this study, we harness all publicly available data from athlete gut microbiome shotgun studies to explore how exercise may influence the gut microbiota through metagenomic assembly supplemented with short read-based taxonomic profiling. Through this analysis, we provide insights into exercise-associated taxa and genes, including the identification and annotation of putative novel species from the analysis of approximately 2,000 metagenome-assembled genomes (MAGs), classified as high-quality (HQ) MAGs and assembled as part of this investigation. Results: Our metagenomic analysis unveiled potential athlete-associated microbiome patterns at both the phylum and species levels, along with their associated microbial genes, across a diverse array of sports and individuals. Specifically, we identified 76 species linked to exercise, with a notable prevalence of the Firmicutes phylum. Furthermore, our analysis detected MAGs representing potential novel species across various phyla, including Bacteroidota, Candidatus Melainabacteria, Elusimicrobia, Firmicutes, Lentisphaerae, Proteobacteria, Tenericutes, and Verrucomicrobiota. Conclusion: In summary, this catalog of MAGs and their corresponding genes stands as the most extensive collection yet compiled from athletes. Our analysis has discerned patterns in genes associated with exercise. This underscores the value of employing shotgun metagenomics, specifically a MAG recovery strategy, for pinpointing sport-associated microbiome signatures. Furthermore, the identification of novel MAGs holds promise for developing probiotics and deepening our comprehension of the intricate interplay between fitness and the microbiome.},
}
@article {pmid39741560,
year = {2024},
author = {Hazzard, AA and McCrorey, M and Salman, T and Johnson, DE and Luo, Z and Fu, X and Keegan, AP and Benitez, A and Fitting, S and Jiang, W},
title = {Cannabis use, oral dysbiosis, and neurological disorders.},
journal = {NeuroImmune pharmacology and therapeutics},
volume = {3},
number = {3-4},
pages = {183-193},
pmid = {39741560},
issn = {2750-6665},
support = {R25 GM072643/GM/NIGMS NIH HHS/United States ; },
abstract = {Cannabis (marijuana) is a leafy plant that has medical, recreational, and other uses. Cannabis is socially accepted and widely used throughout the United States. Though cannabis use is increasingly gaining popularity, studies detail the deleterious effects of chronic cannabis smoking on mental health, as well as the immunosuppressive properties of cannabinoids. Additionally, oral dysbiosis induced by cannabis smoking serves as a novel catalyst for neurological abnormalities, potentially possible through microbial translocation via the oral-brain axis. This review summarizes the effects and link of smoking cannabis on neurological abnormalities, immunity, and oral microbiome.},
}
@article {pmid39741321,
year = {2024},
author = {Shao, L and Cai, G and Fu, J and Zhang, W and Ye, Y and Ling, Z and Ye, S},
title = {Gut microbial 'TNFα-sphingolipids-steroid hormones' axis in children with autism spectrum disorder: an insight from meta-omics analysis.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {1165},
pmid = {39741321},
issn = {1479-5876},
support = {LY22C010001//Natural Science Foundation of Zhejiang Province/ ; 2022KY1451//Zhejiang Provincial Medical and Health Science and Technology Plan/ ; 2022KY971//Zhejiang Provincial Medical and Health Science and Technology Plan/ ; 31870839//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Autism Spectrum Disorder/microbiology/blood/metabolism ; *Gastrointestinal Microbiome ; *Tumor Necrosis Factor-alpha/metabolism/blood ; *Sphingolipids/blood/metabolism ; Child ; *Steroids/blood/metabolism ; Metabolomics ; Male ; Female ; Hormones/blood/metabolism ; Metagenomics ; Child, Preschool ; Dysbiosis/microbiology ; Feces/microbiology ; },
abstract = {BACKGROUND: Autism spectrum disorder (ASD) is a persistent neurodevelopmental disorder affecting brains of children. Mounting evidences support the associations between gut microbial dysbiosis and ASD, whereas detailed mechanisms are still obscure.<br><br>METHODS: Here we probed the potential roles of gut microbiome in ASD using fecal metagenomics and metabolomics.<br><br>RESULTS: Children with ASD were found to be associated with augmented serum cytokines milieu, especially TNF&#x3b1;. Metagenomic analysis generated 29 differential species and 18 dysregulated functional pathways such as Bifidobacterium bifidum, Segatella copri, and upregulated 'Sphingolipid metabolism' in children with ASD. Metabolomics revealed steroid hormone dysgenesis in children with ASD with lower abundances of metabolites such as estriol, estradiol and deoxycorticosterone. A three-way association analysis showed positive correlations between TNF&#x3b1; and microbial function potentials such as 'Bacterial toxins' and 'Lysosome', indicating the contribution of microbial dysbiosis to neuroinflammation. TNF&#x3b1; also correlated positively with 'Sphingolipid metabolism', which further showed negative correlations with metabolites estriol and deoxycorticosterone. Such results, in consistent with current findings, revealed the contribution of increased TNF&#x3b1; to upregulated sphingolipid metabolism, which further impaired steroid hormone biosynthesis.<br><br>CONCLUSION: Our study proposed the gut microbial 'TNF&#x3b1;-sphingolipids-steroid hormones' axis in children with ASD, which may provide new perspectives for developing gut microbiome-based treatments in the future.},
}
@article {pmid39741173,
year = {2024},
author = {Zhao, W and Shi, L and Han, Y and Wang, X and Wang, J and Xu, S and Zhang, X and Huang, Z},
title = {Development of a microbiome for phenolic metabolism based on a domestication approach from lab to industrial application.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1716},
