@article {pmid39902230,
year = {2024},
author = {Ronan, V},
title = {An open window: the crucial role of the gut-brain axis in neurodevelopmental outcomes post-neurocritical illness.},
journal = {Frontiers in pediatrics},
volume = {12},
number = {},
pages = {1499330},
doi = {10.3389/fped.2024.1499330},
pmid = {39902230},
issn = {2296-2360},
abstract = {Among patients admitted to the pediatric intensive care unit, approximately 10% are discharged with a new functional morbidity. For those who were admitted with a neurocritical illness, the number can be as high as 60%. The most common diagnoses for a neurocritical illness admission include traumatic brain injury, status epilepticus, post-cardiac arrest, hypoxic ischemic encephalopathy, meningo/encephalitis, and stroke. The gut-brain axis is crucial to childhood development, particularly neurodevelopment. Alterations on either side of the bidirectional communication of the gut-brain axis have been shown to alter typical development and have been associated with autism spectrum disorder, anxiety, sleep disturbances, and learning disabilities, among others. For those patients who have experienced a direct neurologic insult, subsequent interventions may contribute to dysbiosis, which could compound injury to the brain. Increasing data suggests the existence of a critical window for both gut microbiome plasticity and neurodevelopment in which interventions could help or could harm and warrant further investigation.},
}

@article {pmid39902218,
year = {2025},
author = {Lucchese, A and Marcolina, M and Mancini, N and Ferrarese, R and Acconciaioco, S and Gherlone, E and Bonini, C and Manuelli, M and Polimeni, A},
title = {A comparison of the alterations of oral microbiome with fixed orthodontic therapy and clear aligners: a systematic review.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2372751},
doi = {10.1080/20002297.2024.2372751},
pmid = {39902218},
issn = {2000-2297},
abstract = {AIM: The oral microbiome plays a fundamental role in maintaining homeostasis of the oral cavity. In the last decade there has been an increasing use of clear aligners, which guarantee aesthetics and comfort for the patient. The aim of this work is to conduct a systematic review regarding the alterations in bacterial flora and oral health with aligner and fixed orthodontic therapy.

DESIGN: A systematic review was conducted following the PRISMA Statement. Using the search strategy "(clear aligners OR Invisalign) AND (fixed therapy OR fixed orthodont * therapy) NOT (thermoplastic retainers) AND (oral microbiome OR oral microbiota * OR oral microbiology * OR oral health)", in the main scientific databases. Two scales were applied to assess the quality of scientific evidence: ROBINS-I and RoB 2.

RESULTS: A total of 484 articles emerged of which 9 met our inclusion/exclusion criteria. Afterwards the application of the rating scales, 1 article was found to be at low risk of bias, 6 at moderate and 2 at serious risk of bias.

CONCLUSION: Both therapies cause an alteration of the oral microbiome, but the changes induced by the aligners seem to be compatible with a better oral health compared to fixed appliances.},
}

@article {pmid39902217,
year = {2025},
author = {Al-Maweri, SA and Al-Mashraqi, AA and Al-Qadhi, G and Al-Hebshi, N and Ba-Hattab, R},
title = {The association between the oral microbiome and hypertension: a systematic review.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2459919},
doi = {10.1080/20002297.2025.2459919},
pmid = {39902217},
issn = {2000-2297},
abstract = {BACKGROUND: This study systematically reviewed the available evidence regarding the potential association between oral microbiota and hypertension.

METHODS: A comprehensive search of online databases was conducted by two independent investigators for all relevant articles. All observational studies that assessed the association between oral microbiota and hypertension were included. Quality appraisal was conducted using the NOS tool.

RESULTS: A total of 17 studies comprising 6007 subjects were included. The studies varied with respect to sample type and microbial analysis method. All studies, except one, found significant differences in microbial composition between hypertensive and normotensive subjects. However, there were substantial inconsistencies regarding the specific differences identified. Still, a few taxa were repeatedly found enriched in hypertension including Aggregatibacter, Kingella, Lautropia, and Leptotrachia besides the red complex periodontal pathogens. When considering only studies that controlled for false discovery rates and confounders, Atopobium, Prevotella, and Veillonella were identified as consistently associated with hypertension.

CONCLUSION: There are significant differences in the oral microbiome between hypertensive and normotensive subjects. Despite the heterogeneity between the included studies, a subset of microbial taxa seems to be consistently enriched in hypertension. Further studies are highly recommended to explore this association.

REGISTRATION: PROSPERO database (ID: CRD42023495005).},
}

@article {pmid39902181,
year = {2024},
author = {Veerapandian, R and Paudyal, A and Schneider, SM and Lee, STM and Vediyappan, G},
title = {A mouse model of immunosuppression facilitates oral Candida albicans biofilms, bacterial dysbiosis and dissemination of infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1467896},
doi = {10.3389/fcimb.2024.1467896},
pmid = {39902181},
issn = {2235-2988},
mesh = {Animals ; *Biofilms/growth & development/drug effects ; *Disease Models, Animal ; *Candida albicans/physiology ; *Dysbiosis/microbiology ; Mice ; *Candidiasis, Oral/microbiology ; *Tongue/microbiology ; Enterococcus faecalis/physiology ; Mouth/microbiology ; Liver/microbiology ; Immunosuppression Therapy ; },
abstract = {Opportunistic pathogens are a major threat to people, especially those with impaired immune systems. Two of the most important microbes in this category are the fungus Candida albicans and Gram-positive bacteria of the genus Enterococcus, which share overlapping niches in the oral cavity, gastrointestinal and urogenital tracts. The clinical importance of oral C. albicans biofilm and its interaction with the host under immunosuppressive conditions remains largely understudied. Here, we used a mouse model of oropharyngeal candidiasis (OPC) with cortisone acetate injection on alternate days and a continuous supply of C. albicans in drinking water for three days, resulting in immunosuppression. Results showed abundant growth of resident oral bacteria and a strong C. albicans biofilm on the tongue consisting of hyphae which damaged papillae, the epidermal layer, and invaded tongue tissue with the accumulation of inflammatory cells as demonstrated by Grocott's methenamine silver and hematoxylin and eosin staining, respectively. The dispersed microbes from the oral biofilm colonized the gastrointestinal (GI) tract and damaged its integrity, disseminating microbes to other organs. Although no visible damage was observed in the kidney and liver, except increased lipid vacuoles in the liver cells, C. albicans was found in the liver homogenate. Intriguingly, we found co-occurrence of Enterococcus faecalis in the tongue, liver, and stool of immunosuppressed control and C. albicans infected organs. Targeted 16S rRNA and ITS2 amplicon sequencing of microbes from the fecal samples of mice confirmed the above results in the stool samples and revealed an inverse correlation of beneficial microbes in the dysbiosis condition. Our study shows that mucosal-oral infection of C. albicans under immunosuppressed conditions causes tissue damage and invasion in local and distant organs; the invasion may be aided by the overgrowth of the resident endogenous Enterobacteriaceae and other members, including the opportunistic pathogen Enterococcus faecalis.},
}

Animals
*Biofilms/growth & development/drug effects
*Disease Models, Animal
*Candida albicans/physiology
*Dysbiosis/microbiology
Mice
*Candidiasis, Oral/microbiology
*Tongue/microbiology
Enterococcus faecalis/physiology
Mouth/microbiology
Liver/microbiology
Immunosuppression Therapy

@article {pmid39901928,
year = {2025},
author = {Demirci, M and Çubuk, C and Dasdemir, F and Saribas, AS and Balcıoglu, EB and Ozbey, D and Yorulmaz, D and Olmez Hanci, T and Basa, S and Kocazeybek, BS},
title = {Comparative microbial metagenomic analysis of drinking water plants and wastewater treatment plants in Istanbul.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1488268},
doi = {10.3389/fmicb.2025.1488268},
pmid = {39901928},
issn = {1664-302X},
abstract = {INTRODUCTION: Wastewater treatment plants (WWTPs) and drinking-water treatment plants (DWTPs) are critical for public health due to the potential risks posed by microorganisms that may persist after treatment. The aim of this study was to detect the microbiome profiles of waters from both DWTPs and WWTPs under the Istanbul Water and Sewerage Administration (ISKI), identify the antimicrobial resistance profiles in all these facilities, and observe the differences in the microbiome between the inlet and outlet of different WWTPs.

METHODS: A total of 52 samples were examined, comprising 18 samples from DWTPs and 34 samples from WWTPs. All water samples underwent pre-isolation filtration. DNA isolation was conducted using filter material, followed by sequencing on a NovaSeq 6000 instrument. Kraken2 tools and R scripts were used for statistical analysis and data visualization.

RESULTS: The microbial metagenomic analysis identified 71 phyla, 113 classes, 217 orders, 480 families, and 1,282 genera across all samples. There were unclassified microbes (53.14% vs. 58.75%), Eukaryota (3.64% vs. 3.5%), Archaea (0.08% vs. 0.03%), bacteria (42% vs. 36.25%), and viruses (0.02% vs. 0.04%) in the raw water and ozonation unit outlet of DWTPs. The inlet and outlet of WWTPs showed unclassified microbes (52.68% vs. 59.62%), Eukaryota (0.6% vs. 1.72%), Archaea (0.26% vs. 0.15%), bacteria (46.43% vs. 38.43%), and viruses (0.05% vs. 0.04%). No statistically significant results were found in the analysis of raw waters collected from DWTPs and samples taken from the ozonation unit outlet-from the phylum level to the genus level (p > 0.05). The inlet and outlet points of WWTPs showed no statistically significant results from the phylum to species levels (p > 0.05). The most detected genera were Desulfobacter (4.82%) in preliminary WWTPs, Thauera (1.93%) in biological WWTPs, Pseudomonas (1.44%) in advanced biological WWTPs, Acidovorax (1.85%) in biological package WWTPs, and Pseudomonas (11.55%) in plant-based WWTPs. No antimicrobial resistance gene markers were detected in water samples from raw water inlets and ozonation unit outlets from DWTPs, membrane wastewater recovery plants, or ultraviolet (UV) recycling facilities. The ANT(3″), Erm, and Sul resistance gene markers were detected in all raw WWTPs samples.

DISCUSSION: There were no significant microbial risk differentiation between biological WWTPs and advanced biological WWTPs. The data could serve as preliminary information for future research. More extensive studies are needed, with multiple sample tracking in these facilities and their feeding basins.},
}

@article {pmid39901817,
year = {2025},
author = {Galvin, S and Honari, B and Anishchuk, S and Healy, CM and Moran, GP},
title = {Oral Leukoplakia Microbiome Predicts the Degree of Dysplasia and is Shaped by Smoking and Tooth Loss.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.15272},
pmid = {39901817},
issn = {1601-0825},
support = {/HRBI_/Health Research Board/Ireland ; },
abstract = {OBJECTIVE: This study aimed to determine if the oral potentially malignant disorder, oral leukoplakia (OLK), exhibited microbiome changes that predict the degree of dysplasia and the risk of malignant progression.

RESULTS: We examined the microbiome in 216 swabs of OLK from 177 patients. Compared to healthy controls (n = 120 swabs from 61 patients), who were less likely to smoke and had better oral health, OLK patients exhibited an increased abundance of Rothia mucilaginosa, Streptococcus parasanguinis and S. salivarius, resembling acetaldehyde generating communities described previously. Compared to the patients' healthy contralateral normal (CLN) mucosa (n = 202), which acts as a matched control for oral health parameters, OLK exhibited increased S. infantis, Leptotrichia spp., Bergeyella spp., Porphyromonas spp. and F. nucleatum. Machine learning with clinical and microbiome data could discriminate high-risk dysplasia (moderate to severe) from low-risk dysplasia (none or mild) (sensitivity 87.4%; specificity 76.5%). Follow-up swabs were recovered from 58 patients, eight of whom progressed to a higher grade of dysplasia or OSCC and these eight patients exhibited a higher abundance of Fusobacterium species at their initial presentation.

CONCLUSIONS: Our study suggests that the OLK microbiome has potential to be an aid to the prediction of dysplasia grade and the risk of malignant transformation.},
}

@article {pmid39901675,
year = {2025},
author = {Sultana, A and Hussain, MS and Maqbool, M and Agrawal, M and Bisht, AS and Khurrana, N and Singh, G and Kumar, R},
title = {The Gut Connection: A Narrative Review on the In-depth Analysis of Gut Microbiota and Metabolites in Depression.},
journal = {Current reviews in clinical and experimental pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0127724328332998250118182255},
pmid = {39901675},
issn = {2772-4336},
abstract = {Depression is a prevalent mood disorder with significant public health implications. Despite extensive research, its precise causes remain inadequately understood. Recently, interest has surged in the role of the gut microbiome and its metabolites in the pathophysiology of depression. This review aims to provide a comprehensive overview of the relationship between gut microbiota, its metabolites, and depression while exploring potential mechanisms influencing the efficacy of antidepressant medications. A narrative review methodology was employed, synthesizing recent studies utilizing a multi-omics approach. We examined alterations in gut microbiome composition and metabolite production in individuals diagnosed with depression, discussing the technical tools and methods commonly applied in this research area. The findings indicate that individuals with depression show significant alterations in gut microbiome composition, notably an imbalance in Firmicutes, Bacteroidetes, and Actinobacteria. Changes in metabolite production, including short-chain fatty acids, tryptophan, and bile acids, were also observed. Moreover, the review highlights that antidepressant medications may exert their therapeutic effects by modulating gut microbiota and its metabolites. This review emphasizes the intricate interplay between gut microbiota, its metabolites, and depression, revealing critical insights into the mechanisms underlying antidepressant efficacy. We recommend that future research focus on elucidating these interactions to develop innovative therapeutic strategies, potentially transforming the management of depression through microbiota-targeted approaches.},
}

@article {pmid39901379,
year = {2025},
author = {Zhou, LS and Yang, Y and Mou, L and Xia, X and Liu, M and Xu, LJ and Liu, R and Liu, JP and Zhang, HY and Ao, XJ and Liu, CJ and Xiao, Q and Liu, SX},
title = {Melatonin Ameliorates Age-Related Sarcopenia via the Gut-Muscle Axis Mediated by Serum Lipopolysaccharide and Metabolites.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {16},
number = {1},
pages = {e13722},
doi = {10.1002/jcsm.13722},
pmid = {39901379},
issn = {2190-6009},
support = {21JR7RA372//Natural Science Foundation Project of Gansu Province, China/ ; CSTB2022NSCQ-MSX1666//Natural Science Foundation Project of Chongqing, China/ ; },
mesh = {Animals ; *Melatonin/pharmacology/therapeutic use ; *Sarcopenia/metabolism ; Mice ; *Lipopolysaccharides ; Male ; *Muscle, Skeletal/drug effects/metabolism ; Gastrointestinal Microbiome/drug effects ; Aging ; Disease Models, Animal ; Apoptosis/drug effects ; },
abstract = {BACKGROUND: Sarcopenia affects the quality of life and increases adverse outcomes in the elderly. However, as a potential safe and effective remedy to many age-related disorders, little is known about the protective effect of melatonin against sarcopenia, especially the underlying mechanisms of pathophysiology related to the gut-muscle axis.

METHODS: The young (4 months) and old-aged (24 months) wild-type C57BL/6J male mice were included in this study, of which the old-aged mice in the experimental group were treated with 10 mg/kg/day of melatonin for 16 weeks. After that, muscle strength, muscle mass and the cross-sectional area (CSA) of the gastrocnemius muscle fibres were measured. Then, the putative pathways, based on the data obtained from 16S rDNA sequencing of the gut microbiota, RNA sequencing of gastrocnemius muscle and serum untargeted metabolomics, were screened out by the integrated multiomics analysis and validated using immunohistochemistry, ELISA and TUNEL staining. C2C12 myoblasts were treated with LPS. Flow cytometric analysis and western blotting were applied to detect cell apoptosis and protein expressions of Tnfrsf12a and caspase8, respectively. In addition, the mediation analysis was carried out to infer the causal role of the microbiome in contributing to the skeletal muscle through metabolites.

RESULTS: Melatonin treatment ameliorated age-related declines in muscle strength (p < 0.05), muscle mass (p < 0.01) and CSA of the gastrocnemius muscle fibres (p < 0.01), as well as changed the gut microbial composition (beta-diversity analysis; R = 0.513, p = 0.005). The integrated multiomics analysis implied two main mechanisms about the impact of melatonin-related modifications in the gut microbiota on sarcopenia. First, a lower serum lipopolysaccharide (LPS) level associated with the altered gut microbiota was observed in melatonin-treated mice (p < 0.001) and was most relevant to the transcription level of Tnfrsf12a in skeletal muscle (R = 0.926, p < 0.001). Further bioinformatics analyses and in vitro experiments showed that LPS could contribute to skeletal muscle apoptosis by regulating the Tnfrsf12a/caspase-8 signalling pathway. Second, melatonin significantly altered serum metabolites (variable importance on projection (VIP) > 1.5, p < 0.05). Mediation models showed that changes in the gut microbiome also influenced skeletal muscle through these metabolites (27 linkages; BH-adjusted p < 0.05).