pmid = {39741173},
issn = {2399-3642},
mesh = {*Microbiota ; Wastewater/microbiology ; Phenols/metabolism ; Bacteria/genetics/metabolism/classification ; Phenol/metabolism ; },
abstract = {Despite a lot of efforts devoted to construct efficient microbiomes, there are still major obstacles to moving from the lab to industrial applications due to the inapplicability of existing technologies or limited understanding of microbiome variation regularity. Here we show a domestication strategy to cultivate an effciient and resilient functional microbiome for addressing phenolic wastewater challenges, which involves directional domestication in shaker, laboratory water test in small-scale, gas test in pilot scale, water test in pilot scale, and engineering application in industrial scale. The domestication process includes the transition from water to gas, which provided complex transient environment for screening of a more adaptable and robust microbiome, thereby mitigating the performance disparities encountered when transitioning from laboratory experimentation to industrial engineering applications. Within the domestication and application processes for treating phenolic resin wastewater, a powerful functional microbiome was built by self-assembly. This leads to an augmented biodiversity and the development of more intricate phenol and formaldehyde metabolic pathways. The incorporation of increased stochastic processes and random network characteristics further suggested the stability of the microbial community during the application phase. This study elucidates the self-assembly process of microbial communities during the artificial construction process, showcasing their adaptive evolution under different adverse conditions. It serves as a noteworthy case study for the artificial construction of a microbiome for the engineering application of treating industrial wastewater.},
}
@article {pmid39741169,
year = {2024},
author = {Bathia, J and Miklós, M and Gyulai, I and Fraune, S and Tökölyi, J},
title = {Environmental microbial reservoir influences the bacterial communities associated with Hydra oligactis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {32167},
pmid = {39741169},
issn = {2045-2322},
mesh = {Animals ; *Hydra/microbiology ; *Microbiota ; *Bacteria/classification/isolation &amp; purification/genetics ; *Lakes/microbiology ; Water Microbiology ; Hungary ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The objective to study the influence of microbiome on host fitness is frequently constrained by spatial and temporal variability of microbial communities. In particular, the environment serves as a dynamic reservoir of microbes that provides potential colonizers for animal microbiomes. In this study, we analyzed the microbiome of Hydra oligactis and corresponding water samples from 15 Hungarian lakes to reveal the contribution of environmental microbiota on host microbiome. Correlation analyses and neutral modeling revealed that differences in Hydra microbiota are associated with differences in environmental microbiota. To further investigate the influence of environmental bacterial community on the host microbiome, field-collected Hydra polyps from three populations were cultured in native water or foreign water. Our results show that lake water bacteria significantly contribute to Hydra microbial communities, but the compositional profile remained stable when cultured in different water sources. Longitudinal analysis of the in vitro experiment revealed a site-specific change in microbiome that correlated with the source water quality. Taken together, our findings demonstrate that while freshwater serves as a critical microbial reservoir, Hydra microbial communities exhibit remarkable resilience to environmental changes maintaining stability despite potential invasion. This dual approach highlights the complex interplay between environmental reservoirs and host microbiome integrity.},
}
@article {pmid39740900,
year = {2025},
author = {Palkovsky, M and Modrackova, N and Neuzil-Bunesova, V and Liberko, M and Soumarova, R},
title = {The Bidirectional Impact of Cancer Radiotherapy and Human Microbiome: Microbiome as Potential Anti-tumor Treatment Efficacy and Toxicity Modulator.},
journal = {In vivo (Athens, Greece)},
volume = {39},
number = {1},
pages = {37-54},
pmid = {39740900},
issn = {1791-7549},
mesh = {Humans ; *Neoplasms/radiotherapy/microbiology ; *Gastrointestinal Microbiome/radiation effects/drug effects ; *Microbiota/radiation effects ; Radiotherapy/adverse effects/methods ; Treatment Outcome ; },
abstract = {Microbiome and radiotherapy represent bidirectionally interacting entities. The human microbiome has emerged as a pivotal modulator of the efficacy and toxicity of radiotherapy; however, a reciprocal effect of radiotherapy on microbiome composition alterations has also been observed. This review explores the relationship between the microbiome and extracranial solid tumors, particularly focusing on the bidirectional impact of radiotherapy on organ-specific microbiome. This article aims to provide a systematic review on the radiotherapy-induced microbial alteration in-field as well as in distant microbiomes. In this review, particular focus is directed to the oral and gut microbiome, its role in the development and progression of cancer, and how it is altered throughout radiotherapy. This review concludes with recommendations for future research, such as exploring microbiome modification to optimize radiotherapy-induced toxicities or enhance its anti-cancer effects.},
}
@article {pmid39740876,
year = {2025},
author = {Ahrend, H and Buchholtz, A and Stope, MB},
title = {Microbiome and Mucosal Immunity in the Intestinal Tract.},
journal = {In vivo (Athens, Greece)},
volume = {39},
number = {1},
pages = {17-24},
pmid = {39740876},
issn = {1791-7549},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Immunity, Mucosal ; *Intestinal Mucosa/immunology/microbiology ; Inflammatory Bowel Diseases/immunology/microbiology ; Animals ; },
abstract = {The human bowel is exposed to numerous biotic and abiotic external noxious agents. Accordingly, the digestive tract is frequently involved in malfunctions within the organism. Together with the commensal intestinal flora, it regulates the immunological balance between inflammatory defense processes and immune tolerance. Pathological changes in this system often cause chronic inflammatory bowel diseases including Crohn's disease and ulcerative colitis. This review article highlights the complex interaction between commensal microorganisms, the intestinal microbiome, and the intestinal epithelium-localized local immune system. The main functions of the human intestinal microbiome include (i) protection against pathogenic microbial colonization, (ii) maintenance of the barrier function of the intestinal epithelium, (iii) degradation and absorption of nutrients and (iv) active regulation of the intestinal immunity. The local intestinal immune system consists primarily of macrophages, antigen-presenting cells, and natural killer cells. These cells regulate the commensal intestinal microbiome and are in turn regulated by signaling factors of the epithelial cells and the microbiome. Deregulated immune responses play an important role and can lead to both reduced activity of the commensal microbiome and pathologically increased activity of harmful microorganisms. These aspects of chronic inflammatory bowel disease have become the focus of attention in recent years. It is therefore important to consider the immunological-microbial context in both the diagnosis and treatment of inflammatory bowel diseases. A promising holistic approach would include the most comprehensive possible diagnosis of the immune and microbiome status of the patient, both at the time of diagnostics and during therapy.},
}
@article {pmid39740617,
year = {2024},
author = {Gao, Z and Zhou, R and Chen, Z and Qian, H and Xu, C and Gao, M and Huang, X},
title = {Genetic prediction of blood metabolites mediating the relationship between gut microbiota and postpartum depression: A mendelian randomization study.},
journal = {Journal of psychiatric research},
volume = {181},
number = {},
pages = {614-622},
doi = {10.1016/j.jpsychires.2024.12.025},
pmid = {39740617},
issn = {1879-1379},
abstract = {BACKGROUND: Observational studies have suggested an association between gut microbiota(GM) and postpartum depression (PPD). However, the causal relationship remains unclear, and the role of blood metabolites in this association remains elusive.<br><br>METHODS: This study firstly elucidated the causal relationship among 196&#xa0;GM taxa, 224 blood metabolites, and PPD from a genetic perspective, employing two-sample Mendelian randomization (MR). Subsequently, a two-step mediation MR approach was employed to explore the role of blood metabolites as potential mediators. To validate the relevant findings, we further selected other data (GM and blood metabolites) from the IEU Open GWAS and GWAS Catalog for analysis. Our primary analysis utilized the inverse variance weighted method. To enhance the robustness of our results, we also applied MR-Egger method, weighted median method, Cochran's Q test, MR-Egger regression, and MR-PRESSO.<br><br>RESULTS: MR analysis results revealed a nominal association (p&#xa0;<&#xa0;0.05) between 13&#xa0;GM taxa, 6 blood metabolites, and PPD. After multiple-testing correction (PFDR < 0.1), Bifidobacteriales (PFDR&#xa0;=&#xa0;0.034), Bifidobacteriaceae (PFDR&#xa0;=&#xa0;0.055) and Guanosine (PFDR&#xa0;=&#xa0;0.081) showed significant causal relationships with PPD. In our validation results, the higher level of Alphaproteobacteria (OR: 1.057, 95% CI: 1.024-1.091; p&#xa0;=&#xa0;0.0006) retained a causal relationship with a higher risk of PPD. Finally, mediation analysis revealed that the impact of Odoribacter on PPD was mediated indirectly through Hyodeoxycholate, with a mediation proportion of 16.8%.<br><br>CONCLUSION: Our findings elucidated the underlying mechanisms between the GM, blood metabolites, and PPD. These findings contribute to the prevention and diagnosis of PPD, offering novel insights into microbiome-based therapies and metabolite-targeted interventions for the treatment of PPD.},
}
@article {pmid39740607,
year = {2024},
author = {Seymour, KA and Strain, M and Ashley-Koch, A and Muehlbauer, MJ and Ilkayeva, OR and George, TK and Hill, D and Ellison, M and Ito, S and Lagoo-Deenadayalan, S and Plichta, JK and Purves, JT and Thacker, JKM and Nalley, J and Kirk, AD and Hwang, ES and Bain, JR},
title = {Acute perioperative alterations in metabolism: A pilot study using mass spectrometry-based metabolomics.},
journal = {Surgery},
volume = {180},
number = {},
pages = {109055},
doi = {10.1016/j.surg.2024.109055},
pmid = {39740607},
issn = {1532-7361},
abstract = {OBJECTIVE: To characterize early physiologic stresses imposed by surgery by applying metabolomic analyses to deeply phenotype pre- and postoperative plasma and urine of patients undergoing elective surgical procedures.<br><br>BACKGROUND: Patients experience perioperative stress through depletion of metabolic fuels. Bowel stasis or injury might allow more microbiome-derived uremic toxins to enter the blood, while the liver and kidney are simultaneously clearing analgesic and anesthetic drugs. Metabolomics provides a broad-scale snapshot of small-molecule chemicals generated in vital energetic and detoxification pathways, enabling a mechanistic understanding of surgical stressors.