CONCLUSIONS: Our study revealed functional insights and a putative causality for the role of the gut-muscle axis in the mechanism of melatonin ameliorating age-related sarcopenia, namely, inhibition of the LPS-induced Tnfrsf12a/caspase-8 signalling pathway or serum metabolites as intermediates in the gut-muscle axis.},
}

Animals
*Melatonin/pharmacology/therapeutic use
*Sarcopenia/metabolism
Mice
*Lipopolysaccharides
Male
*Muscle, Skeletal/drug effects/metabolism
Gastrointestinal Microbiome/drug effects
Aging
Disease Models, Animal
Apoptosis/drug effects

@article {pmid39901297,
year = {2025},
author = {Azouggagh, L and Ibáñez-Escriche, N and Martínez-Álvaro, M and Varona, L and Casellas, J and Negro, S and Casto-Rebollo, C},
title = {Characterization of microbiota signatures in Iberian pig strains using machine learning algorithms.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {13},
pmid = {39901297},
issn = {2524-4671},
support = {PID2020-114705RB-I00//Ministerio de Ciencia e Innovación/ ; PID2020-114705RB-I00//Ministerio de Ciencia e Innovación/ ; PID2020-114705RB-I00//Ministerio de Ciencia e Innovación/ ; PID2020-114705RB-I00//Ministerio de Ciencia e Innovación/ ; PID2020-114705RB-I00//Ministerio de Ciencia e Innovación/ ; PID2020-114705RB-I00//Ministerio de Ciencia e Innovación/ ; PID2020-114705RB-I00//Ministerio de Ciencia e Innovación/ ; },
abstract = {BACKGROUND: There is a growing interest in uncovering the factors that shape microbiome composition due to its association with complex phenotypic traits in livestock. Host genetic variation is increasingly recognized as a major factor influencing the microbiome. The Iberian pig breed, known for its high-quality meat products, includes various strains with recognized genetic and phenotypic variability. However, despite the microbiome's known impact on pigs' productive phenotypes such as meat quality traits, comparative analyses of gut microbial composition across Iberian pig strains are lacking. This study aims to explore the gut microbiota of two Iberian pig strains, Entrepelado (n = 74) and Retinto (n = 63), and their reciprocal crosses (n = 100), using machine learning (ML) models to identify key microbial taxa relevant for distinguishing their genetic backgrounds, which holds potential application in the pig industry. Nine ML algorithms, including tree-based, kernel-based, probabilistic, and linear algorithms, were used.

RESULTS: Beta diversity analysis on 16 S rRNA microbiome data revealed compositional divergence among genetic, age and batch groups. ML models exploring maternal, paternal and heterosis effects showed varying levels of classification performance, with the paternal effect scenario being the best, achieving a mean Area Under the ROC curve (AUROC) of 0.74 using the Catboost (CB) algorithm. However, the most genetically distant animals, the purebreds, were more easily discriminated using the ML models. The classification of the two Iberian strains reached the highest mean AUROC of 0.83 using Support Vector Machine (SVM) model. The most relevant genera in this classification performance were Acetitomaculum, Butyricicoccus and Limosilactobacillus. All of which exhibited a relevant differential abundance between purebred animals using a Bayesian linear model.

CONCLUSIONS: The study confirms variations in gut microbiota among Iberian pig strains and their crosses, influenced by genetic and non-genetic factors. ML models, particularly CB and RF, as well as SVM in certain scenarios, combined with a feature selection process, effectively classified genetic groups based on microbiome data and identified key microbial taxa. These taxa were linked to short-chain fatty acids production and lipid metabolism, suggesting microbial composition differences may contribute to variations in fat-related traits among Iberian genetic groups.},
}

@article {pmid39901227,
year = {2025},
author = {Maestro-Gaitán, I and Redondo-Nieto, M and González-Bodí, S and Rodríguez-Casillas, L and Matías, J and Bolaños, L and Reguera, M},
title = {Insights into quinoa endophytes: core bacterial communities reveal high stability to water stress and genotypic variation.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {16},
pmid = {39901227},
issn = {2524-6372},
support = {CONSOLIDACIÓN 2022 (CNS2022-135167)//Agencia Estatal de Investigación/ ; CEX2020-000999-S-20-4//Agencia Estatal de Investigación/ ; PID2019-105748RA-I00 AEI/10.13039/501100011033//Agencia Estatal de Investigación/ ; },
abstract = {BACKGROUND: Plant endophytes, comprising non-pathogenic bacteria, fungi, and archaea, inhabit various plant parts, including roots, stems, leaves, and seeds. These microorganisms play a crucial role in plant development by enhancing germination, growth, and stress resilience. Seed endophytes, in particular, represent the most adapted and conserved segment of plant microbiota, significantly influencing the initial stages of plant growth and microbial community establishment. This study investigates the impact of environmental and genotypic factors on the endophytic communities of Chenopodium quinoa Willd. (quinoa), a crop notable for its adaptability and nutritional value.

RESULTS: We aimed to characterize the core endophytic communities in quinoa seeds and roots from two distinct genotypes under well-watered (WW) and water-deficit (WD) conditions, utilizing various soil infusions as inoculants to explore potential changes in these endophytes. Our findings reveal distinct changes with quinoa seeds exhibiting a high degree of conservation in their endophytic microbiome, even between maternal and offspring seeds, with specific bacterial taxa showing only minor differences. Tissue specificity emerged as a key factor, with seeds maintaining a stable microbial community, while roots exhibited more pronounced shifts, highlighting the tissue-dependent patterns of microbial enrichment.

CONCLUSIONS: The results highlight the stability and conservation of endophytic communities in quinoa seeds, even under varying water conditions and across different genotypes, emphasizing the role of tissue specificity in shaping microbial associations. These findings suggest that quinoa-associated endophytes, particularly those conserved in seeds, may play a crucial role in enhancing drought resilience. Understanding the dynamics of plant-microbe interactions in quinoa is vital for developing stress-resilient crop varieties, supporting sustainable agricultural practices, and ensuring food security in the face of climate change and environmental challenges.},
}

@article {pmid39901058,
year = {2025},
author = {Richardson, M and Zhao, S and Lin, L and Sheth, RU and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH},
title = {SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.},
journal = {Nature microbiology},
volume = {10},
number = {2},
pages = {527-540},
pmid = {39901058},
issn = {2058-5276},
support = {MCB-2025515//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; 2R01AI132403, 1R01DK118044, 1R01EB031935, 1R21AI146817//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; N00014-18-1-2237//United States Department of Defense | United States Navy | ONR | Office of Naval Research Global (ONR Global)/ ; 1016691//Burroughs Wellcome Fund (BWF)/ ; HR0011-23-2-0001//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; W911NF-22-2-0210//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Feces/microbiology ; Inulin/metabolism ; RNA, Ribosomal, 16S/genetics ; Metagenome ; },
abstract = {The local arrangement of microbes can profoundly impact community assembly, function and stability. However, our understanding of the spatial organization of the human gut microbiome at the micron scale is limited. Here we describe a high-throughput and streamlined method called Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) to capture spatial co-localization in a complex microbial consortium. The method obtains microbial composition of micron-scale subcommunities through split-and-pool barcoding. SAMPL-seq analysis of the healthy human gut microbiome identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These co-localized microbes organize into spatially distinct groups or 'spatial hubs' dominated by Bacteroidaceae, Ruminococcaceae and Lachnospiraceae families. Using inulin as a dietary perturbation, we observed reversible spatial rearrangement of the gut microbiome where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock insights into microbiomes at the micron scale.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing/methods
Feces/microbiology
Inulin/metabolism
RNA, Ribosomal, 16S/genetics
Metagenome

@article {pmid39900806,
year = {2025},
author = {Stanton, C and Koc, F and Kelleher, S and Ross, P and Magnier, C and McMahon, CJ},
title = {Rebuttal to Gut Microbiome in Children with Congenital Heart Disease After Cardiopulmonary Bypass Surgery (GuMiBear Study).},
journal = {Pediatric cardiology},
volume = {},
number = {},
pages = {},
pmid = {39900806},
issn = {1432-1971},
}

@article {pmid39900569,
year = {2025},
author = {Priest, T and Oldenburg, E and Popa, O and Dede, B and Metfies, K and von Appen, WJ and Torres-Valdés, S and Bienhold, C and Fuchs, BM and Amann, R and Boetius, A and Wietz, M},
title = {Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1326},
pmid = {39900569},
issn = {2041-1723},
mesh = {Arctic Regions ; *Seasons ; *Microbiota/genetics ; *Seawater/microbiology ; *Oceans and Seas ; Metagenomics/methods ; Bacteria/genetics/classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; DNA Barcoding, Taxonomic ; Metagenome ; Phylogeny ; },
abstract = {Deciphering how microbial communities are shaped by environmental variability is fundamental for understanding the structure and function of ocean ecosystems. While seasonal environmental gradients have been shown to structure the taxonomic dynamics of microbiomes over time, little is known about their impact on functional dynamics and the coupling between taxonomy and function. Here, we demonstrate annually recurrent, seasonal structuring of taxonomic and functional dynamics in a pelagic Arctic Ocean microbiome by combining autonomous samplers and in situ sensors with long-read metagenomics and SSU ribosomal metabarcoding. Specifically, we identified five temporal microbiome modules whose succession within each annual cycle represents a transition across different ecological states. For instance, Cand. Nitrosopumilus, Syndiniales, and the machinery to oxidise ammonia and reduce nitrite are signatures of early polar night, while late summer is characterised by Amylibacter and sulfur compound metabolism. Leveraging metatranscriptomes from Tara Oceans, we also demonstrate the consistency in functional dynamics across the wider Arctic Ocean during similar temporal periods. Furthermore, the structuring of genetic diversity within functions over time indicates that environmental selection pressure acts heterogeneously on microbiomes across seasons. By integrating taxonomic, functional and environmental information, our study provides fundamental insights into how microbiomes are structured under pronounced seasonal changes in understudied, yet rapidly changing polar marine ecosystems.},
}

Arctic Regions
*Seasons
*Microbiota/genetics
*Seawater/microbiology
*Oceans and Seas
Metagenomics/methods
Bacteria/genetics/classification/metabolism
RNA, Ribosomal, 16S/genetics
Ecosystem
DNA Barcoding, Taxonomic
Metagenome
Phylogeny

@article {pmid39900290,
year = {2025},
author = {Ward, CP and Perelman, D and Durand, LR and Robinson, JL and Cunanan, KM and Sudakaran, S and Sabetan, R and Madrigal-Moeller, MJ and Dant, C and Sonnenburg, ED and Sonnenburg, JL and Gardner, CD},
title = {Effects of fermented and fiber-rich foods on maternal & offspring microbiome study (FeFiFo-MOMS) - Study design and methods.},
journal = {Contemporary clinical trials},
volume = {},
number = {},
pages = {107834},
doi = {10.1016/j.cct.2025.107834},
pmid = {39900290},
issn = {1559-2030},
abstract = {BACKGROUND: Recent research underscores the crucial role of the gut microbiota in human health, particularly during states of altered homeostasis, including pregnancy. Additionally, it is not well understood how dietary changes during pregnancy affect the development of microbiomes of both mother and child.

METHODS: Here, we describe the study design and methods for our randomized controlled trial, the fermented and fiber-rich foods on maternal and offspring microbiome study (FeFiFo-MOMS). We enrolled 135 women during early pregnancy, randomizing them to one of four diet arms: increased fiber, increased fermented foods, increase in both, and no dietary intervention as a comparator arm. Samples were collected across pregnancy continuing to 18 months post-birth for clinical, microbiome, and immune marker analysis.

RESULTS: Our trial design intended to investigate the effects of dietary interventions-specifically, increased intake of high-fiber and fermented foods-on maternal gut microbiota diversity and its subsequent transmission to infants.

CONCLUSION: The FeFiFo-MOMS trial was designed to provide valuable insights into the modifiable dietary factors that could influence maternal and infant health through microbiota-mediated mechanisms and examine the broader implications of diet on pregnant mothers' and infants' health and disease.

CLINICALTRIALS: govID:NCT05123612.},
}

@article {pmid39900146,
year = {2025},
author = {Antoine, D and Tao, J and Singh, S and Singh, PK and Marin, BG and Roy, S},
title = {Neonatal exposure to morphine results in prolonged pain hypersensitivity during adolescence, driven by gut microbial dysbiosis and gut-brain axis-mediated inflammation.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.01.021},
pmid = {39900146},
issn = {1090-2139},
abstract = {Opioids, such as morphine, are used in the Neonatal Intensive Care Unit (NICU) for pain relief in neonates. However, the available evidence concerning the benefits and harms of opioid therapy in neonates remains limited. While previous studies have reported that neonatal morphine exposure (NME) results in long-term heightened pain sensitivity, the underlying mechanisms are not well understood. This study proposes that dysbiosis of the gut microbiome contributes to pain hypersensitivity following NME. Using an adolescent female murine model, pain sensitivity was evaluated using tail flick and hot plate assays for thermal pain and the Von Frey assay for mechanical pain. Gut microbiome composition was assessed using 16 s rRNA sequencing, while transcriptomic changes in midbrain samples were investigated using bulk RNA-sequencing. NME induced prolonged hypersensitivity to thermal and mechanical pain in adolescence, accompanied by persistent gut microbial dysbiosis and sustained systemic inflammation, characterized by elevated circulating cytokine levels (e.g., IL-1α, IL-12p70, IFN-γ, IL-10). Transplantation of the microbiome from NME adolescents recapitulated pain hypersensitivity in naïve adolescent mice, while neonatal probiotic intervention with Bifidobacterium infantis (B. infantis) reversed the hypersensitivity by preventing gut dysbiosis and associated systemic inflammation. Furthermore, transcriptomic analysis of the midbrain tissues revealed that NME upregulated several genes and key signaling pathways, including those related to immune activation and excitatory signaling, which were notably mitigated by neonatal B. infantis administration. Together, these findings highlight the critical role of the gut-brain axis in modulating pain sensitivity and suggest that targeting the gut microbiome offers a promising therapeutic strategy for managing neurobiological disorders following early opioid exposure.},
}

@article {pmid39900089,
year = {2025},
author = {Fretheim, H and Barua, I and Bakland, G and Dhainaut, A and Halse, AK and Carstens, MN and Didriksen, H and Midtvedt, Ø and Lundin, KEA and Aabakken, L and Sarna, VK and Zaré, HK and Khanna, D and Distler, O and Midtvedt, T and Bækkevold, ES and Olsen, IC and Domanska, D and Pesonen, ME and Molberg, Ø and Hoffmann-Vold, AM},
title = {Faecal microbiota transplantation in patients with systemic sclerosis and lower gastrointestinal tract symptoms in Norway (ReSScue): a phase 2, randomised, double-blind, placebo-controlled trial.},
journal = {The Lancet. Rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2665-9913(24)00334-5},
pmid = {39900089},
issn = {2665-9913},
abstract = {BACKGROUND: Gastrointestinal tract involvement is highly prevalent in systemic sclerosis, with few treatment options. We assessed the efficacy and safety of faecal microbiota transplantation using standardised anaerobic cultivated human intestinal microbiome (ACHIM) as a novel treatment option for patients with systemic sclerosis and symptomatic lower gastrointestinal tract involvement.

METHODS: In this phase 2, randomised, double-blind, placebo-controlled trial done at four university hospitals in Norway, we enrolled adults aged 18-85 years with systemic sclerosis and moderate-to-severe lower gastrointestinal tract symptoms (bloating or diarrhoea). Participants were randomly assigned 1:1 to intestinal infusions of placebo or ACHIM at weeks 0 and 2, stratified by worst symptom (bloating or diarrhoea). The primary endpoint was change in worst lower gastrointestinal tract symptom (bloating or diarrhoea) from week 0 to week 12, measured using the University of California Los Angeles Scleroderma Clinical Trial Consortium Gastrointestinal Tract 2.0 scoring system in the intention-to-treat population. Safety was assessed at weeks 0, 2, 4, 6, and 12 in all participants who received at least one infusion. A person with lived experience of systemic sclerosis was involved in the study planning and conduct. This trial was registered at ClinicalTrials.gov, NCT04300426.

FINDINGS: Between Sept 24, 2020, and Jan 14, 2022, 67 participants were enrolled and randomly allocated to placebo (n=34) or ACHIM (n=33). Mean age was 58·91 years (SD 11·59). 62 (93%) of 67 participants were women, five (7%) were men, and 50 (75%) were anti-centromere antibody positive. Change in worst lower gastrointestinal tract symptom from week 0 to week 12 did not differ between participants who received ACHIM (-0·13, 95% CI -0·37 to 0·11) and participants who received placebo (-0·33, -0·57 to -0·09; average marginal effect 0·20, 95% CI -0·12 to 0·52; p=0·22). Adverse events, mostly mild and short-lived gastrointestinal tract symptoms, were reported by 16 (48%) of 33 participants in the ACHIM group and 19 (56%) of 34 in the placebo group. During gastroscopy, one participant had a duodenal perforation.

INTERPRETATION: Faecal microbiota transplantation with ACHIM was well tolerated in participants with systemic sclerosis but did not result in an improvement in lower gastrointestinal tract symptoms.

FUNDING: KLINBEFORSK.