<br><br>METHODS: We performed metabolomic analysis of paired preoperative and early-recovery plasma (n&#xa0;= 34) and urine (n&#xa0;= 35) from patients who underwent elective surgeries, spanning cardiovascular, gastrointestinal, hernia, oncologic, and urologic procedures. Mass spectrometry-based metabolomics analyses were performed together with the analysis of select metabolites and macromolecules via conventional clinical assays.<br><br>RESULTS: Fuel stress during elective surgery manifested in changes across all major metabolic pathways, encompassing lipolysis, glycolysis-Krebs cycle, ketogenesis, and glycogenolysis. A common signature of enhanced amino acid oxidation and urea-cycle activity emerged, which was especially pronounced in patients given citrulline boluses before visceral procedures. Excretion of amino acid-derived catabolite toxins increased during surgery, notably those derived from gut microbes, as did an extract of disposable surgical plasticware, bis(2-ethylhexyl)phthalate.<br><br>CONCLUSION: Elective surgery imposes broad-scale early and measurable metabolic changes. The use of citrulline-enriched preoperative carbohydrate drinks needs further study to limit metabolic burden. Attention to perioperative nutrition and intraoperative control of gut-microbial toxins might reduce metabolic derangements and lead to better postoperative outcomes.},
}
@article {pmid39740549,
year = {2024},
author = {Zveushe, OK and Nkoh, JN and de Dios, VR and Manjoro, TT and Suanon, F and Zhang, H and Chen, W and Lin, L and Zhou, L and Zhang, W and Sesu, F and Li, J and Han, Y and Dong, F},
title = {Enhancing hexavalent chromium stable reduction via sodium alginate encapsulation of newly isolated fungal and bacterial consortia.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {136994},
doi = {10.1016/j.jhazmat.2024.136994},
pmid = {39740549},
issn = {1873-3336},
abstract = {Chromium [Cr(VI)]-induced soil pollution is a serious environmental threat. Bioremediation utilizes specific microbes capable of transforming Cr(VI) into the less toxic Cr(III), however, microbial efficacy can be inhibited by elevated pollutant concentrations and competition from indigenous microbial communities. Thus, this study explored the potential of single and multi-domain microbial consortia encapsulated in alginate to overcome these shortcomings. The results revealed that (i) fungal treatments demonstrated an elevated tolerance and reduction ability for Cr(VI) compared to bacterial treatments; (ii) combined application of fungi and bacteria was more effective in degrading Cr(VI) in soil compared to the individual treatments; (iii) microbial encapsulation improved microbial response to Cr(VI) toxicity thereby increasing their lifespan and Cr(VI) degrading ability; (iv) microbial consortia significantly decreased soil pH, electrical conductivity, and redox potential while simultaneously increasing soil enzyme activities (urease, sucrase, phosphatase, catalase, and laccase); and (v) The improved tolerance in the inoculated treatment resulted in increased microbial diversity and a substantial variation in microbial community structures, with 10,753 bacterial and 2697 fungal amplicon sequence variants identified across the treatment groups. This study underscores the critical importance of microbial diversity in bioremediation, emphasizing that encapsulation with the right material could improve the effectiveness of environmental remediation strategies.},
}
@article {pmid39740548,
year = {2024},
author = {Wu, J and Lv, D and Lin, W and Mao, Y and Xia, Y and Feng, L and Zhao, T and Mao, X and Shu, F and Guo, H},
title = {Chronic exposure to liquid crystal monomer EBCN at environmentally relevant concentrations induces testicular dysfunction via the gut-testis axis.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {137033},
doi = {10.1016/j.jhazmat.2024.137033},
pmid = {39740548},
issn = {1873-3336},
abstract = {4-Cyano-4'-ethoxybiphenyl (EBCN) is a representative cyano liquid crystal monomer (LCM). While prior studies have documented the widespread occurrence of LCMs in diverse environmental and biological samples, research on their reproductive effects in vivo remains limited. This study employed 35-day and 70-day exposure models in mice to assess the short-term and long-term effects of environmentally relevant concentrations of EBCN on testicular health. Our findings indicate that EBCN exposure, irrespective of duration, had minimal impact on body weight, testis weight, and testicular organ coefficient. However, it induced dose-dependent reductions in seminiferous tubule area, sperm count, accompanied by decreases in Leydig cells and spermatogenic cells, along with disruptions in sex hormone levels. Moreover, EBCN exposure led to the upregulation of inflammatory factors in serum, partially attributable to the activation of necroptosis-related pathways. Additionally, 16S rRNA sequencing and metabolomic analysis revealed a decline in gut microbiome diversity and a decrease in anti-inflammatory metabolites, specifically L-carnosine, in the intestine, potentially contributing to the observed testicular toxicity. Supplementation with exogenous L-carnosine mitigated EBCN-induced testicular dysfunction by inhibiting the expression of necroptosis-related genes. In conclusion, our study suggests that prolonged EBCN exposure at environmentally relevant concentrations adversely impacts testicular function via the gut-testis axis.},
}
@article {pmid39740526,
year = {2024},
author = {Rojas-Velazquez, D and Kidwai, S and Liu, TC and El-Yacoubi, MA and Garssen, J and Tonda, A and Lopez-Rincon, A},
title = {Understanding Parkinson's: The microbiome and machine learning approach.},
journal = {Maturitas},
volume = {193},
number = {},
pages = {108185},
doi = {10.1016/j.maturitas.2024.108185},
pmid = {39740526},
issn = {1873-4111},