TRANSLATION: For the Norwegian translation of the abstract see Supplementary Materials section.},
}

@article {pmid39900010,
year = {2025},
author = {Faust, KB and Lupatsii, M and Römer, F and Graspeuntner, S and Waschina, S and Zimmermann, S and Humberg, A and Fortmann, MI and Hanke, K and Böckenholt, K and Dirks, J and Silwedel, C and Rupp, J and Herting, E and Göpel, W and Härtel, C},
title = {Use of Macrogol to accelerate feeding advancement in extremely preterm infants.},
journal = {Neonatology},
volume = {},
number = {},
pages = {1-19},
doi = {10.1159/000543050},
pmid = {39900010},
issn = {1661-7819},
abstract = {Introduction Delayed enteral nutrition is associated with a higher risk for adverse outcomes in extremely preterm infants. Limited evidence exists on therapeutic options to support meconium evacuation and increase gastrointestinal motility. The aim of this study was to determine the effect of macrogol on feeding tolerance and microbiome establishment in preterm infants < 27 weeks of gestation. Methods We investigated the impact of early macrogol administration in two observational cohort studies: the multi-center German-Neonatal-Network (GNN) study comparing extremely preterm infants born in Neonatal intensive care units (NICUs) using macrogol in the first week of life in >30% of their infants as compared to the remaining units, and the single center Immunoregulation-of-the-Newborn (IRoN) study including gut microbiome assessment of infants born before and after implementation of macrogol use in this NICU. Results In the GNN study cohort including 4290 infants, advancement to full enteral feedings was significantly faster in macrogol-using NICUs compared to the remaining NICUs (median/SD: 14/16.5 vs. 16/16.7days, p=0.001). Risk for short-term outcomes such as sepsis or abdominal complications was not elevated in units with regular use of macrogol. In the IRoN cohort (n=68), macrogol treated infants had a shorter time to reach full enteral feeding (median/SD: Macrogol 12/4.8, Control 16/6.6days, p=0.004). Higher Bifidobacterium longum abundance in the gut microbiome correlated with acceleration to full enteral nutrition. Conclusion Our observational data suggests that early off-label use of macrogol may support feeding advancement in highly vulnerable babies. These data provide a basis for a randomized controlled trial.},
}

@article {pmid39899987,
year = {2024},
author = {Tluway, F and Agongo, G and Baloyi, V and Boua, PR and Kisiangani, I and Lingani, M and Mashaba, RG and Mohamed, SF and Nonterah, EA and Ntimana, CB and Rouamba, T and Mathema, T and Madala, S and Maghini, DG and Choudhury, A and Crowther, NJ and Hazelhurst, S and Sengupta, D and Ansah, P and Choma, SSR and Debpuur, C and Gómez-Olivé, FX and Kahn, K and Micklesfield, LK and Norris, SA and Oduro, AR and Sorgho, H and Tindana, P and Tinto, H and Tollman, S and Wade, A and Ramsay, M and , },
title = {Cohort Profile: Africa Wits-INDEPTH partnership for Genomic studies (AWI-Gen) in four sub-Saharan African countries.},
journal = {International journal of epidemiology},
volume = {54},
number = {1},
pages = {},
doi = {10.1093/ije/dyae173},
pmid = {39899987},
issn = {1464-3685},
support = {/HG/NHGRI NIH HHS/United States ; },
}

@article {pmid39899882,
year = {2025},
author = {Mansoori Moghadam, Z and Zhao, B and Raynaud, C and Strohmeier, V and Neuber, J and Lösslein, AK and Qureshi, S and Gres, V and Ziegelbauer, T and Baasch, S and Schell, C and Warnatz, K and Inohara, N and Nunez, G and Clavel, T and Rosshart, SP and Kolter, J and Henneke, P},
title = {Reactive oxygen species regulate early development of the intestinal macrophage-microbiome interface.},
journal = {Blood},
volume = {},
number = {},
pages = {},
doi = {10.1182/blood.2024025240},
pmid = {39899882},
issn = {1528-0020},
abstract = {Controlled development of cellular intestinal immunity in the face of dynamic microbiota emergence constitutes a major challenge in very early life, and a bottleneck for sustained growth and well-being. Early-onset inflammatory bowel disease (IBD) represents an extreme disturbance of intestinal immunity. It is a hallmark, and often the first manifestation of chronic granulomatous disease (CGD), caused by inborn defects in the NADPH oxidase NOX2 and thus the failure to produce reactive oxygen species (ROS) in phagocytes. However, in contrast to the known role of ROS in antimicrobial defense, the mechanisms underlying intestinal immunopathology in CGD remain enigmatic. This is partly due to the incomplete recapitulation of the CGD-IBD phenotype in established mouse models. We found that mice deficient in the NOX2 subunits p47phox or gp91phox showed similar baseline disturbances in lamina-propria macrophage differentiation, but they responded differently to chemically-induced colitis. Although p47phox and gp91phox-deficient mice differed markedly in microbiota composition, cross-fostering failed to equalize discrepant IBD phenotypes and microbiota, pointing at extremely early and functionally important microbiota fixation under specific pathogen-free housing conditions. In contrast, neonatal acquisition of a complex wild-mouse-microbiota triggered spontaneous IBD, granuloma formation and secondary sepsis with intestinal pathogens in both NOX2-deficient mouse lines, which was in part dependent on NOX2 in intestinal macrophages. Thus, in experimental CGD, the aberrant development of tissue immunity and the microbiota are closely intertwined immediately after birth.},
}

@article {pmid39899646,
year = {2025},
author = {de Oliveira, DA and Oliveira, R and Braga, BV and Straker, LC and Rodrigues, LS and Bueno, LL and Fujiwara, RT and Lopes-Torres, EJ},
title = {Experimental trichuriasis: Changes in the immune response and bacterial translocation during acute phase development illustrated with 3D model animation.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {2},
pages = {e0012841},
doi = {10.1371/journal.pntd.0012841},
pmid = {39899646},
issn = {1935-2735},
abstract = {Trichuriasis, a well-known type of soil-transmitted helminthiasis, is a neglected gastrointestinal nematode disease predominantly affecting children in tropical regions and is caused by Trichuris trichiura. The potential zoonotic transmission of this disease is indicated by its presence in nonhuman primates. Chronic infection leads to mucosal damage, bacterial translocation, and intense inflammatory infiltration; however, the progression of these processes remains poorly understood. This study tracks the acute phase of experimental trichuriasis, providing detailed insights into nematode tissue migration stages, inflammatory infiltration, cytokine production, and 2D/3D imaging of the bacterial translocation process. We showed a mixed immune response (Th1, Th2, and Th17) initiated by larval-induced lesions in the intestine tissue and modulated by L4 larvae and adult worms in the cecum, with systemic changes observed in the mesenteric lymph nodes, peritoneal macrophages, and spleen. Despite the disruption of the intestinal mucosa within the first 10 days post-infection (d.p.i.), bacterial invasion becomes evident only after the development of the nematode into the L3 larval stage (17 d.p.i.), intensifying with lesions caused by the L4 larvae (22 d.p.i.) and adult worms (35 d.p.i.). Our multidimensional approach, which incorporates microscopy tools, micro-CT, physiological evaluations, tissue/organ assessments, and immunological parameters, demonstrates the ability of larvae to breach the intestinal mucosa, further indicating the timing of extensive bacterial infiltration. Additionally, a 3D animation illustrates how adult worm attachment mechanisms may facilitate bacterial translocation. This study provides significant insights into the immunological and pathological mechanisms of trichuriasis progression, highlighting the complex interplay among host immune responses, the gut microbiome, and parasite survival strategies, all of which are crucial aspects for future therapeutic development.},
}

@article {pmid39899616,
year = {2025},
author = {Oyono, MG and Kenmoe, S and Ebogo Belobo, JT and Mbah Ntepe, LJ and Kameni, M and Kamguia, LM and Mpotje, T and Nono, JK},
title = {Diagnostic, prognostic, and therapeutic potentials of gut microbiome profiling in human schistosomiasis: A comprehensive systematic review.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {2},
pages = {e0012844},
doi = {10.1371/journal.pntd.0012844},
pmid = {39899616},
issn = {1935-2735},
abstract = {BACKGROUND: Several studies have highlighted alteration in the gut microbiome associated with the onset and progression of diseases. Recognizing the potential of gut microbiota as biomarkers, this systematic review seeks to synthesize current data on the intricate relationship between the host gut microbiome profiles and their usefulness for the development of diagnostic, prognostic and therapeutic approaches to control human schistosomiasis.

METHODS: A systematic literature review was carried out by searching for relevant studies published until date, that is May 2024, using Medline, Embase, Global Health, Web of Science, and Global Index Medicus databases. The keywords used to select articles were "Gut microbiome", "Gut Microbiota", "Schistosomiasis", "Bilharziasis ", and "Human". Extracted data were analysed qualitatively from the selected articles.

RESULTS: Of the 885 articles retrieved and screened, only 13 (1.47%) met the inclusion criteria and were included in this review. Of the included studies, 6 (46.2%) explored alterations of gut microbiome in schistosome-infected patients, 4 (30.7%) in patients with liver pathologies, and 3 (23.1%) in patients treated with praziquantel. Bacteria from the genera Bacteroides, Faecalibacterium, Blautia and Megasphaera were associated with S. japonicum and S. haematobium infection in school-aged children, whereas infection with S. mansoni rather associated with Klebsiella and Enterobacter. The gut microbiota signature in patient with schistosomiasis-induced liver pathology was reported only for S. japonicum, and the genus Prevotella appeared as a non-invasive biomarker of S. japonicum-associated liver fibrosis. For S. mansoni-infected school-aged children, it further appeared that the treatment outcome following praziquantel administration associated with the abundance in the gut microbiome of bacteria from the classes Fusobacteriales, Rickettsiales and Neisseriales.

CONCLUSION: The host gut microbiome appears to be a valuable, non-invasive, but still poorly utilized, source of host biomarkers potentially informative for better diagnosing, prognosing and treating schistosomiasis. Further studies are therefore needed to comprehensively define such gut microbial biomarkers of human schistosomiasis and catalyse the informed development of gut microbiome-based tools of schistosomiasis control.},
}

@article {pmid39898934,
year = {2025},
author = {Chen, J and Guo, S and Shi, S},
title = {Effects of water acidifiers on the growth performance, intestinal function and gut microflora in broilers.},
journal = {British poultry science},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/00071668.2025.2454958},
pmid = {39898934},
issn = {1466-1799},
abstract = {1. This study evaluated the effect of acidified drinking water on the gastrointestinal function and intestinal health of broilers.2. A total of 630 one-day-old male broilers (Arbor Acre) were randomly assigned to one of three treatment groups: drinking water treatment (CON), drinking water + 0.5 ml Selko pH®/L (Selko pH), or + 0.85 ml Forticoat®/L (Forticoat) treated groups. Performance data, gut and digesta samples were collected from the broilers at the age of 21 and 42 d.3. The results showed that acidifying drinking water had no significant effect on body weight or average daily gain (ADG). However, addition of Forticoat significantly increased (p < 0.05) feed conversion ratio (FCR) throughout the experimental period and significantly increased (p < 0.05) pepsin activity on d 21. The Selko pH supplemented drinking water significantly increased (p < 0.05) the relative length of the duodenum and jejunum on d 21. The relative length of the jejunum and caecum on d 42 compared to birds receiving CON. The addition of the Forticoat to drinking water significantly increased (p < 0.05) the relative length of the jejunum and caecum on d 42 than for samples from birds in the CON group. In the caecal chyme, abundance of Blautia, Bifidobasterium, Faecalibacterium, Limosilactobacillus and Akkermania spp. on d 21 were significantly higher (p < 0.05) in the caecum of birds receiving Selko pH than those in CON group and the number of Escherichia Shigella in Selko pH and Forticoat group were significantly lower (p < 0.05).4. Overall, adding Seiko pH and Forticoat to drinking water improved pepsin activity, reduced the number of caecal pathogens, increased the number of beneficial bacteria and improved intestinal health in broilers.},
}

@article {pmid39898899,
year = {2025},
author = {Yu, J and Wang, Y and Wei, W and Wang, X},
title = {A review on lipid inclusion in preterm formula: Characteristics, nutritional support, challenges, and future perspectives.},
journal = {Comprehensive reviews in food science and food safety},
volume = {24},
number = {2},
pages = {e70099},
doi = {10.1111/1541-4337.70099},
pmid = {39898899},
issn = {1541-4337},
support = {2021YFD2100700//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Infant Formula/chemistry ; *Infant, Premature/growth & development ; Infant, Newborn ; *Lipids/chemistry ; *Milk, Human/chemistry ; Infant Nutritional Physiological Phenomena ; Nutritional Support/methods ; },
abstract = {The lack of nutrient accumulation during the last trimester and the physiological immaturity at birth make nutrition for preterm infants a significant challenge. Lipids are essential for preterm infant growth, neurodevelopment, immune function, and intestinal health. However, the inclusion of novel lipids in preterm formulas has rarely been discussed. This study discusses specific lipid recommendations for preterm infants according to authoritative legislation based on their physiological characteristics. The gaps in lipid composition, such as fatty acids, triacylglycerols, and complex lipids, between preterm formulas and human milk have been summarized. The focus of this study is mainly on the vital roles of lipids in nutritional support, including long-chain polyunsaturated fatty acids, structural lipids, milk fat global membrane ingredients, and other minor components. These lipids have potential applications in preterm formulas for improving lipid absorption, regulating lipid metabolism, and protecting against intestinal inflammation. The lipidome and microbiome can be used to provide adequately powered evidence of the effects of lipids. This study proposes nutritional strategies for preterm infants and suggests approaches to enhance their lipid quality in preterm formula.},
}

Humans
*Infant Formula/chemistry
*Infant, Premature/growth & development
Infant, Newborn
*Lipids/chemistry
*Milk, Human/chemistry
Infant Nutritional Physiological Phenomena
Nutritional Support/methods

@article {pmid39898649,
year = {2025},
author = {Taylor, BC and Weldon, KC and Ellis, RJ and Franklin, D and Groth, T and Gentry, EC and Tripathi, A and McDonald, D and Humphrey, G and Bryant, M and Toronczak, J and Schwartz, T and Oliveira, MF and Heaton, R and Grant, I and Gianella, S and Letendre, S and Swafford, A and Dorrestein, PC and Knight, R},
title = {Correction for Taylor et al., "Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome".},
journal = {mSystems},
volume = {},
number = {},
pages = {e0130524},
doi = {10.1128/msystems.01305-24},
pmid = {39898649},
issn = {2379-5077},
}

@article {pmid39898646,
year = {2025},
author = {Zhao, Y and Ferri, JT and White, JR and Schollenberger, MD and Peloza, K and Sears, CL and Lipson, EJ and Shaikh, FY},
title = {Gut microbiome features associate with immune checkpoint inhibitor response in individuals with non-melanoma skin cancers: an exploratory study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0255924},
doi = {10.1128/spectrum.02559-24},
pmid = {39898646},
issn = {2165-0497},
abstract = {Immune checkpoint inhibitor (ICI) therapy has yielded revolutionary outcomes among some individuals with skin cancer, but a large percentage of individuals do not benefit from these treatments. The gut microbiota is hypothesized to impact ICI therapy outcomes. However, data on ICI therapy, gut microbiota, and non-melanoma skin cancers are limited. To examine the association of gut microbiota structure and function with non-melanoma skin cancer ICI outcomes, we performed 16S rRNA V1-V2 gene amplicon sequencing of 68 fecal samples collected longitudinally from individuals with basal cell carcinoma (n = 5), Merkel cell carcinoma (n = 5), or cutaneous squamous cell carcinoma (CSCC, n = 11), followed by tumor-dependent differential analyses of bacterial composition and fecal sample analysis by untargeted metabolomics. Across all tumor types, we identified 10 differential bacterial genera between responders (R) or non-responders (NR) to ICI therapy. Among individuals with CSCC, we identified 10 genera and 20 species that differentiated between R and NR and yielded 8 pathways enriched in NR and 12 pathways enriched in R by predicted functional pathway analyses. Untargeted fecal metabolomics to examine putative gut microbiota metabolites associated with CSCC ICI R/NR identified nine KEGG pathways associated with ICI efficacy. In summary, this exploratory study suggests gut microbiota features that are associated with ICI efficacy in individuals with non-melanoma skin cancers and highlights the need for larger studies to validate the results.IMPORTANCEPrior studies examining associations between ICI efficacy and the gut microbiome have focused primarily on individuals with melanoma, for whom ICI therapy was first approved. Meanwhile, data regarding microbiome features associated with ICI responses in individuals with non-melanoma skin cancers (NMSCs) have remained limited. This initial fecal microbiota examination of individuals with NMSCs suggests that larger-scale studies to extend and validate our findings may yield predictive or prognostic biomarkers for individuals with NMSC receiving ICI with potential to provide insight to complementary, effective therapeutic interventions through microbiota modification.},
}

@article {pmid39898356,
year = {2025},
author = {Duan, C and Sheng, J and Ma, X},
title = {Innovative approaches in colorectal cancer screening: advances in detection methods and the role of artificial intelligence.},
journal = {Therapeutic advances in gastroenterology},
volume = {18},
number = {},
pages = {17562848251314829},
pmid = {39898356},
issn = {1756-283X},
abstract = {Colorectal cancer (CRC) is the third most prevalent cancer globally and poses a significant health threat, making early detection crucial. This review paper explored emerging detection methods for early screening of CRC, including gut microbiota, metabolites, genetic markers, and artificial intelligence (AI)-based technologies. Current screening methods have their respective advantages and limitations, particularly in detecting precursors. First, the importance of the gut microbiome in CRC progression is discussed, highlighting how specific microbial alterations can serve as biomarkers for early detection, potentially enhancing diagnostic accuracy when combined with traditional screening methods. Next, research on metabolic reprogramming illustrates the relationship between metabolic changes and CRC, with studies developing metabolite-based detection models that show good sensitivity for early diagnosis. In terms of genetic markers, methylated DNA markers like SEPTIN9 have demonstrated high sensitivity, although further validation across diverse populations is necessary. Lastly, AI technology has shown immense potential in improving adenoma detection rates, significantly enhancing the quality of colonoscopic examinations through image recognition techniques. This review aims to provide a comprehensive perspective on new strategies for CRC screening, emphasizing the potential of noninvasive detection technologies and the prospects of AI and genomics in clinical applications. Despite several challenges, this review advocates for future large-scale prospective studies to validate the effectiveness and cost-effectiveness of these new screening methods while promoting the implementation of screening protocols tailored to individual characteristics.},
}

@article {pmid39898328,
year = {2025},
author = {Thomsen, AR and Monroy Ordonez, EB and Henke, M and Luka, B and Sahlmann, J and Schäfer, H and Verma, V and Schlueter, N and Grosu, AL and Sprave, T},
title = {Evaluating the radiosensitivity of the oral microbiome to predict radiation-induced mucositis in head and neck cancer patients: A prospective trial.},
journal = {Clinical and translational radiation oncology},
volume = {51},
number = {},
pages = {100915},
pmid = {39898328},
issn = {2405-6308},
abstract = {BACKGROUND: Predicting the occurrence and/or severity of oral mucositis (OM) before commencing radiotherapy (RT) remains very difficult. The aim of this prospective trial was to investigate whether the ex-vivo radiation sensitivity of oral keratinocytes from head and neck (H&N) cancer patients correlates with severe OM.