abstract = {OBJECTIVE: Given that Parkinson's disease is a progressive disorder, with symptoms that worsen over time, our goal is to enhance the diagnosis of Parkinson's disease by utilizing machine learning techniques and microbiome analysis. The primary objective is to identify specific microbiome signatures that can reproducibly differentiate patients with Parkinson's disease from healthy controls.<br><br>METHODS: We used four Parkinson-related datasets from the NCBI repository, focusing on stool samples. Then, we applied a DADA2-based script for amplicon sequence processing and the Recursive Ensemble Feature Selection (REF) algorithm for biomarker discovery. The discovery dataset was PRJEB14674, while PRJNA742875, PRJEB27564, and PRJNA594156 served as testing datasets. The Extra Trees classifier was used to validate the selected features.<br><br>RESULTS: The Recursive Ensemble Feature Selection algorithm identified 84 features (Amplicon Sequence Variants) from the discovery dataset, achieving an accuracy of over 80%. The Extra Trees classifier demonstrated good diagnostic accuracy with an area under the receiver operating characteristic curve of 0.74. In the testing phase, the classifier achieved areas under the receiver operating characteristic curves of 0.64, 0.71, and 0.62 for the respective datasets, indicating sufficient to good diagnostic accuracy. The study identified several bacterial taxa associated with Parkinson's disease, such as Lactobacillus, Bifidobacterium, and Roseburia, which were increased in patients with the disease.<br><br>CONCLUSION: This study successfully identified microbiome signatures that can differentiate patients with Parkinson's disease from healthy controls across different datasets. These findings highlight the potential of integrating machine learning and microbiome analysis for the diagnosis of Parkinson's disease. However, further research is needed to validate these microbiome signatures and to explore their therapeutic implications in developing targeted treatments and diagnostics for Parkinson's disease.},
}
@article {pmid39740465,
year = {2024},
author = {BenIsrael, M and Obregon, D and Wanner, P and Fernandes, J and Burken, JG and Aravena, R and Parker, BL and Haack, EA and Tsao, DT and Dunfield, KE},
title = {Active phytoextraction of toluene shifts the microbiome and enhances degradation capacity in hybrid poplar.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123910},
doi = {10.1016/j.jenvman.2024.123910},
pmid = {39740465},
issn = {1095-8630},
abstract = {Hybrid poplars are widely recognized for their effectiveness in remediating subsurface aromatic hydrocarbon contaminants, including benzene, toluene, ethylbenzene, and xylene isomers (BTEX). While BTEX compounds are frequently found in the transpiration streams of poplars at contaminated sites, the microbial dynamics within these trees, particularly in response to hydrocarbon exposure, remain underexplored. This study utilized high-throughput amplicon sequencing to investigate the trunk microbiome in hybrid poplars at a field-scale toluene phytoremediation site. Across the plant growth season (spring to late summer), we observed a significant seasonal increase in bacterial diversity and richness, particularly in trees located in areas with the highest groundwater and in planta toluene concentrations. During late summer, the microbiomes of these trees were enriched with hydrocarbon-degrading taxa, including Acinetobacter, Pseudomonas, Burkholderia, Sandaracinobacter, and Allorhizobium-Rhizobium, and exhibited enhanced capacities for aerobic toluene degradation based on functional predictions. These findings reveal selective pressures exerted by hydrocarbons on endophytic microbial communities and underscore their role in mitigating volatile contaminant emissions. This study advances our understanding of microbial dynamics in phytoremediation systems and highlights the potential for leveraging endophytes to optimize contaminant degradation.},
}
@article {pmid39740461,
year = {2024},
author = {Rana, S and Pandey, H and Shridhar, V and Tiwary, P and Kukreti, S and Arunachalam, K and Singh, V},
title = {Structural and functional analysis of rhizospheric bacterial diversity in the Pranmati basin, Himalayan critical zone observatory.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123872},
doi = {10.1016/j.jenvman.2024.123872},
pmid = {39740461},
issn = {1095-8630},
abstract = {The study explores the structural and functional dynamics of rhizospheric bacterial diversity in the Pranmati basin, focusing on their ecological significance, diversity, and functional roles across dominant vegetation types; Rhododendron arboreum, Myrica esculenta, and Quercus leucotrichophora. The research provides critical insights into soil health and ecosystem functioning by analysing rhizospheric soil properties among the selected vegetations. The research findings reveal that Myrica esculenta exhibits the highest root colonization (95.8%) and moisture content (92.6%), while Quercus leucotrichophora shows the lowest (76.2% and 83.2%), respectively. The microbial community is predominantly composed of Proteobacteria, with 62-65% abundance across different vegetation types. Key genera such as Bacillus, Acinetobacter, and Paenibacillus are notably enriched, highlighting their significant role in phosphate solubilization and nutrient cycling. Venn diagram analysis identified 136 common bacterial species among vegetation types reflecting ecological significance in forest ecosystem. The functional metabolism, diversity indices, and core microbiome analysis underscore the distinct microbial profiles associated with different vegetation types, which are crucial for overall forest soil health. The importance of this research lies in its contribution to environmental management by providing a comprehensive understanding of how microbial communities interact with various vegetation types and influence soil health in the Pranmati basin. These insights are essential for developing targeted strategies to enhance soil fertility and manage forest ecosystems in terms of conservation and restoration efforts in sensitive ecological regions. This study is pioneer as it establishes a functional analysis of rhizospheric bacterial diversity in the Pranmati basin, offering a baseline data for future research on bacterial community structure and their functional role in Himalayan Critical Zone Observatory to the best of our knowledge.},
}
@article {pmid39740430,
year = {2024},
author = {Zhao, X and Chen, J and Li, H and Zhao, Y and Wang, W and Li, W and Wang, Y},
title = {Integration of volatilomics and microbiome diversity reveals key flavor-related metabolic pathways in semi-dried large yellow croaker (Pseudosciaena crocea).},
journal = {Food chemistry},
volume = {470},
number = {},
pages = {142518},
doi = {10.1016/j.foodchem.2024.142518},
pmid = {39740430},
issn = {1873-7072},
abstract = {A complex microbial community is critical for developing unique flavors in semi-dried large yellow croaker (Pseudosciaena crocea). Volatilomics analysis identified hexanal, heptanal, nonanal, phenylacetaldehyde, 1-octen-3-ol, and butanoic acid were identified as the key flavor compounds in the fish. Clostridium sensu stricto was the dominant genus, with a relative abundance of 79.78 % after 4 days of air-drying. Validation results showed a positive association between the accumulation of nonanal, phenylacetaldehyde, and butanoic acid and the presence of Clostridium sensu stricto. Significant correlations were also observed between the genera of Lactobacillus and Microbacterium and the key flavor compounds of hexanal and heptanal. Microorganisms contribute to the metabolism of these compounds, primarily through the metabolism of phenylalanine, linoleic acid, linolenic acid, arachidonic acid, and pyruvate. This flavor-regulating role of microorganisms presents them as potential targets for flavor enhancement in traditional aquatic products.},
}
@article {pmid39740428,
year = {2024},
author = {Yang, L and Xu, F and Zhao, S and Zeng, Y and Wu, Q and Zhang, L and Shi, S and Zhang, F and Li, J and An, Z and Li, H and Wu, H and Song, J and Wu, W},
title = {Airway microbiota dysbiosis and metabolic disorder in ozone and PM2.5 co-exposure induced lung inflammatory injury in mice.},
journal = {Ecotoxicology and environmental safety},
volume = {290},
number = {},
pages = {117626},
doi = {10.1016/j.ecoenv.2024.117626},
pmid = {39740428},
issn = {1090-2414},
abstract = {Co-exposure to ground-level ozone (O3) and fine particles (PM2.5, ≤ 2.5 µm in diameter) has become a primary scenario for air pollution exposure of urbanites in China. Recent studies have suggested a synergistic effect of PM2.5 and O3 on induction of lung inflammatory injury. However, the underlying mechanisms for respiratory toxicity induced by this co-exposure have not been adequately elucidated. In this study, a realistic exposure was based to set up the co-exposure condition of an animal model. Specifically, eighty male C57BL/6 mice (10 months old) were randomly divided into four groups: control, O3, PM2.5 and co-exposure (O3 + PM2.5). Mice in the co-exposure group breathed O3 and orally inhaled PM2.5 suspension. The scenario for O3 exposure was 0.6 ppm, 4 h/d, for 30 consecutive days while that for PM2.5 exposure was oral inhalation of PM2.5 suspension (5.6 mg/kg bw) once every other day and 4 h prior to O3 exposure. After last exposure, bronchoalveolar lavage fluids (BALF) were collected for inflammatory biomarker measurement, 16S rRNA sequencing and metabolite profiling. Lung tissues were processed for histological examination. The results demonstrated that co-exposure to O3 and PM2.5 exacerbated the pathological changes and inflammatory response induced by O3 or PM2.5. Further studies revealed that co-exposure to O3 and PM2.5 increased the abundance of Prevotella in the airways and caused more severe metabolic disorders compared to O3 or PM2.5 exposure. Spearman correlation analysis demonstrated correlations among airway microbiota dysbiosis, metabolic disorder, inflammation, and pathological alterations induced by co-exposure to O3 and PM2.5. In summary, co-exposure to O3 and PM2.5 worsens airway inflammatory injury, possibly through interrelated airway microbiota dysbiosis and metabolic disorder.},
}
@article {pmid39740381,
year = {2024},
author = {Abdullah, and Ahmad, N and Xiao, J and Tian, W and Khan, NU and Hussain, M and Ahsan, HM and Hamed, YS and Zhong, H and Guan, R},
title = {Gingerols: Preparation, encapsulation, and bioactivities focusing gut microbiome modulation and attenuation of disease symptoms.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {136},
number = {},
pages = {156352},
doi = {10.1016/j.phymed.2024.156352},
pmid = {39740381},
issn = {1618-095X},
abstract = {BACKGROUND: Gut dysbiosis, chronic diseases, and microbial recurrent infections concerns have driven the researchers to explore phytochemicals from medicinal and food homologous plants to modulate gut microbiota, mitigate diseases, and inhibit pathogens. Gingerols have attracted attention as therapeutic agents due to their diverse biological activities like gut microbiome regulation, gastro-protective, anti-inflammatory, anti-microbial, and anti-oxidative effects.<br><br>PURPOSE: This review aimed to summarize the gingerols health-promoting potential, specifically focusing on the regulation of gut microbiome, attenuation of disease symptoms, mechanisms of action, and signaling pathways involved.<br><br>METHOD: Research findings from experimental and clinical studies have been summarized regarding gingerols effects on the modulation of gut microbiome and its metabolites, and attenuation of disease symptoms.