METHODS: Oral microbiopsies of healthy gingival mucosa were collected from 63H&N cancer patients undergoing (chemo)RT, of which 58 samples were useable. Keratinocytes from these microbiopsies underwent ex-vivo proliferation, irradiation, and subsequently the cell spreading assay. Tubes with the cell suspension were placed within the irradiation chamber of a [137]Cs Gammacell 40 Exactor (Best Theratronics, Canada) and exposed to 0, 2, 4, 6, or 8 Gy at a dose rate of 0.63 Gy min[-1]. Cell suspension was then immediately pipetted into custom-made polydimethylsiloxane (PDMS) rings.The effect of demographic and clinical parameters on the cell spreading assay were also analyzed. Systematic clinical recording of OM was conducted twice a week by a specially trained examiner.

RESULTS: Most patients had node-positive disease and cancer of the oropharynx or oral cavity. The vast majority of patients received adjuvant RT and concurrent chemotherapy. Overall, 34 (58.6 %) participants developed grade 3 OM after a median dose of 32 Gy. No patient experienced a grade ≥ 4 event. There was a correlation between the cell spreading assay area and grade 3 OM (p < 0.05), equivalent to approximately 0.5 Gy dose. Demographic and clinical parameters had no significant impact on the cell spreading assay (p > 0.05 for all).

CONCLUSIONS: It is necessary to establish reliable predictors of severe OM before treatment in H&N cancer to allow early management of treatment-related sequelae. This prospective trial illustrates that the intrinsic ex-vivo radiosensitivity of oral keratinocytes could be correlated with RT-induced OM in patients with H&N cancer. This novel predictor requires validation in larger prospective cohorts.},
}

@article {pmid39898315,
year = {2025},
author = {Walker, JR and Bente, DA and Burch, MT and Cerqueira, FM and Ren, P and Labonté, JM},
title = {Molecular assessment of oyster microbiomes and viromes reveals their potential as pathogen and ecological sentinels.},
journal = {One health (Amsterdam, Netherlands)},
volume = {20},
number = {},
pages = {100973},
pmid = {39898315},
issn = {2352-7714},
abstract = {Oyster aquaculture world-wide is a booming industry that can provide many benefits to coastal habitats, including economic, ecosystem-level, and cultural benefits. Oysters present several risks for human consumption, including transmission of parasites, and bacterial and viral pathogens. Oyster microbiomes are well-defined, but their connection to the incidence of pathogens, humans or others, is unclear. Furthermore, viruses associated with oysters are largely unknown, and their connection to humans, animals, and ecosystem health has not been explored. Here, we employed a One Health framework and modern molecular techniques, including 16S rRNA amplicon and metagenomic sequencing, to identify links between changes in the microbial and viral communities associated with oysters and the incidence of pathogens detected in oyster tissues and their surrounding environments. In addition, we adapted the BioFire® FilmArray®, commonly used in hospitals, to determine the presence of human pathogens within the sampled oysters. We detected known human pathogens in 50 % of the oysters tested. Within the genomic datasets, we noted that pathogens of humans, animals, and plants in oysters were shared with the nearby water and sediments, suggesting a sink-source dynamic between the oysters and their surroundings. 16S rRNA gene analysis revealed that while oysters share common microbial constituents with their surrounding environments, they enrich for certain bacteria such as Mycoplasmatales, Fusobacteriales, and Spirochaetales. On the contrary, we found that oyster viromes harbored the same viruses in near equal relative abundances as their surrounding environments. Our results show how oysters could be used not only to determine the risk of human pathogens within coastal estuaries but also how oyster viruses could be used as ecosystem-level sentinels.},
}

@article {pmid39897886,
year = {2025},
author = {Qayyum, H and Talib, MS and Ali, A and Kayani, MUR},
title = {Evaluating the potential of assembler-binner combinations in recovering low-abundance and strain-resolved genomes from human metagenomes.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41938},
pmid = {39897886},
issn = {2405-8440},
abstract = {Human-associated microbial communities are a complex mixture of bacterial species and diverse strains prevalent at varying abundances. Due to the inherent limitations of metagenomic assemblers and genome binning tools in recovering low-abundance species (<1 %) and strains, we lack comprehensive insight into these communities. Although many bioinformatics approaches are available for recovering metagenome-assembled genomes, their effectiveness in recovering low-abundance species and strains is often questioned. Moreover, each tool has its trade-offs, making selecting the right tools challenging. In this study, we investigated the combinatory effect of various assemblers and binning tools on the recovery of low-abundance species and strain-resolved genomes from real and simulated human metagenomes. We evaluated the performance of nine combinations of metagenome assemblers and genome binning tools for their potential to recover genomes of useable quality. Our results revealed that the metaSPAdes-MetaBAT2 combination is highly effective in recovering low-abundance species, while MEGAHIT-MetaBAT2 excels in recovering strain-resolved genomes. These findings highlight the significant variation in the performance of different combinations, even when aiming for the same objective. This suggests the profound impact of selecting the right assembler-binner combination for metagenome analyses. We believe this study will be a cornerstone for the scientific community, guiding the choice of tools by highlighting their complementary effects. Furthermore, it underscores the potential of existing tools to address the current challenges in the field improving the recovery of information from metagenomes.},
}

@article {pmid39897812,
year = {2025},
author = {Yang, Y and Lu, Y and Gao, C and Nie, Y and Wang, H and Huang, Y and Dong, H and Sun, Q},
title = {Effects of housing conditions on health and gut microbiome of female cynomolgus monkeys and improvement of welfare by checking menstruation under socially housed condition.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41912},
pmid = {39897812},
issn = {2405-8440},
abstract = {Laboratory non-human primates (NHPs) are commonly subjected to social deprivation in various scientific researches. However, the impact of social deprivation on gut microbiome remains largely unknown. We examined the health status and gut microbiota of female cynomolgus monkeys housed in isolation or social conditions and found that social deprivation brought adverse effects to monkeys by inhibiting their growth, remodeling the immune status, and decreasing the level of beneficial biochemical parameters. 16S rRNA gene sequencing revealed that the gut microbial composition and function differed between grouped and isolated monkeys. Specifically, grouping the single-caged young monkeys to socially housed condition could decrease the relative abundance of Firmicutes and increase the relative abundance of Bacteroidetes, while separating the socially housed middle-aged monkeys into single cages showed the opposite trend. Besides, training female monkeys to detect menstruation under socially-housed condition could increase their body weight change and adjusting their immune status, thus attenuating the adverse effects of separating them to single cages. Our results verified the significant role of grouping in mitigating adverse health and microbiota alterations caused by isolation in female cynomolgus monkeys and emphasized the importance of training NHPs to cooperate with experimental procedures under socially housed condition, which could not only improve the welfare of cynomolgus monkeys but also enhance the accuracy and reliability of scientific results.},
}

@article {pmid39897789,
year = {2025},
author = {Schmidt, JE and Lewis, CA and Firl, AJ and Umaharan, P},
title = {Microbial bioindicators associated with cadmium uptake in sixteen genotypes of Theobroma cacao.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41890},
pmid = {39897789},
issn = {2405-8440},
abstract = {Recent regulatory limits on concentrations of cadmium (Cd), an element of concern for human health, have made Cd reduction a key issue in the global chocolate industry. Research into Cd minimization has investigated soil management, cacao genetic variation, and postharvest processing, but has overlooked the cacao-associated microbiome despite promising evidence in other crops that root-associated microorganisms could help reduce Cd uptake. A novel approach combining both amplicon and metagenomic sequencing identified microbial bioindicators associated with leaf and stem Cd accumulation in sixteen field-grown genotypes of Theobroma cacao. Sequencing highlighted over 200 amplicon sequence variants (ASVs) whose relative abundance was related to cacao leaf and stem Cd content or concentration. The two highest-accumulating genotypes, PA 32 and TRD 94, showed enrichment of four ASVs belonging to the genus Haliangium, the family Gemmataceae, and the order Polyporales. ASVs whose relative abundance was most negatively associated with plant Cd were identified as Paenibacillus sp. (β = -2.21), Candidatus Koribacter (β = -2.17), and Candidatus Solibacter (β = -2.03) for prokaryotes, and Eurotiomycetes (β = -4.58) and two unidentified ASVs (β = -4.32, β = -3.43) for fungi. Only two ASVs were associated with both leaf and stem Cd, both belonging to the Ktedonobacterales. Of 5543 C d-associated gene families, 478 could be assigned to GO terms, including 68 genes related to binding and transport of divalent heavy metals. Screening for Cd-related bioindicators prior to planting or developing microbial bioamendments could complement existing strategies to minimize the presence of Cd in the global cacao supply.},
}

@article {pmid39897714,
year = {2025},
author = {Morshead, ML and Tanguay, RL},
title = {Advancements in the Developmental Zebrafish Model for Predictive Human Toxicology.},
journal = {Current opinion in toxicology},
volume = {41},
number = {},
pages = {},
pmid = {39897714},
issn = {2468-2934},
abstract = {The rapid assessment of chemical hazards to human health, with reduced reliance on mammalian testing, is essential in the 21st century. Early life stage zebrafish have emerged as a leading model in the field due to their amenability to high throughput developmental toxicity testing while retaining the benefits of using a whole vertebrate organism with high homology with humans. Zebrafish are particularly well suited for a variety of study areas that are more challenging in other vertebrate model systems including microbiome work, transgenerational studies, gene-environment interactions, molecular responses, and mechanisms of action. The high volume of data generated from zebrafish screening studies is highly valuable for QSAR modeling and dose modeling for use in predictive hazard assessment. Recent advancements and challenges in using early life stage zebrafish for predictive human toxicology are reviewed.},
}

@article {pmid39897551,
year = {2025},
author = {Yu, C and Sun, R and Yang, W and Gu, T and Ying, X and Ye, L and Zheng, Y and Fan, S and Zeng, X and Yao, S},
title = {Exercise ameliorates osteopenia in mice via intestinal microbial-mediated bile acid metabolism pathway.},
journal = {Theranostics},
volume = {15},
number = {5},
pages = {1741-1759},
pmid = {39897551},
issn = {1838-7640},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Fecal Microbiota Transplantation/methods ; *Bone Diseases, Metabolic/metabolism/therapy ; *Bile Acids and Salts/metabolism ; Female ; *Physical Conditioning, Animal/physiology ; Ovariectomy ; Mice, Inbred C57BL ; Disease Models, Animal ; Osteoporosis/metabolism/therapy ; RNA, Ribosomal, 16S/genetics ; Bone and Bones/metabolism ; Metabolomics/methods ; },
abstract = {Rationale: Physical exercise is essential for skeletal integrity and bone health. The gut microbiome, as a pivotal modulator of overall physiologic states, is closely associated with skeletal homeostasis and bone metabolism. However, the potential role of intestinal microbiota in the exercise-mediated bone gain remains unclear. Methods: We conducted microbiota depletion and fecal microbiota transplantation (FMT) in ovariectomy (OVX) mice and aged mice to investigate whether the transfer of gut ecological traits could confer the exercise-induced bone protective effects. The study analyzed the gut microbiota and metabolic profiles via 16S rRNA gene sequencing and LC-MS untargeted metabolomics to identify key microbial communities and metabolites responsible for bone protection. Transcriptome sequencing and RNA interference were employed to explore the molecular mechanisms. Results: We found that gut microbiota depletion hindered the osteogenic benefits of exercise, and FMT from exercised osteoporotic mice effectively mitigated osteopenia. Comprehensive profiling of the microbiome and metabolome revealed that the exercise-matched FMT reshaped intestinal microecology and metabolic landscape. Notably, alterations in bile acid metabolism, specifically the enrichment of taurine and ursodeoxycholic acid, mediated the protective effects on bone mass. Mechanistically, FMT from exercised mice activated the apelin signaling pathway and restored the bone-fat balance in recipient MSCs. Conclusion: Our study underscored the important role of the microbiota-metabolic axis in the exercise-mediated bone gain, heralding a potential breakthrough in the treatment of osteoporosis.},
}

Animals
*Gastrointestinal Microbiome/physiology
Mice
*Fecal Microbiota Transplantation/methods
*Bone Diseases, Metabolic/metabolism/therapy
*Bile Acids and Salts/metabolism
Female
*Physical Conditioning, Animal/physiology
Ovariectomy
Mice, Inbred C57BL
Disease Models, Animal
Osteoporosis/metabolism/therapy
RNA, Ribosomal, 16S/genetics
Bone and Bones/metabolism
Metabolomics/methods

@article {pmid39897492,
year = {2025},
author = {Keleher, JG and Strope, TA and Estrada, NE and Griggs Mathis, AM and Easson, CG and Fiore, C},
title = {Freshwater sponges in the southeastern U.S. harbor unique microbiomes that are influenced by host and environmental factors.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18807},
pmid = {39897492},
issn = {2167-8359},
mesh = {*Porifera/microbiology ; *Microbiota ; Animals ; *Fresh Water/microbiology ; North Carolina ; *Symbiosis ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Marine, and more recently, freshwater sponges are known to harbor unique microbial symbiotic communities relative to the surrounding water; however, our understanding of the microbial ecology and diversity of freshwater sponges is vastly limited compared to those of marine sponges. Here we analyzed the microbiomes of three freshwater sponge species: Radiospongilla crateriformis, Eunapius fragilis, and Trochospongilla horrida, across four sites in western North Carolina, U.S.A. Our results support recent work indicating that freshwater sponges indeed harbor a distinct microbiome composition compared to the surrounding water and that these varied across sampling site indicating both environmental and host factors in shaping this distinct community. We also sampled sponges at one site over 3 months and observed that divergence in the microbial community between sponge and water occurs at least several weeks after sponges emerge for the growing season and that sponges maintain a distinct community from the water as the sponge tissue degrades. Bacterial taxa within the Gammproteobacteria, Alphproteobacteria, Bacteroidota (Flavobacteriia in particular), and Verrucomicrobia, were notable as enriched in the sponge relative to the surrounding water across sponge individuals with diverging microbial communities from the water. These results add novel information on the assembly and maintenance of microbial communities in an ancient metazoan host and is one of few published studies on freshwater sponge microbial symbiont communities.},
}

*Porifera/microbiology
*Microbiota
Animals
*Fresh Water/microbiology
North Carolina
*Symbiosis
Bacteria/classification/genetics/isolation & purification

@article {pmid39897478,
year = {2024},
author = {Li, Y and Wu, X},
title = {Vaginal microbiome distinction in women with HPV+, cervical intraepithelial neoplasia, and cervical cancer, a retrospective study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1483544},
pmid = {39897478},
issn = {2235-2988},
mesh = {Humans ; Female ; *Vagina/microbiology/virology ; *Microbiota ; *Uterine Cervical Dysplasia/microbiology/virology ; *Uterine Cervical Neoplasms/virology/microbiology ; *Papillomavirus Infections/virology/microbiology ; Adult ; Retrospective Studies ; Middle Aged ; *Genotype ; Papillomaviridae/genetics/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/isolation & purification/genetics ; Lactobacillus/isolation & purification/genetics ; Young Adult ; Gardnerella/isolation & purification/genetics ; },
abstract = {INTRODUCTION: The vaginal microbiota is a complex and dynamic micro-ecosystem that plays a pivotal role in protecting the host from various pathogens. Previous studies have investigated the diversity of the vaginal microbiome and its association with health outcomes, particularly the development of HPV-related disorders. This study aimed to investigate the correlation between the vaginal microbiota, HPV infection, cervical intraepithelial neoplasias (CINs), and cervical cancers in 69 women.

METHODS: DNA was extracted from vaginal samples, followed by HPV genotyping through PCR and sequenced of the16S rRNA gene.

RESULTS: Our results revealed that Lactobacillus was the predominant bacterium across all groups, with prevalence rates of 60.2% in women with HPV+, 63.9% in CINI, 97.7% in CINII, 52.0% in CINIII, 36.9% in cervical cancer, and 70.9% in NILM (normal cytology). Additionally, an elevated proportion of Gardnerella was identified as a high-risk bacterium associated with HPV infection, potentially contributing to the progression of cervical lesions. High-risk HPV genotypes, particularly HPV16, 52, and 33, were found to be more prevalent among women with HPV+, CIN, and cervical cancer. We also observed significantly higher alpha diversity in the vaginal microbiome of women with HPV+ and CIN, as indicated by increased Sobs, Shannon, Ace, and Chao indices, compared to the NILM group.

CONCLUSION: These findings suggest that HPV infection and its associated pathological conditions are closely linked to alterations in the vaginal microbiome. This underscores the need for further research to unravel the intricate relationship between HPV genotype infections and vaginal microbiota, which could pave the way for new diagnostic and therapeutic approaches.},
}

Humans
Female
*Vagina/microbiology/virology
*Microbiota
*Uterine Cervical Dysplasia/microbiology/virology
*Uterine Cervical Neoplasms/virology/microbiology
*Papillomavirus Infections/virology/microbiology
Adult
Retrospective Studies
Middle Aged
*Genotype
Papillomaviridae/genetics/isolation & purification/classification
RNA, Ribosomal, 16S/genetics
Bacteria/classification/isolation & purification/genetics
Lactobacillus/isolation & purification/genetics
Young Adult
Gardnerella/isolation & purification/genetics

@article {pmid39897450,
year = {2025},
author = {Knudsen, B and Narain, S and Moore, BB and Corr, PG and Frame, LA},
title = {Information About the Gut Microbiome's Connection to Health and Disease can Impact Knowledge: Feasibility of an Education-Based Intervention in a General Internal Medicine Clinic.},
journal = {American journal of lifestyle medicine},
volume = {},
number = {},
pages = {15598276251317129},
pmid = {39897450},
issn = {1559-8284},
abstract = {The gut microbiome (gMicrobiome)-a dynamic ecosystem of microorganisms-is emerging as a correlate of healthy lifestyle. Patients may not be aware of this. General Internal Medicine patients completed surveys evaluating gMicrobiome knowledge, lifestyle knowledge, dietary intake, physical activity, sleep, and stress. Surveys were given pre-/post-education (n = 112) and at 1 month follow-up (n = 60). The educational-module comprised a video and handout describing how lifestyle enhances gMicrobiome and health outcomes. Post-educational-module, 9 of 19 (47%) statements showed favorable change in knowledge (P < 0.05). Two statements reached statistical significance at 1-month follow-up: "Exercise influences the types of bacteria present in the digestive system" [7 (12%) to 24 (41%), P = 0.004] and "An inactive lifestyle promotes the growth of healthy types of digestive system bacteria" [12 (20%) to 24 (41%), P = 0.035]. We observed a small but favorable change in knowledge but not behavior. Large lifestyle changes are challenging to adopt, and education alone is necessary but insufficient for change. Our results confirm that education is a viable first step to establish the importance of pursuing lifestyle changes, perhaps moving from pre-contemplation to contemplation. Baseline knowledge in our participants was higher than anticipated, indicating that this intervention may have been too introductory. Future interventions should investigate baseline knowledge.},
}

@article {pmid39897390,
year = {2025},
author = {Gubler, S and Zaugg, A and Yi, R and Sherren, E and Milner, E and Conyer, W and May, T and Jack, T and Heaton, T and Christopherson, J and Higbee, P and Powers, E and Takara, M and Linder, A and Boyack, B and Pauga, F and Salmon, M and Thomas, M and Shiraki, M and Deng, S and Savage, PB},
title = {Design, synthesis, antimicrobial activity, stability, and mechanism of action of bioresorbable ceragenins.},
journal = {RSC medicinal chemistry},
volume = {},
number = {},
pages = {},
pmid = {39897390},
issn = {2632-8682},
abstract = {Device-related infections (DRIs) from bacterial/fungal biofilms that form on surfaces are a major cause of death in first-world countries. DRIs and the increasing prevalence of antibiotic resistant strains require development of new antimicrobials for improved antimicrobial prophylaxis. New antimicrobial prophylaxis practices necessitate novel agents to combat a broad spectrum of both fungi and bacteria, to be less toxic to patients, and to be locally administrable to prevent perturbations to a patient's microbiome. A class of antimicrobials that we have previously developed to fit these criteria is ceragenins. Here we describe the design, synthesis, and characterization of a new series of ceragenins that is composed of and degrades into endogenous compounds: cholic acid, B alanine, and glycerides. From this series we identify an optimized bioresorbable ceragenin that has comparable antimicrobial activities to other ceragenins, degrades rapidly through the action of lipase and at pH 7.2, and has a similar mechanism of action to previously developed ceragenins.},
}

@article {pmid39896799,
year = {2024},
author = {Dong, Y and Han, M and Qi, Y and Wu, Y and Zhou, Z and Jiang, D and Gai, Z},
title = {Enhancement of host defense against Helicobacter pylori infection through modulation of the gastrointestinal microenvironment by Lactiplantibacillus plantarum Lp05.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1469885},
pmid = {39896799},
issn = {1664-3224},
mesh = {Animals ; *Helicobacter Infections/immunology/microbiology ; *Helicobacter pylori ; Mice ; *Probiotics/therapeutic use/administration & dosage ; *Gastrointestinal Microbiome ; *Mice, Inbred C57BL ; Gastric Mucosa/microbiology/immunology/metabolism/pathology ; Disease Models, Animal ; Male ; Oxidative Stress ; },
abstract = {OBJECTIVE: This study aimed to assess the impact of Lactiplantibacillus plantarum Lp05 (Lp05) on the gastrointestinal microbiome and pathophysiological status of mice infected with Helicobacter pylori (H. pylori), exploring its potential as a probiotic treatment for H. pylori infections.

METHODS: In vitro, the interaction between Lp05 and H. pylori was analyzed using laser confocal and scanning electron microscopy. In vivo, C57BL/6 mice infected with H. pylori were treated with Lp05 and divided into six groups: control, model, quadruple therapy, and three dosage levels of Lp05 (2×10[7], 2×10[8], 2×10[9] CFU/mouse/day). Over six weeks, the impact of Lp05 on the gastrointestinal microbiome and physiological markers was assessed. Measurements included digestive enzymes (α-amylase, pepsin, cellulase), inflammatory markers (interleukin-17A, interleukin-23, interleukin-10, interferon-β, interferon-γ, FoxP3, endothelin, IP-10, TGF-β1), oxidative stress markers (catalase, malondialdehyde, superoxide dismutase, myeloperoxidase), and tissue pathology (via modified Warthin-Starry silver and H&E staining). Microbial community structure in the stomach and intestines was evaluated through 16S rRNA gene sequencing.

RESULTS: In vitro studies showed Lp05 and H. pylori formed co-aggregates, with Lp05 potentially disrupting H. pylori cell structure, reducing its stomach colonization. In vivo, Lp05 significantly lowered gastric mucosal urease activity and serum H. pylori-IgG antibody levels in infected mice (p < 0.01). It also mitigated pathological changes in the stomach and duodenum, decreased inflammatory responses (ET, IL-17A, IL-23, TGF-beta1, and IP-10, p < 0.01 for all), and enhanced antioxidant enzyme activities (CAT and SOD, p < 0.01) while reducing MDA and MPO levels (p < 0.01), combating oxidative stress from H. pylori infection. Lp05 treatment significantly modified the intestinal and gastric microbiota, increasing beneficial bacteria like Lactobacillus and Ligilactobacillus, and decreasing harmful bacteria such as Olsenella, linked to pathological conditions.

CONCLUSION: Lp05 effectively modulates the gastrointestinal microbiome, reduces inflammation and oxidative stress, and suppresses H. pylori, promising for probiotic therapies with further research needed to refine its clinical use.},
}

Animals
*Helicobacter Infections/immunology/microbiology
*Helicobacter pylori
Mice
*Probiotics/therapeutic use/administration & dosage
*Gastrointestinal Microbiome
*Mice, Inbred C57BL
Gastric Mucosa/microbiology/immunology/metabolism/pathology
Disease Models, Animal
Male
Oxidative Stress

@article {pmid39896755,
year = {2025},
author = {Zhao, B and Zhou, H and Lin, K and Xu, J and Zhou, B and Xie, D and Ma, J and Yang, L and Su, C and Yang, L},
title = {Antimicrobial peptide DP7 alleviates dextran sulfate sodium (DSS)-induced colitis via modifying gut microbiota and regulating intestinal barrier function.},
journal = {MedComm},
volume = {6},
number = {2},
pages = {e70085},
pmid = {39896755},
issn = {2688-2663},
abstract = {Inflammatory bowel diseases (IBDs), such as Crohn's disease (CD) and ulcerative colitis (UC), represent a growing global health concern. Restoring the balance of the gut microbiota, a crucial factor in intestinal health, offers potential for treating IBD. DP7, a novel antimicrobial peptide with potent antibacterial activity, was investigated for its anti-inflammatory effects in a dextran sulfate sodium (DSS)-induced UC mouse model. DP7 significantly ameliorated key disease parameters, including disease activity index, weight loss, and shortened colon length, while preserving colonic epithelial integrity and reducing inflammatory infiltration. Further analysis revealed potential targets of DP7, highlighting the significant role of Muribaculaceae bacteria during inflammatory states. To further explore the role of the gut microbiota in DP7's efficacy, fecal microbiota transplantation (FMT) was performed using feces from DP7-treated mice. FMT successfully ameliorated colitis in recipient mice, providing further evidence for the crucial role of the gut microbiome in IBD treatment and DP7's ability to modulate the gut microbiota for therapeutic benefit. Moreover, our findings suggest that DP7's modulation of the immune system is intricately linked to the complex microbial environment. Our findings demonstrate that DP7 effectively mitigates inflammation, attenuates barrier dysfunction, and shapes the gut microbiota, suggesting its potential as a therapeutic agent for UC.},
}

@article {pmid39896730,
year = {2025},
author = {Trumbo, PR and Ard, J and Bellisle, F and Drewnowski, A and Gilbert, JA and Kleinman, R and Misra, A and Sievenpiper, J and Tahiri, M and Watson, KE and Hill, J},
title = {Perspective: Current Scientific Evidence and Research Strategies in the Role of Almonds in Cardiometabolic Health.},
journal = {Current developments in nutrition},
volume = {9},
number = {1},
pages = {104516},
pmid = {39896730},
issn = {2475-2991},
abstract = {Almonds are consumed by individuals around the world. Because almonds are rich in protein, unsaturated fatty acids, and fiber, a significant amount of research has been conducted on their role in affecting various cardiometabolic endpoints (body weight, blood pressure, blood cholesterol levels, and glycemic response). The most current meta-analyses on almond consumption and various health-related endpoints suggest that almond consumption does not result in weight gain and results in small reductions in LDL cholesterol and diastolic blood pressure, as well as improved glycemic responses in certain populations (i.e. Asian Indians). A number of research gaps on almond consumption and cardiometabolic health were identified that should be addressed to further understand their role in the various cardiometabolic endpoints, including the mechanisms of action interactions with the microbiome with regular consumption and their role as part of a healthy dietary pattern for both individuals and the general population.},
}

@article {pmid39896720,
year = {2024},
author = {Coltro, EP and Cafferati Beltrame, L and da Cunha, CR and Zamparette, CP and Feltrin, C and Benetti Filho, V and Vanny, PA and Beduschi Filho, S and Klein, TCR and Scheffer, MC and Palmeiro, JK and Wagner, G and Sincero, TCM and Zárate-Bladés, CR},
title = {Evaluation of the resistome and gut microbiome composition of hospitalized patients in a health unit of southern Brazil coming from a high animal husbandry production region.},
journal = {Frontiers in antibiotics},
volume = {3},
number = {},
pages = {1489356},
pmid = {39896720},
issn = {2813-2467},
abstract = {INTRODUCTION: Antimicrobial resistance (AMR) poses a significant threat to global public health. The One Health approach, which integrates human, animal, and environmental health, highlights the roles of agricultural and hospital settings in the propagation of AMR. This study aimed to analyze the resistome and gut microbiome composition of individuals from a high-intensity animal husbandry area in the western region of Santa Catarina, Southern Brazil, who were subsequently admitted to the University Hospital in the city of Florianopolis, located in the eastern part of the same state.

METHODS: Rectal swab samples were collected upon admission and discharge. Metagenomic sequencing and resistome analysis were employed to identify antimicrobial resistance genes (ARGs) and their associated bacterial taxa. Additionally, the impact of the hospital environment on the resistome and microbiome profiles of these patients was assessed.

RESULTS: A total of 247 genetic elements related to AMR were identified, with 66.4% of these elements present in both admission and discharge samples. Aminoglycoside resistance genes were the most prevalent, followed by resistance genes for tetracyclines and lincosamides. Notably, unique resistance genes, including dfrF and mutations in gyrB, were identified at discharge. ARGs were associated with 55 bacterial species, with Lactobacillus fermentum, harboring the ermB gene. (MLSB), detected in both admission and discharge samples. The most prevalent bacterial families included Mycobacteriaceae, Enterobacteriaceae, and Bacteroidaceae. Among these, Mycobacteriaceae was the most abundant, with ARGs primarily associated with mutations in the 16S rRNA gene, RNA polymerase subunits, and gyrases.

DISCUSSION: The study revealed a high prevalence of genes related to aminoglycoside and tetracycline resistance, with a notable increase in certain resistance determinants at discharge, likely influenced by extended antimicrobial use. The presence of mcr genes, associated with colistin resistance, in both admission and discharge samples from a single patient highlights a concerning trend in AMR, particularly in relation to animal husbandry. These findings underscore the substantial impact of antimicrobial use on resistance development and the complex dynamics of the resistome in hospital settings. They also emphasize the influence of local factors, such as intensive animal production, on resistance patterns and advocate for ongoing surveillance and policy development to manage multidrug-resistant bacteria eVectively.},
}

@article {pmid39896683,
year = {2025},
author = {McManus, D and Copsel, SN and Pffeifer, BJ and Wolf, D and Barreras, H and Ma, S and Khodor, A and Komai, S and Burgos da Silva, M and Hazime, H and Gallardo, M and van den Brink, MR and Abreu, MT and Hill, GR and Perez, VL and Levy, RB},
title = {Pretransplant targeting of TNFRSF25 and CD25 stimulates recipient Tregs in target tissues ameliorating GVHD post-HSCT.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.16.633453},
pmid = {39896683},
issn = {2692-8205},
abstract = {The current approach to minimize transplant-associated complications, including graft-versus-host disease (GVHD) includes long-term pharmacological immune suppression frequently accompanied by unwanted side effects. Advances in targeted immunotherapies regulating alloantigen responses in the recipient continue to reduce the need for pan-immunosuppression. Here, in vivo targeting of the TNF superfamily receptor 25 (TNFRSF25) and the high affinity IL-2 receptor with a TL1A-Ig fusion protein and low dose IL-2, respectively, was used to pretreat recipient mice prior to allogeneic-HSCT (aHSCT). Pretreatment induced Treg expansion persisting early post-aHSCT leading to diminished GVHD and improved transplant outcomes. Expansion was accompanied by an increase in frequency of stable and functionally active Tregs as evidenced by in vitro assays using cells from major GVHD target tissues including colon, liver, and eye. Importantly, pretreatment supported epithelial cell function/integrity, a diverse microbiome including reduction of pathologic bacteria overgrowth and promotion of butyrate producing bacteria, while maintaining physiologic levels of obligate/facultative anaerobes. Notably, using a sphingosine 1-phosphate receptor agonist to sequester T cells in lymphoid tissues, we found that the increased tissue Treg frequency included resident CD69 [+] CD103 [+] FoxP3 [+] hepatic Tregs. In contrast to infusion of donor Treg cells, the strategy developed here resulted in the presence of immunosuppressive target tissue environments in the recipient prior to the receipt of donor allo-reactive T cells and successful perseveration of GVL responses. We posit strategies that circumvent the need of producing large numbers of ex-vivo manipulated Tregs, may be accomplished through in vivo recipient Treg expansion, providing translational approaches to improve aHSCT outcomes.},
}