<br><br>RESULTS: Gingerols are phenolic compounds characterized by a common 3-methoxy-4-hydroxyphenyl moiety in their chemical structures, and further divided into different gingerol types, including gingerols (major), shogaols, paradols, gingerdiols, gingerdiones, and zingerones (minor). Advanced extraction techniques (e.g., ionic liquid-based-, enzyme-assisted-, microwave-assisted-, pressurized liquid-, ultrasound-assisted-, and supercritical fluid extractions) were reported as optimal alternatives to conventional methods for gingerols extraction. Research studies reported that gingerols positively modulated the composition of gut microbiome that helped to combat disease symptoms (e.g., obesity by decreasing weight gain- (Lactobacillus reuteri and Lachnospiraceae) and increasing weight loss associated-bacteria (Akkermansia, Muribaculaceae, and Alloprevotella). Gingerols intervention also ameliorated ulcerative colitis by increasing relative abundance of the beneficial bacteria (Akkermansia, Lachnospiraceae NK4A136, and Muribaculaceae_norank), and decreasing pathogenic microorganisms (Bacteroides, Parabacteroides, and Desulfovibrio). Emerging delivery systems (e.g., microcapsules, nanoparticles, nanostructured lipid carriers, nanoemulsions, and nanoliposomes) can enhance the bioavailability and therapeutic efficacy of gingerols by preserving their inherent properties and addressing challenges of stability, solubility, and absorption.<br><br>CONCLUSION: Gingerols are promising therapeutic agents to modulate gut microbiome (increase beneficial bacteria and inhibit pathogenic microbes), and attenuate chronic disease symptoms such as diabetes, colitis, obesity, oxidative stress, and cancer. Despite significant progress, challenges persist in transforming research findings into industrial applications, such as stability and solubility during processing and low bioavailability in the distal gut to impart desirable health benefits.},
}
@article {pmid39740378,
year = {2024},
author = {Chen, L and Xu, S and Wang, S and Chen, H and Han, Y},
title = {Xiaohuafuning tang intervenes liver-depression-and-spleen-deficiency syndrome chronic-atrophic-gastritis by reshaping amino acid metabolism through gut Microbiota.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {136},
number = {},
pages = {156346},
doi = {10.1016/j.phymed.2024.156346},
pmid = {39740378},
issn = {1618-095X},
abstract = {BACKGROUND: Xiaohua Funing Tang (XHFND) is a decoction formula of traditional Chinese medicine (TCM) and possesses the potential to manage chronic atrophic gastritis (CAG) with liver depression and spleen deficiency (LDSD), but the mechanisms were still unclear.<br><br>PURPOSE: Our aim is to reveal the overall synergistic mechanisms of XHFND against CAG with LDSD.<br><br>METHODS: Based on a CAG rat model with LDSD, this study combined metabolomics, gut microbiota, and network pharmacology techniques to demonstrate the XHFND mechanisms with multiple components and targets.<br><br>RESULTS: Through the integration analysis of gut microbiome and metabolome using metorigin, we found that XHFND regulates arginine metabolism levels in the urea cycle by regulating the gut ecological environment and the host. The XHFND mainly promotes aspartate 1 metabolism by regulating the abundance of odoribacter, bacteroides, phocaeicola, lachnospire, and intestinimonas, intervened in the imbalance of arginine metabolism in CAG rats with LDSD, suppresses the pathogenic Th17 cell differentiation, and inhibits the gastric mucosa damage in rats. Through Cytoscape analysis of network pharmacology and metabolomics integration, we found that XHFND might regulate host phospholipid metabolism through PTEN and PIK3CA to inhibit the PI3K-AKT-TSC axis and then inhibit mTORC1 to control arginine metabolism in the urea cycle and produce polyamines, thereby inhibiting the pathogenic Th17 cell differentiation and preventing rat gastric mucosa damage. Intervention in arginine metabolism in the urea cycle is the primary pathway in which XHFND exerts its therapeutic effects. XHFND may mainly control the pathogenic Th17 cell differentiation in the gastric mucosa of model rats through the pathway.<br><br>CONCLUSION: This study indicated that XHFND might intervene in treating CAG with LDSD from multiple levels and perspectives to suppress the pathogenic Th17 cell differentiation, which aligns with the characteristics of TCM treatment. This study presents experimental evidence for the clinical use of XHFND and promotes the development of drugs for the therapy of CAG with LDSD.},
}
@article {pmid39740376,
year = {2024},
author = {Xia, L and Li, C and Zhao, J and Sun, Q and Mao, X},
title = {Rebalancing immune homeostasis in combating disease: The impact of medicine food homology plants and gut microbiome.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {136},
number = {},
pages = {156150},
doi = {10.1016/j.phymed.2024.156150},
pmid = {39740376},
issn = {1618-095X},
abstract = {BACKGROUND: Gut microbiota plays an important role in multiple human physiological processes and an imbalance in it, including the species, abundance, and metabolites can lead to diseases. These enteric microorganisms modulate immune homeostasis by presenting a myriad of antigenic determinants and microbial metabolites. Medicinal and food homologous (MFH) plants, edible herbal materials for both medicine and food, are important parts of Traditional Chinese Medicine (TCM). MFH plants have drawn much attention due to their strong biological activity and low toxicity. However, the interplay of MFH and gut microbiota in rebalancing the immune homeostasis in combating diseases needs systematic illumination.<br><br>PURPOSE: The review discusses the interaction between MFH and gut microbiota, including the effect of MFH on the major group of gut microbiota and the metabolic effect of gut microbiota on MFH. Moreover, how gut microbiota influences the immune system in terms of innate and adaptive immunity is addressed. Finally, the immunoregulatory mechanisms of MFH in regulation of host pathophysiology via gut microbiota are summarized.