@article {pmid39896561,
year = {2025},
author = {Ghaddar, BC and Blaser, MJ and De, S},
title = {Revisiting the cancer microbiome using PRISM.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.21.634087},
pmid = {39896561},
issn = {2692-8205},
abstract = {Recent controversy around the cancer microbiome highlights the need for improved microbial analysis methods for human genomics data. We developed PRISM, a computational approach for precise microorganism identification and decontamination from low-biomass sequencing data. PRISM removes spurious signals and achieves excellent performance when benchmarked on a curated dataset of 62,006 known true- and false-positive taxa. We then use PRISM to detect microbes in 8 cancer types from the CPTAC and TCGA datasets. We identify rich microbiomes in gastrointestinal tract tumors in CPTAC and identify bacteria in a subset of pancreatic tumors that are associated with altered glycoproteomes, more extensive smoking histories, and higher tumor recurrence risk. We find relatively sparse microbes in other cancer types and in TCGA, which we demonstrate may reflect differing sequencing parameters. Overall, PRISM does not replace gold-standard controls, but it enables higher-confidence analyses and reveals tumor-associated microorganisms with potential molecular and clinical significance.},
}

@article {pmid39896492,
year = {2025},
author = {Siguenza, N and Bailey, S and Sadegi, M and Gootin, H and Tiu, M and Price, JD and Ramer-Tait, A and Zarrinpar, A},
title = {Gut Competition Dynamics of Live Bacterial Therapeutics Are Shaped by Microbiome Complexity, Diet, and Therapeutic Transgenes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.21.634159},
pmid = {39896492},
issn = {2692-8205},
abstract = {Competitive exclusion is conventionally believed to prevent the establishment of a secondary strain of the same bacterial species in the gut microbiome, raising concerns for the deployment of live bacterial therapeutics (LBTs), especially if the bacterial chassis is a strain native to the gut. In this study, we investigated factors influencing competition dynamics in the murine gut using isogenic native Escherichia coli strains. We found that competition outcomes are context-dependent, modulated by microbiome complexity, LBT transgene expression, intestinal inflammation, and host diet. Furthermore, we demonstrated that native LBTs can establish long-term engraftment in the gut alongside a parental strain, with transgene-associated fitness effects influencing competition. We identified various interventions, including strategic dosing and dietary modulation, that significantly enhanced LBT colonization levels by 2 to 3 orders of magnitude. These insights provide a framework for optimizing LBT engraftment and efficacy, supporting their potential translation for human therapeutic applications.},
}

@article {pmid39896159,
year = {2025},
author = {Kapoor, MP and Abe, A and Morishima, S and Nakajima, A and Ozeki, M and Sato, N},
title = {Dietary intervention of prebiotic partially hydrolyzed guar gum improves skin viscoelasticity, stratum corneum hydration, and reduction of trans-epidermal water loss: a randomized, double-blind, and placebo-controlled clinical study in healthy humans.},
journal = {Journal of clinical biochemistry and nutrition},
volume = {76},
number = {1},
pages = {96-115},
pmid = {39896159},
issn = {0912-0009},
abstract = {Dietary fiber-rich diets are gaining popularity as an alternative therapy for skin health. Plant-based prebiotic partially hydrolyzed guar gum (PHGG) dietary fiber promotes gastrointestinal health, which is imperative for skin health through the gut microbiome. In this randomized, double-blind, and placebo-controlled study, the purpose was to assess the therapeutic effects of PHGG on skin hydration, trans-epidermal water loss (TEWL), and skin viscoelastic properties during the winter season. Healthy male and female subjects (n = 70; 9 male and 61 female; mean age: 45.5 ± 8.1 years) were recruited. They received either the 5 ‍g PHGG dietary fiber (n = 35) or a 5 ‍g placebo (n = 35) for twelve weeks. Skin moisture, TEWL, skin elasticity and skin color parameters, and related features were assessed at baseline, after 6 and 12 weeks, and questionnaires to evaluate the study outcomes. The results confirmed the improvement in skin conditions throughout the winter season by restoring skin hydration, reducing TEWL, and improving skin elasticity parameters. After 6 weeks of PHGG intake, there was a substantial decrease in TEWL and improvement in viscoelasticity metrics when compared to placebo. Subject satisfaction with efficacy reflected these encouraging findings, and PHGG was well tolerated, with no adverse events occurring during the study period.},
}

@article {pmid39896100,
year = {2025},
author = {Gutzeit, O and Gulati, A and Izadifar, Z and Stejskalova, A and Rhbiny, H and Cotton, J and Budnik, B and Shahriar, S and Goyal, G and Junaid, A and Ingber, DE},
title = {Cervical mucus in linked human Cervix and Vagina Chips modulates vaginal dysbiosis.},
journal = {npj women's health},
volume = {3},
number = {1},
pages = {5},
pmid = {39896100},
issn = {2948-1716},
abstract = {This study explores the protective role of cervicovaginal mucus in maintaining vaginal health, particularly in relation to bacterial vaginosis (BV), using organ chip technology. By integrating human Cervix and Vagina Chips, we demonstrated that cervical mucus significantly reduces inflammation and epithelial damage caused by a dysbiotic microbiome commonly associated with BV. Proteomic analysis of the Vagina Chip, following exposure to mucus from the Cervix Chip, revealed differentially abundant proteins, suggesting potential biomarkers and therapeutic targets for BV management. Our findings highlight the essential function of cervical mucus in preserving vaginal health and underscore the value of organ chip models for studying complex interactions within the female reproductive tract. This research provides new insights into the mechanisms underlying vaginal dysbiosis and opens avenues for developing targeted therapies and diagnostic tools to enhance women's reproductive health.},
}

@article {pmid39896099,
year = {2025},
author = {Iwami, N and Komiya, S and Asada, Y and Tatsumi, K and Habara, T and Kuramoto, T and Seki, M and Yoshida, H and Takeuchi, K and Shiotani, M and Mukaida, T and Odawara, Y and Mio, Y and Kamiya, H},
title = {"Shortening time to pregnancy in infertile women by personalizing treatment of microbial imbalance through Emma & Alice: A multicenter prospective study".},
journal = {Reproductive medicine and biology},
volume = {24},
number = {1},
pages = {e12634},
pmid = {39896099},
issn = {1445-5781},
abstract = {PURPOSE: To evaluate the impact of Endometrial Microbiome Metagenomic Analysis and Analysis of Infectious Chronic Endometritis (EMMA & ALICE) on pregnancy outcomes following recommended treatments in women with recurrent implantation failure (RIF) or recurrent pregnancy loss (RPL).

METHODS: This prospective, multicenter cohort study included 527 women under 42 years old with RIF or RPL across 14 IVF centers in Japan. Endometrial samples were analyzed using EMMA & ALICE, and patients received antibiotics, probiotics, or no treatment based on test results. Pregnancy outcomes were assessed using Kaplan-Meier survival analysis and multivariate generalized linear models.

RESULTS: Amongst participants, 43.4% had a normal Lactobacillus-dominated microbiota, 20.9% had dysbiosis, and 35.7% had mild dysbiosis or ultralow biomass. Kaplan-Meier analysis revealed significantly higher ongoing pregnancy rates in the dysbiosis group treated with antibiotics and probiotics compared to other groups (p = 0.031). Post-treatment, ongoing pregnancy rates in the dysbiosis and mild dysbiosis groups were comparable to the normal group.

CONCLUSIONS: EMMA & ALICE-guided antimicrobial and probiotic treatments improved pregnancy outcomes, enabling the dysbiosis group to achieve pregnancy earlier than the normal group. Addressing uterine dysbiosis may reduce the time to pregnancy in patients with RIF and RPL.

TRIAL REGISTRATION: University Hospital Medical Information Network (UMIN), UMIN000036917.},
}

@article {pmid39895839,
year = {2025},
author = {Zhang, Z and Bi, C and Wu, R and Qu, M},
title = {Association of the newly proposed dietary index for gut microbiota and constipation: a cross-sectional study from NHANES.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1529373},
pmid = {39895839},
issn = {2296-861X},
abstract = {OBJECTIVE: The dietary index for gut microbiota. DI-GM is an innovative metric designed to capture the diversity of the gut microbiome, yet its association with constipation remains unstudied.

METHODS: In this cross-sectional study, 11,405 adults aged 20 and older were selected from the National Health and Nutrition Examination Survey 2005-2010 for the sample. Constipation was defined as fewer than three defecation frequencies per week using bowel health questionnaire (BHQ). Fewer than three bowel movements per week were considered as constipation by Bowel Health Questionnaire (BHQ). DI-GM was derived from dietary recall data, including avocado, broccoli, chickpeas, coffee, cranberries, fermented dairy, fiber, green tea, soybean and whole grains as beneficial elements, red meat, processed meat, refined grains, and high fat as detrimental components. Multivariable weighted logistic was employed to investigate the association of DI-GM with constipation. Secondary analyses included subgroup analyses, restricted cubic spline (RCS), and multiple imputation.

RESULTS: A higher DI-GM and beneficial gut microbiota score were associated with a lower prevalence of constipation (DI-GM: OR = 0.82, 95% CI = 0.75, 0.90; beneficial gut microbiota score: OR = 0.77, 95% CI = 0.67, 0.89). After grouping DI-GM, in the fully adjusted model, participants with DI-GM ≥ 6 were significantly negatively correlated with both the prevalence of constipation (OR = 0.48, 95% CI = 0.33, 0.71). RCS indicated a non-linear relationship between DI-GM and constipation. Subgroup analyses by age, sex and common complications showed no statistically significant interactions (p > 0.05).

CONCLUSION: The newly proposed DI-GM was inversely related with the prevalence of constipation. When treating patients with constipation, it is necessary for clinicians to provide timely and effective dietary interventions incorporating the DI-GM for patients with constipation to avoid further deterioration of the condition.},
}

@article {pmid39895797,
year = {2025},
author = {Gao, Y and Zheng, H and Ye, M and Zhou, G and Chen, J and Qiang, X and Bai, J and Lu, X and Tang, Q},
title = {Characteristics and function of the gut microbiota in patients with rectal neuroendocrine tumors.},
journal = {Journal of Cancer},
volume = {16},
number = {4},
pages = {1040-1050},
pmid = {39895797},
issn = {1837-9664},
abstract = {The gut microbiota plays a significant role in the initiation and progression of tumors, but its role in rectal neuroendocrine tumors (rNETs) remains unclear. Fecal samples were collected from 19 healthy individuals and 21 rNET patients,with the rNET cohort further divided into metastatic (rNETs-M) and non-metastatic (rNETs-nM) groups. Using metagenomic high-throughput sequencing, we analyzed the diversity, species composition, and functional characteristics of the gut microbiota. We applied a random forest model to identify potential microbial biomarkers for predicting rNET and specifically distinguishing rNETs-M cases. Alpha diversity analysis revealed that species diversity was lower in the rNETs group than in the control group. In contrast, the rNETs-M group exhibited higher species diversity than the rNETs-nM group. Beta diversity analysis demonstrated significant differences in community structure between the rNETs and control groups between the rNET-M and rNETs-nM groups. Notably, in the rNETs group, the abundance of potential pathogens such as Escherichia coli and Shigella was elevated.Furthermore, the rNETs-M group exhibited an increased abundance of potential pathogens such as Alistipes. KEGG enrichment analysis indicated that these distinct microbiota play a significant role in environmental information processing, genetic information processing, and metabolic pathways. Random forest analysis and ROC curve results identified Lachnospira pectinoschiza (AUC=0.885), Parasutterella muris (AUC=0.862), Sodaliphilus pleomorphus(AUC=0.956), Methylobacterium iners (AUC=0.971) as biomarkers with significant discriminatory value.},
}

@article {pmid39895695,
year = {2025},
author = {Cumbo, F and Joshi, J and Thurnher, D and Maniakas, A},
title = {Editorial: The role of the microbiome in head and neck cancer.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1545067},
doi = {10.3389/fonc.2025.1545067},
pmid = {39895695},
issn = {2234-943X},
}

@article {pmid39895632,
year = {2025},
author = {Gazzaniga, FS and Kasper, DL},
title = {The gut microbiome and cancer response to immune checkpoint inhibitors.},
journal = {The Journal of clinical investigation},
volume = {135},
number = {3},
pages = {},
doi = {10.1172/JCI184321},
pmid = {39895632},
issn = {1558-8238},
mesh = {*Gastrointestinal Microbiome/drug effects/immunology ; Humans ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Animals ; *Neoplasms/immunology/drug therapy/microbiology/therapy ; Mice ; *Fecal Microbiota Transplantation ; Immunotherapy ; },
abstract = {Immune checkpoint inhibitors (ICIs) are widely used for cancer immunotherapy, yet only a fraction of patients respond. Remarkably, gut bacteria impact the efficacy of ICIs in fighting tumors outside of the gut. Certain strains of commensal gut bacteria promote antitumor responses to ICIs in a variety of preclinical mouse tumor models. Patients with cancer who respond to ICIs have a different microbiome compared with that of patients who don't respond. Fecal microbiota transplants (FMTs) from patients into mice phenocopy the patient tumor responses: FMTs from responders promote response to ICIs, whereas FMTs from nonresponders do not promote a response. In patients, FMTs from patients who have had a complete response to ICIs can overcome resistance in patients who progress on treatment. However, the responses to FMTs are variable. Though emerging studies indicate that gut bacteria can promote antitumor immunity in the absence of ICIs, this Review will focus on studies that demonstrate relationships between the gut microbiome and response to ICIs. We will explore studies investigating which bacteria promote response to ICIs in preclinical models, which bacteria are associated with response in patients with cancer receiving ICIs, the mechanisms by which gut bacteria promote antitumor immunity, and how microbiome-based therapies can be translated to the clinic.},
}

*Gastrointestinal Microbiome/drug effects/immunology
Humans
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Animals
*Neoplasms/immunology/drug therapy/microbiology/therapy
Mice
*Fecal Microbiota Transplantation
Immunotherapy

@article {pmid39895627,
year = {2025},
author = {Scharschmidt, TC and Segre, JA},
title = {Skin microbiome and dermatologic disorders.},
journal = {The Journal of clinical investigation},
volume = {135},
number = {3},
pages = {},
doi = {10.1172/JCI184315},
pmid = {39895627},
issn = {1558-8238},
mesh = {Humans ; *Microbiota/immunology ; *Skin/microbiology/immunology/pathology ; *Dermatitis, Atopic/microbiology/immunology/pathology ; *Skin Diseases/microbiology/immunology ; Animals ; },
abstract = {Human skin acts as a physical barrier to prevent the entry of pathogenic microbes while simultaneously providing a home for commensal bacteria and fungi. Microbiome sequencing studies have demonstrated the unappreciated diversity and selectivity of these microbes. Functional studies have demonstrated the impact of specific strains to tune the immune system, sculpt the microbial community, provide colonization resistance, and promote epidermal barrier integrity. Recent studies have integrated the microbiome, immunity, and tissue integrity to understand their interplay in common disorders such as atopic dermatitis. In this Review, we explore microbiome shifts associated with cutaneous disorders with an eye toward how the microbiome can be mined to identify new therapeutic opportunities.},
}

Humans
*Microbiota/immunology
*Skin/microbiology/immunology/pathology
*Dermatitis, Atopic/microbiology/immunology/pathology
*Skin Diseases/microbiology/immunology
Animals

@article {pmid39895623,
year = {2025},
author = {Bordelon, RC and Herath, M and Speer, AL},
title = {Innervation of Human Intestinal Organoids.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {215},
pages = {},
doi = {10.3791/67702},
pmid = {39895623},
issn = {1940-087X},
mesh = {*Organoids/cytology ; Humans ; Animals ; Mice ; *Pluripotent Stem Cells/cytology ; *Intestine, Small/cytology ; Enteric Nervous System/cytology ; Neural Crest/cytology ; Cell Differentiation/physiology ; },
abstract = {The complexity of intestinal cytoarchitecture and function poses significant challenges for the creation of the bioengineered small intestine. Techniques for generating human intestinal organoids (HIOs) resembling human small intestine have been previously reported. HIOs contain epithelium and mesenchyme but lack other critical components of functional intestine such as the enteric nervous system (ENS), immune cells, vasculature, and microbiome. Two independent research groups have published distinct methods to innervate HIOs with an ENS. Here we discuss a unique method of incorporating the ENS into an HIO-derived bioengineered small intestine, which utilizes components of these prior reports to optimize progenitor cell identity as well as developmental timing. Human pluripotent stem cells (hPSCs) are differentiated to independently generate HIOs and enteric neural crest cells (ENCCs) by temporal regulation of differentiation markers over a period of several days per published protocols. Once HIOs reach the mid-hindgut spheroid stage (approximately day 8), day 15-21 ENCC spheroids are dissociated, co-cultured with HIOs, and suspended within clear three-dimensional (3D) basement membrane matrix droplets. HIO + ENCC co-cultures are maintained in vitro for 28-40 days before transplantation into >9-week-old immunodeficient mice for further development and maturation. Transplanted HIOs (tHIOs) with ENS can be harvested 4-20 weeks later. This method integrates elements from two previously published techniques by utilizing ENCCs generated from hPSCs and co-culturing them with HIOs at an early stage of development to maximize exposure to early developmental cues that likely contribute to the formation of a more mature intestinal morphology.},
}

*Organoids/cytology
Humans
Animals
Mice
*Pluripotent Stem Cells/cytology
*Intestine, Small/cytology
Enteric Nervous System/cytology
Neural Crest/cytology
Cell Differentiation/physiology

@article {pmid39895585,
year = {2025},
author = {Li, Y and Mai, Y and Jiao, Y and Yuan, Y and Qu, Y and Zhang, Y and Wang, M and Zhang, W and Lu, X and Lin, Z and Liang, C and Li, J and Mao, T and Xie, C},
title = {Alterations in the Tongue Coating Microbiome in Patients With Diarrhea-Predominant Irritable Bowel Syndrome: A Cross-Sectional Study.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {2},
pages = {e70001},
doi = {10.1111/apm.70001},
pmid = {39895585},
issn = {1600-0463},
support = {2022-1-4201//Capital's Funds for Health Improvement and Research/ ; 7242232//Beijing Natural Science Foundation Proposed Program/ ; JCYJ20240813153504007//Shenzhen Science and Technology Program/ ; CACM-2022-QNRC2-A02//China Association of Chinese Medicine Young Talent Support Project/ ; CYJH2024057//Young Talents Program for Traditional Chinese Medicine Clinical Practice under the Eagle Plan of China Association of Chinese Medicine/ ; K2023A01//Qihuang Excellent Youth Science and Technology Talent Cultivation Plan of Beijing University of Chinese Medicine/ ; DFRCZY-2024GJRC010//National High Level Chinese Medicine Hospital Clinical Research Funding/ ; },
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; Adult ; Male ; Female ; *Tongue/microbiology ; Cross-Sectional Studies ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Diarrhea/microbiology ; Microbiota/genetics ; Dysbiosis/microbiology ; Bacteria/classification/genetics/isolation & purification ; Young Adult ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; Gastrointestinal Microbiome/genetics ; Sequence Analysis, DNA ; },
abstract = {The gut microbiota plays a critical role in the occurrence and development of IBS-D, however, IBS-D-associated tongue coating microbiome dysbiosis has not yet been clearly defined. To address this, we analyzed the structure and composition of the tongue coating microbiome in 23 IBS-D patients and 12 healthy controls using 16S rRNA high-throughput sequencing analysis. The 16S rRNA sequencing results revealed that the overall observed OTUs of tongue coating microbiome in IBS-D patients exhibited a significant decrease compared with the healthy controls. Alpha diversity analysis showed that the diversity and community richness were significantly reduced in IBS-D patients, and PCoA revealed a distinct clustering of tongue coating microbiome between the IBS-D patients and healthy controls. Microbial comparisons at the genus level showed that the abundance of Veillonella, Prevotella in IBS-D patients was higher than those in healthy controls, while Streptococcus, Haemophilus, Granulicatella, and Rothia were significantly reduced compared with the healthy volunteers. Functional analysis results showed significant differences in 88 functional metabolic pathways between the IBS-D patients and the healthy controls, including fatty acid biosynthesis. These findings identified the structure, composition, functionality of tongue coating microbiome in IBS-D patients, and hold promise the potential for therapeutic targets during IBS-D management.},
}

Humans
*Irritable Bowel Syndrome/microbiology
Adult
Male
Female
*Tongue/microbiology
Cross-Sectional Studies
*RNA, Ribosomal, 16S/genetics
Middle Aged
*Diarrhea/microbiology
Microbiota/genetics
Dysbiosis/microbiology
Bacteria/classification/genetics/isolation & purification
Young Adult
High-Throughput Nucleotide Sequencing
DNA, Bacterial/genetics
Gastrointestinal Microbiome/genetics
Sequence Analysis, DNA

@article {pmid39895304,
year = {2025},
author = {Markley, JD and Bajaj, JS},
title = {Rethinking Antibiotic Prophylaxis for Spontaneous Bacterial Peritonitis in Patients with Cirrhosis: First, Do No Harm.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciaf047},
pmid = {39895304},
issn = {1537-6591},
abstract = {Antibiotic prophylaxis for spontaneous bacterial peritonitis (SBPPr) in patients with cirrhosis has been considered standard of care since the 1990s and is currently recommended by several major gastroenterological societies. However, the evidence supporting this practice is weak and there is no clear mortality benefit. The unintended consequences of this strategy are not insignificant, both at the patient and population level. Recent evidence suggests that SBPPr may even cause harm. Since the widespread implementation of SBPPr three decades ago, our overall approach to antibiotic use has shifted. We now recognize the growing threat of antimicrobial resistance (AMR), the potential harms of antibiotics, and the vital role of antimicrobial stewardship. In light recent developments and evidence, there is an urgent need for infectious disease, antimicrobial stewardship, and hepatology leaders to collaborate to develop an updated and cohesive approach to SBPPr.},
}

@article {pmid39895284,
year = {2025},
author = {Costa de Almeida, T and Sabino, YNV and Brasiel, PGA and Rocha, BMO and de Cássia Ávila Alpino, G and Rocha, VN and Dias, VC and Diniz, CG and Paiva, AD and Silva, VLD and Dutra Medeiros, J and Potente Dutra Luquetti, SC and Barbosa Ferreira Machado, A},
title = {Maternal kefir intake during lactation impacts the breast milk and gut microbiota of the Wistar rat's offspring.},
journal = {International journal of food sciences and nutrition},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/09637486.2025.2461142},
pmid = {39895284},
issn = {1465-3478},
abstract = {Environmental factors can play fundamental role in health in childhood and adulthood during critical developmental periods like lactation. The maternal intake of probiotics like kefir during lactation could benefit newborns' intestinal health. This study aimed to evaluate the effects of maternal kefir intake during lactation on bacterial breast milk composition and the gut microbiota of offspring Wistar male rats at weaning. Lactating Wistar rats and their pups were divided into four groups based on litter size and maternal kefir intake. Sequencing of the 16S rRNA gene in breast milk revealed the predominance of the Proteobacteria, Firmicutes, and Actinobacteriota phyla. Offspring gut microbiota exhibited clustering tendencies in kefir groups with varying genus abundance. Additionally, maternal kefir intake led to increased levels of butyrate acid in offspring faeces (> +30%, p > 0.05). These findings show that the lactation period could be a window of opportunity to program intestinal health through microbiota modulation.},
}

@article {pmid39895076,
year = {2025},
author = {Jung, S},
title = {Advances in functional analysis of the microbiome: Integrating metabolic modeling, metabolite prediction, and pathway inference with Next-Generation Sequencing data.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {1},
pages = {e.2411006},
doi = {10.71150/jm.2411006},
pmid = {39895076},
issn = {1976-3794},
support = {2022R1A2C1007345//National Research Foundation of Korea/ ; //Ministry of Science and ICT/ ; },
mesh = {*Microbiota/genetics ; Humans ; *High-Throughput Nucleotide Sequencing ; *Metabolic Networks and Pathways/genetics ; Bacteria/genetics/metabolism/classification ; Computational Biology/methods ; Models, Biological ; },
abstract = {This review explores current advancements in microbiome functional analysis enabled by next-generation sequencing technologies, which have transformed our understanding of microbial communities from mere taxonomic composition to their functional potential. We examine approaches that move beyond species identification to characterize microbial activities, interactions, and their roles in host health and disease. Genome-scale metabolic models allow for in-depth simulations of metabolic networks, enabling researchers to predict microbial metabolism, growth, and interspecies interactions in diverse environments. Additionally, computational methods for predicting metabolite profiles offer indirect insights into microbial metabolic outputs, which is crucial for identifying biomarkers and potential therapeutic targets. Functional pathway analysis tools further reveal microbial contributions to metabolic pathways, highlighting alterations in response to environmental changes and disease states. Together, these methods offer a powerful framework for understanding the complex metabolic interactions within microbial communities and their impact on host physiology. While significant progress has been made, challenges remain in the accuracy of predictive models and the completeness of reference databases, which limit the applicability of these methods in under-characterized ecosystems. The integration of these computational tools with multi-omic data holds promise for personalized approaches in precision medicine, allowing for targeted interventions that modulate the microbiome to improve health outcomes. This review highlights recent advances in microbiome functional analysis, providing a roadmap for future research and translational applications in human health and environmental microbiology.},
}

*Microbiota/genetics
Humans
*High-Throughput Nucleotide Sequencing
*Metabolic Networks and Pathways/genetics
Bacteria/genetics/metabolism/classification
Computational Biology/methods
Models, Biological

@article {pmid39895074,
year = {2025},
author = {Lee, KA and Ul-Haq, A and Seo, H and Jo, S and Kim, S and Song, HY and Kim, HS},
title = {Characteristics of skin microbiome associated with disease severity in systemic sclerosis.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {1},
pages = {e.2409018},
doi = {10.71150/jm.2409018},
pmid = {39895074},
issn = {1976-3794},
support = {//Korea Health Industry Development Institute/ ; HI21C1888//Ministry of Health and Welfare/ ; //National Research Foundation of Korea/ ; RS-2023-00219563//Ministry of Science and ICT/ ; //Soonchunhyang University Research Fund/ ; },
mesh = {Humans ; *Scleroderma, Systemic/microbiology ; *Skin/microbiology/pathology ; *Microbiota ; Female ; Middle Aged ; Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Severity of Illness Index ; Aged ; Biomarkers ; Metagenomics ; },
abstract = {Systemic sclerosis (SSc) is a chronic autoimmune disorder characterised by skin fibrosis and internal organ involvement. Disruptions in the microbial communities on the skin may contribute to the onset of autoimmune diseases that affect the skin. However, current research on the skin microbiome in SSc is lacking. This study aimed to investigate skin microbiome associated with disease severity in SSc. Skin swabs were collected from the upper limbs of 46 healthy controls (HCs) and 36 patients with SSc. Metagenomic analysis based on the 16S rRNA gene was conducted and stratified by cutaneous subtype and modified Rodnan skin score (mRSS) severity. Significant differences in skin bacterial communities were observed between the HCs and patients with SSc, with further significant variations based on subtype and mRSS severity. The identified biomarkers were Bacteroides and Faecalibacterium for patients with diffuse cutaneous SSc with high mRSS (≥ 10) and Mycobacterium and Parabacteroides for those with low mRSS (< 10). Gardnerella, Abies, Lactobacillus, and Roseburia were the biomarkers in patients with limited cutaneous SSc (lcSS) and high mRSS, whereas Coprococcus predominated in patients with lcSS and low mRSS. Cutaneous subtype analysis identified Pediococcus as a biomarker in the HCs, whereas mRSS analysis revealed the presence of Pseudomonas in conjunction with Pediococcus. In conclusion, patients with SSc exhibit distinct skin microbiota compared with healthy controls. Bacterial composition varies by systemic sclerosis cutaneous subtype and skin thickness.},
}

Humans
*Scleroderma, Systemic/microbiology
*Skin/microbiology/pathology
*Microbiota
Female
Middle Aged
Male
*RNA, Ribosomal, 16S/genetics
Adult
*Bacteria/classification/genetics/isolation & purification
Severity of Illness Index
Aged
Biomarkers
Metagenomics

@article {pmid39895049,
year = {2025},
author = {Lu, ZJ and Shi, WJ and Qiao, LK and Ma, DD and Zhang, JG and Yao, CR and Li, SY and Long, XB and Ying, GG},
title = {Benzimidazole Fungicide Carbendazim Induces Gut Inflammation through the TLR5/NF-κB Pathway in Grass Carp.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12695},
pmid = {39895049},
issn = {1520-5851},
abstract = {Fungicides have been increasingly used across various sectors, including agriculture and textiles. The biocidal properties of fungicides may negatively impact the stability of intestinal microbiota, thereby posing a threat to intestinal health. In this study, we investigated the mechanisms of intestinal damage and functional abnormalities in grass carp following a 42-day exposure to the widely used fungicide carbendazim at environmentally relevant concentrations (0.2 to 20 μg/L). Histopathological observations, mRNA and protein expression analyses, biochemical analysis, quantification of short-chain fatty acids (SCFAs), cytokines, lipopolysaccharide (LPS), and 16S ribosomal ribonucleic acid (rRNA), as well as internal transcribed spacer (ITS) sequencing, were performed. At environmentally relevant concentrations, carbendazim strongly induced intestinal inflammation, leading to increased transcriptional and translational levels of genes involved in the toll-like receptor five (TLR5)/nuclear factor kappa B (NF-κB) pathway, including TLR5, NF-κB, interleukin-1 beta (IL-1β), and tumor necrosis factor-alpha (TNFα). Additionally, carbendazim damaged intestinal barriers and reduced the expression of tight junction proteins (e.g., occludin and zonula occludens-1/2), goblet cells, and immunoglobulin M levels, while also disrupting the gut microbiome, leading to intestinal metabolic disorders, particularly decreases in SCFAs and increases in LPS. Treatment with the TLR5 antagonist TH1020 mitigated intestinal inflammation caused by carbendazim, subsequently improving mechanical barrier function. Overall, our findings provide new insights into the toxicological mechanisms underlying intestinal damage caused by carbendazim in grass carp, indicating that carbendazim poses a significant threat to nontarget organisms. Given its widespread detection in the environment, these results underscore the substantial ecological risks to the gut health of fish living in carbendazim-contaminated water bodies.},
}

@article {pmid39895020,
year = {2025},
author = {Mazurel, D and Brandt, BW and Boomsma, M and Crielaard, W and Lagerweij, M and Exterkate, RAM and Deng, DM},
title = {Streptococcus mutans and Caries: A Systematic Review and Meta-Analysis.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345241303880},
doi = {10.1177/00220345241303880},
pmid = {39895020},
issn = {1544-0591},
abstract = {It has been questioned whether Streptococcus mutans can still be considered the major etiological agent for caries. The main argument is that most evidence has been based on single-species identification. The composition of the oral microbiome was not analyzed. This systemic review aims to assess the prevalence and abundance of S. mutans in caries-active (CA) and caries-free (CF) subjects based on clinical studies in which the microbiome was investigated. Three databases (PubMed, Cochrane, Embase) were searched until May 22, 2023, for eligible publications that included CA and CF subjects and reported the detection of both S. mutans and the oral microbial community, using DNA-based methods. The clinical and microbial outcomes were summarized and further analyzed using a random-effects model. Of 22 eligible studies, 3 were excluded due to the high risk of bias. In the remaining 19 studies, 16 reported the prevalence of S. mutans, 11 reported its relative abundance, and 8 reported both parameters. The prevalence of S. mutans in CA was either similar to (n = 4) or higher than (n = 12) the CF group. The reported relative abundance in CA was higher than CF in all 11 studies, although the values varied from 0.001% to 5%. Meta-analysis confirmed the significance of these findings. The summary of microbial community data did not reveal other caries-associated bacterial genera/species than S. mutans. In conclusion, the collected evidence based on microbiome studies suggests a strong association between the prevalence and abundance of S. mutans and caries experience. While the cariogenic role of S. mutans in the oral ecosystem should be recognized, its actual function warrants further exploration.},
}

@article {pmid39894829,
year = {2025},
author = {Li, Z and Azad, MAK and Meng, C and Kong, X and Gui, J and Lin, W and Cui, Y and Lan, W and He, Q},
title = {Metabolomics, network pharmacology, and microbiome analyses uncover the mechanisms of the Chinese herbal formula for the improvement of meat quality in spent hens.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {17},
pmid = {39894829},
issn = {1674-9782},
support = {2022YFC3400700//National Key Research and Development Project/ ; SXHZ2020007//City-School Cooperation Project of the Fuyang Science and Technology Special Fund/ ; JCYJ20200109114242138//Basic Research Program of Shenzhen Municipal Government/ ; KTP20210345//Special Commissioner for Rural Science and Technology of Guangdong Province/ ; },
abstract = {BACKGROUND: Meat originating from the spent hen is an important source of poultry meat production; however, multiple factors cause the decline in the meat quality of spent hens. Chinese herbs have been widely used as medicine for a long time to prevent diseases and as nutrient supplements to improve the product quality. This experiment explored the effects of adding 1.0% Chinese herbal formula (CHF, including 0.30% Leonurus japonicus Houtt., 0.20% Salvia miltiorrhiza Bge., 0.25% Ligustrum lucidum Ait., and 0.25% Taraxacum mongolicum Hand.-Mazz.) for 120 d to the spent hens' diet through metabolomics, network pharmacology, and microbiome strategies.

RESULTS: The results indicated that CHF supplementation improved the meat quality by reducing drip loss (P < 0.05), b* value (P = 0.058), and shear force (P = 0.099) and increasing cooked meat percentage (P = 0.054) and dry matter (P < 0.05) of breast muscle. The addition of CHF improved the nutritional value of breast muscle by increasing (P < 0.05) the content of C18:2n-6, n-6/n-3 polyunsaturated fatty acids (PUFA), total PUFA, PUFA-to-saturated fatty acids (SFA) ratio, and hypocholesterolemic-to-hypercholesterolemic ratio, and tending to increase serine content (P = 0.069). The targeted metabolomics analysis revealed that the biosynthesis of SFA, linoleic acid metabolism, fatty acid degradation, fatty acid elongation, and fatty acid biosynthesis pathways were enriched by CHF supplementation. Furthermore, the network pharmacology analysis indicated that CHF was closely associated with oxidative stress and lipid metabolism. The CHF supplementation increased the glutathione peroxidase level (P < 0.05) and upregulated gene expression related to the Nrf2 pathway (including HO-1, P < 0.05; Nrf2, P = 0.098; CAT, P = 0.060; GPX1, P = 0.063; and SOD2, P = 0.052) and lipid metabolism (including PPARγ, P < 0.05; SREBP1, P = 0.059; and CPT1A, P = 0.058). Additionally, CHF supplementation increased Firmicutes and decreased Bacteroidetes, Spirochaetes, and Synergistetes abundances (P < 0.05), which may contribute to better meat quality.