<br><br>METHODS: Literature was searched, analyzed, and collected using databases, including PubMed, Web of Science, and Google Scholar using relevant keywords. The obtained articles were screened and summarized by the research content of MFH and gut microbiota in immune regulation.<br><br>RESULTS: The review demonstrates the interaction between MFH and gut microbiota in disease prevention and treatment. Not only do the intestinal microorganisms and intestinal mucosa constitute an important immune barrier of the human body, but also lymphoid tissue and diffused immune cells within the mucosa participate in the response of innate immunity and adaptive immunity. MFH modulates immune regulation by affecting intestinal flora, helps maintain the balance of the immune system and interfere with the occurrence and development of a broad category of diseases.<br><br>CONCLUSION: Being absorbed from the gastrointestinal tract, MFH can have profound effects on gut microbiota. In turn, the gut microbiota also actively participate in the bioconversion of complex constituents from MFH, which could further influence their physiological and pharmacological properties. The review deepens the understanding of the relationship among MFH, gut microbiota, immune system, and human diseases and further promotes the progression of additional relevant research.},
}
@article {pmid39739369,
year = {2025},
author = {Zhang, Z and Liang, Y and Mo, S and Zhao, M and Li, Y and Zhang, C and Shan, X and Liu, S and Liao, J and Luo, X and Zhu, J and Wang, C and Jiang, Q and Hou, C and Hong, W and Lai, N and Chen, Y and Xu, L and Lu, W and Wang, J and Wang, Z and Yang, K},
title = {Oral administration of pioglitazone inhibits pulmonary hypertension by regulating the gut microbiome and plasma metabolome in male rats.},
journal = {Physiological reports},
volume = {13},
number = {1},
pages = {e70174},
pmid = {39739369},
issn = {2051-817X},
support = {82170065//National Natural Science Foundation of China (NSFC)/ ; 82241012//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; *Pioglitazone/pharmacology/administration &amp; dosage ; Male ; *Gastrointestinal Microbiome/drug effects ; *Metabolome/drug effects ; Rats ; *Rats, Sprague-Dawley ; *Hypertension, Pulmonary/drug therapy/metabolism ; *Probiotics/administration &amp; dosage/pharmacology ; Administration, Oral ; Hypoxia/metabolism ; Indoles/pharmacology/administration &amp; dosage ; Pyrroles/pharmacology/administration &amp; dosage ; },
abstract = {The oral administrated thiazolidinediones (TZDs) have been widely reported to alleviate experimental pulmonary hypertension (PH). However, previous studies mainly focused on their beneficial effects on the cardiopulmonary vascular system but failed to determine their potential roles on gut microenvironment. This study aims to investigate the effects of pioglitazone, an oral TZD drug, on gut microbiome in classic PH rat models induced by hypoxia (HPH) or SU5416/hypoxia (SuHx-PH) and evaluate the therapeutic potential of supplementation of selective probiotics for experimental PH. Pioglitazone remarkably inhibited the PH pathogenesis in both models and reshaped the gut microbiome and plasma metabolome. Correlation analyses represented strong and unique association between the protective metabolites and bacteria genera (Roseburia, Lactobacillus, and Streptococcus) that were positively stimulated by pioglitazone. Supplementation of selective probiotics Roseburia intestinalis (R. intestinalis) partially attenuated SuHx-PH and rebuilt a novel gut microbiome and host metabolome. This study reports for the first time that oral administration of pioglitazone protects PH by regulating the gut microbiome and host metabolome, providing novel insights for the TZD drugs. The data also supports that modulation of gut microbiota by supplementation of selective probiotics could be a novel effective therapeutic strategy for the treatment of PH.},
}
@article {pmid39739202,
year = {2024},
author = {Bard, NW and Davies, TJ and Cronk, QCB},
title = {Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14056},
doi = {10.1111/1755-0998.14056},
pmid = {39739202},
issn = {1755-0998},
support = {RGPIN-2019-04041//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2020-04439//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Relatively little is known of the host associations and compatibility of fungal plant pathogens and endophytes. Publicly available plant genomic DNA can be mined to detect incidental fungal DNA, but taxonomic assignment can be challenging due to short lengths and variable discriminative power among different genomic regions and taxa. Here, we introduce a computationally lightweight and accessible Snakemake pipeline for rapid detection and classification (identification and assignment to taxonomic rank) of pathogenic and endophytic fungi (and other fungi associated with plants) that targets the internal transcribed spacer (ITS) region, a fungal barcode standard. We include methods for maximising query sequence length, which gives higher support for ITS1 and ITS2 taxonomic classifications by extending to other fragments of the ITS region and providing taxon-specific local cut-off and confidence scores. We demonstrate our pipeline with a case study using public genomic sequence data for six diverse plant species, including four species within Betula, an ecologically and economically important broadleaved forest tree genus, a shrub and a grass. Our pipeline classified fungi within minutes to a few hours per host individual, with 204 different fungal genera identified at high confidence (≥ 70%). Our pipeline detected and classified pathogenic and endophytic genera known to associate with Betula, and many others with no prior record of association. Our pip