CONCLUSIONS: Our results suggest that CHF supplementation improved the quality and nutritional value of meat, which will provide a theoretical basis for the utilization of CHF as a feed additive in spent hens' diets.},
}

@article {pmid39894814,
year = {2025},
author = {El Leithy, AA and Youssef, ASE and Nassar, A and Aziz, RK and Khaled, NM and Mahrous, MT and Farahat, GN and Mohamed, AH and Bakr, YM},
title = {Long-read 16S rRNA amplicon sequencing reveals microbial characteristics in patients with colorectal adenomas and carcinoma lesions in Egypt.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {8},
pmid = {39894814},
issn = {1757-4749},
abstract = {BACKGROUND: Colorectal cancer (CRC) is among the five leading causes of cancer incidence and mortality. During the past decade, the role of the gut microbiota and its dysbiosis in colorectal tumorigenesis has been emphasized. Metagenomics and amplicon-based microbiome profiling provided insights into the potential role of microbial dysbiosis in the development of CRC.

AIM: To address the scarcity of information on differential microbiome composition of tumor tissue in comparison to adenomas and the lack of such data from Egyptian patients with CRC.

MATERIALS AND METHODS: Long-read nanopore sequencing of 16S rRNA amplicons was used to profile the colonic microbiota from fresh colonoscopic biopsy samples of Egyptian patients with CRC and patients with colonic polyps.

RESULTS: Species richness of CRC lesions was significantly higher than that in colonic polyps (p-value = 0.0078), while evenness of the CRC group was significantly lower than the colonic polyps group (p-value = 0.0055). Both species richness and Shannon diversity index of the late onset CRC samples were significantly higher than those of the early onset ones. The Firmicutes-to-Bacteroidetes (F/B) ratio was significantly higher in the CRC group than in the colonic polyps group (p-value = 0.0054), and significantly higher in samples from early-onset CRC. The Enterococcus spp. were significantly overabundant in patients with rectal cancer and early-onset CRC, while Staphylococcus spp. were significantly higher in patients with sigmoid cancer and late-onset CRC. In addition, the relative abundance of Fusobacterium nucleatum was significantly higher in CRC patients.

CONCLUSION: Differentiating trends were identified at phylum, genus, and species levels, despite the inter-individual differences. In summary, this study addressed the microbial dysbiosis associated with CRC and colonic polyps groups, paving the way for a better understanding of the pathogenesis of early and late-onset CRC in Egyptian patients.},
}

@article {pmid39894796,
year = {2025},
author = {Palrasu, M and Kakar, K and Marudamuthu, A and Hamida, H and Thada, S and Zhong, Y and Staley, S and Busbee, PB and Li, J and Garcia-Buitrago, M and Nagarkatti, M and Nagarkatti, P},
title = {AhR Activation Transcriptionally Induces Anti-Microbial Peptide Alpha-Defensin 1 Leading to Reversal of Gut Microbiota Dysbiosis and Colitis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2460538},
doi = {10.1080/19490976.2025.2460538},
pmid = {39894796},
issn = {1949-0984},
mesh = {Animals ; *alpha-Defensins/metabolism/genetics ; *Receptors, Aryl Hydrocarbon/metabolism/genetics ; *Dysbiosis/microbiology ; *Colitis/microbiology/chemically induced/metabolism ; *Gastrointestinal Microbiome ; Mice ; Humans ; Mice, Inbred C57BL ; Crohn Disease/microbiology/metabolism/drug therapy ; Epithelial Cells/metabolism/microbiology ; Intestinal Mucosa/metabolism/microbiology ; Disease Models, Animal ; Male ; Female ; Basic Helix-Loop-Helix Transcription Factors/metabolism/genetics ; },
abstract = {Alpha-defensin 1 is a small antimicrobial peptide that acts as the first line of defense against pathogens. It is induced following microbial cues and inflammatory signals in neutrophils and Paneth cells in the small intestine, which suggests that it plays a role in microbial homeostasis in the gut. The gut microbial products also serve as ligands for the aryl hydrocarbon receptor (AhR), an environmental sensor. In the current study, we investigated if there is any crosstalk between AhR and alpha-defensin 1. Interestingly, we found a positive correlation between AhR and alpha-defensin 1 protein levels in ileal tissues from active Crohn's' (CD) patients and epithelial cells (IECs) from multiple models of murine colitis. In vitro downregulation of AhR led to inhibition of α-defensin 1, while activation of AhR induced α-defensin 1 in IECs. AhR directly targeted the dioxin response element 3 (DRE3) region on the α-defensin 1 promoter in IECs. AhR-mediated induction of α-defensin 1 in colitis mice reversed the gut microbial dysbiosis and alleviated colitis. Our data identify a novel signaling pathway in which AhR acts as a transcription factor for α-defensin 1, leading to regulation of homeostasis between gut microbiota, intestinal mucosa, and mucosal immunity.},
}

Animals
*alpha-Defensins/metabolism/genetics
*Receptors, Aryl Hydrocarbon/metabolism/genetics
*Dysbiosis/microbiology
*Colitis/microbiology/chemically induced/metabolism
*Gastrointestinal Microbiome
Mice
Humans
Mice, Inbred C57BL
Crohn Disease/microbiology/metabolism/drug therapy
Epithelial Cells/metabolism/microbiology
Intestinal Mucosa/metabolism/microbiology
Disease Models, Animal
Male
Female
Basic Helix-Loop-Helix Transcription Factors/metabolism/genetics

@article {pmid39894735,
year = {2025},
author = {Dizman, N and Roberts, M and McQuade, J},
title = {Beyond the Microbiome: The Role of the Metabolome and Diet in Antitumor Immunity.},
journal = {European urology focus},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.euf.2025.01.010},
pmid = {39894735},
issn = {2405-4569},
abstract = {Microbiome-derived or -modulated metabolites (short-chain fatty acids, bile acids, and amino acids) could mediate antitumor immunity. Diet offers an actionable route for manipulating both the microbiome and the metabolome. Diet- and microbiome-directed trials with robust translational correlates are eagerly awaited.},
}

@article {pmid39894724,
year = {2025},
author = {Kleebayoon, A and Wiwanitkit, V},
title = {Effects of Electronic Cigarettes on Oral Microbiome and Metabolome in 3D Tissue-Engineered Models: Comment.},
journal = {International dental journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.identj.2025.01.004},
pmid = {39894724},
issn = {1875-595X},
}

@article {pmid39894593,
year = {2025},
author = {Pack, A},
title = {Developing a Personalized Approach to Obstructive Sleep Apnea.},
journal = {Sleep medicine clinics},
volume = {20},
number = {1},
pages = {127-134},
doi = {10.1016/j.jsmc.2024.10.008},
pmid = {39894593},
issn = {1556-4088},
mesh = {Humans ; *Precision Medicine/methods ; *Sleep Apnea, Obstructive/therapy/diagnosis ; },
abstract = {All areas of medicine are focused on developing a personalized approach to diagnosis and treatment of specific conditions. This is based on the fundamental concept that all subjects with apparently the same disorder are different. There are multiple reasons for these differences. These include differences in the sequence of DNA, differences in the environment, differences in epigenetics, some of which may be driven by environmental differences and differences in the microbiome. These different factors will result in variations in multiple aspects of the phenotype. This includes different pathways to disease, different symptoms, different pattern of comorbidities and risk for adverse outcomes, and different physiological changes during sleep as a result of breathing episodes.},
}

Humans
*Precision Medicine/methods
*Sleep Apnea, Obstructive/therapy/diagnosis

@article {pmid39894225,
year = {2025},
author = {Kim, SY and Woo, SY and Kim, HL and Chang, YS and Ryu, S and Kim, HN},
title = {A shotgun metagenomic study identified short-chain fatty acid-producing species and their functions in the gut microbiome of adults with depressive symptoms: Large-scale shotgun sequencing data of the gut microbiota using a cross-sectional design.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jad.2025.01.149},
pmid = {39894225},
issn = {1573-2517},
abstract = {BACKGROUND: The gut-brain axis is emerging as a novel mechanism to explain depressive disorders.

METHODS: We performed shotgun metagenomic sequencing of stool samples obtained from 133 individuals with depression and 532 without depression. This study examined the taxonomy, functional pathways, and predicted metabolites profiles associated with depressive symptoms, using generalized linear models. To explore links between the taxonomic and functional pathway results, we compared the relative abundance of specific species contributing to pathways significantly associated with depressive symptoms.

RESULTS: Taxonomic composition suggested a disruption in short-chain fatty acid (SCFA)-producing capacity of the gut microbiome in the depressed group. Pathways related to SCFA biosynthesis were also depleted in this group. Faecalibacterium prausnitzii, a well-known SCFA-producing bacterium, was significantly decreased in the depressed group and was identified as a major contributor to the depleted pathways. When inferring the metabolites related to depression from metagenomic data, higher levels of docosapentaenoic acid, stearoyl ethanolamide, putrescine, and bilirubin were more likely to be found in the depressed group.

CONCLUSION: The present findings highlight the altered gut microbiota and associated SCFA-related pathways in individuals with depression. The depletion of F. prausnitzii and its contribution to SCFA production suggest that it is a potential therapeutic target for depression.},
}

@article {pmid39894030,
year = {2025},
author = {The Lancet Microbe, },
title = {Brain microbiome: is it all in our heads?.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101075},
doi = {10.1016/j.lanmic.2025.101075},
pmid = {39894030},
issn = {2666-5247},
}

@article {pmid39893935,
year = {2025},
author = {Luo, Y and Gao, J and Su, X and Li, H and Li, Y and Qi, W and Han, X and Han, J and Zhao, Y and Zhang, A and Zheng, Y and Qian, F and He, H},
title = {Unraveling the immunological landscape and gut microbiome in sepsis: a comprehensive approach to diagnosis and prognosis.},
journal = {EBioMedicine},
volume = {113},
number = {},
pages = {105586},
doi = {10.1016/j.ebiom.2025.105586},
pmid = {39893935},
issn = {2352-3964},
abstract = {BACKGROUND: Comprehensive and in-depth research on the immunophenotype of septic patients remains limited, and effective biomarkers for the diagnosis and treatment of sepsis are urgently needed in clinical practice.

METHODS: Blood samples from 31 septic patients in the Intensive Care Unit (ICU), 25 non-septic ICU patients, and 18 healthy controls were analyzed using flow cytometry for deep immunophenotyping. Metagenomic sequencing was performed in 41 fecal samples, including 13 septic patients, 10 non-septic ICU patients, and 18 healthy controls. Immunophenotype shifts were evaluated using differential expression sliding window analysis, and random forest models were developed for sepsis diagnosis or prognosis prediction.

FINDINGS: Septic patients exhibited decreased proportions of natural killer (NK) cells and plasmacytoid dendritic cells (pDCs) in CD45[+] leukocytes compared with non-septic ICU patients and healthy controls. These changes statistically mediated the association of Bacteroides salyersiae with sepsis, suggesting a potential underlying mechanism. A combined diagnostic model incorporating B.salyersia, NK cells in CD45[+] leukocytes, and C-reactive protein (CRP) demonstrated high accuracy in distinguishing sepsis from non-sepsis (area under the receiver operating characteristic curve, AUC = 0.950, 95% CI: 0.811-1.000). Immunophenotyping and disease severity analysis identified an Acute Physiology and Chronic Health Evaluation (APACHE) II score threshold of 21, effectively distinguishing mild (n = 19) from severe (n = 12) sepsis. A prognostic model based on the proportion of total lymphocytes, Helper T (Th) 17 cells, CD4[+] effector memory T (TEM) cells, and Th1 cells in CD45[+] leukocytes achieved robust outcome prediction (AUC = 0.906, 95% CI: 0.732-1.000), with further accuracy improvement when combined with clinical scores (AUC = 0.938, 95% CI: 0.796-1.000).

INTERPRETATION: NK cell subsets within innate immunity exhibit significant diagnostic value for sepsis, particularly when combined with B. salyersiae and CRP. In addition, T cell phenotypes within adaptive immunity are correlated with sepsis severity and may serve as reliable prognostic markers.

FUNDING: This project was supported by the National Key R&D Program of China (2023YFC2307600, 2021YFA1301000), Shanghai Municipal Science and Technology Major Project (2023SHZDZX02, 2017SHZDZX01), Shanghai Municipal Technology Standards Project (23DZ2202600).},
}

@article {pmid39893882,
year = {2025},
author = {Xia, F and Fan, T and Wang, M and Yang, L and Ding, D and Wei, J and Zhou, Y and Jiang, D and Deng, S},
title = {Biodegradation of CAHs and BTEX in groundwater at a multi-polluted pesticide site undergoing natural attenuation: Insights from identifying key bioindicators using machine learning methods based on microbiome data.},
journal = {Ecotoxicology and environmental safety},
volume = {291},
number = {},
pages = {117609},
doi = {10.1016/j.ecoenv.2024.117609},
pmid = {39893882},
issn = {1090-2414},
abstract = {Groundwater pollution, particularly in retired pesticide sites, is a significant environmental concern due to the presence of chlorinated aliphatic hydrocarbons (CAHs) and benzene, toluene, ethylbenzene, and xylene (BTEX). These contaminants pose serious risks to ecosystems and human health. Natural attenuation (NA) has emerged as a sustainable solution, with microorganisms playing a crucial role in pollutant biodegradation. However, the interpretation of the diverse microbial communities in relation to complex pollutants is still challenging, and there is limited research in multi-polluted groundwater. Advanced machine learning (ML) algorithms help identify key microbial indicators for different pollution types (CAHs, BTEX plumes, and mixed plumes). The accuracy and Area Under the Curve (AUC) achieved by Support Vector Machines (SVM) were impressive, with values of 0.87 and 0.99, respectively. With the assistance of model explanation methods, we identified key bioindicators for different pollution types which were then analyzed using co-occurrence network analysis to better understand their potential roles in pollution degradation. The identified key genera indicate that oxidation and co-metabolism predominantly drive dechlorination processes within the CAHs group. In the BTEX group, the primary mechanism for BTEX degradation was observed to be anaerobic degradation under sulfate-reducing conditions. However, in the CAHs&BTEX groups, the indicative genera suggested that BTEX degradation occurred under iron-reducing conditions and reductive dechlorination existed. Overall, this study establishes a framework for harnessing the power of ML alongside co-occurrence network analysis based on microbiome data to enhance understanding and provide a robust assessment of the natural attenuation degradation process at multi-polluted sites.},
}

@article {pmid39893588,
year = {2025},
author = {Ha, S and Kim, J and Seo, HW and Kim, L and Yi, YS and Seo, SE and Kim, KH and Kim, S and An, JE and Kim, GJ and Ko, KC and Jun, S and Ryu, CM and Kwon, OS},
title = {Siderophore-Functionalized Nanodrug for Treating Antibiotic-Resistant Bacteria.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.4c06501},
pmid = {39893588},
issn = {1936-086X},
abstract = {The development of nanodrugs targeting multidrug-resistant bacteria, while sparing the beneficial constituents of the microbiome, has emerged as a promising approach to combat disease and curb the rise of antimicrobial resistance. In this investigation, we devised a siderophore-functionalized nanodrug based on a gold nanoparticle construct (AuNP-NSC; Gold nanoparticle_N-heterocyclic_Siderophore_Cyanine7), offering an innovative treatment modality against drug-resistant bacterial pathogens. As a proof of concept, the efficacy of this nanodrug delivery and antimicrobial therapy was evaluated against the notoriously resistant bacterium P. aeruginosa. N-Heterocyclic carbenes (NHCs) exhibit a strong affinity for transition metals, forming highly stable complexes resistant to ligand displacement. The entry of siderophore-conjugated nanodrugs into bacteria is facilitated through specific receptors on the outer membrane. In our study, AuNP-NSC was specifically targeted and imported into resistant Gram-negative P. aeruginosa via binding with ferric iron. Treatment with the developed nanodrug significantly inhibited the proliferation of antibiotic-resistant P. aeruginosa, reducing bacterial counts by more than 95% and mitigating drug resistance. Furthermore, AuNP-NSC markedly diminished P. aeruginosa-induced skin lesions and forestalled systemic organ failure triggered by secondary sepsis in mouse models. These findings underscore the potential of nanodrugs as specialized therapeutic agents for the management of antibiotic-resistant bacterial infections.},
}

@article {pmid39893498,
year = {2025},
author = {Zhao, H and Zhou, X and Song, Y and Zhao, W and Sun, Z and Zhu, J and Yu, Y},
title = {Multi-omics analyses identify gut microbiota-fecal metabolites-brain-cognition pathways in the Alzheimer's disease continuum.},
journal = {Alzheimer's research & therapy},
volume = {17},
number = {1},
pages = {36},
pmid = {39893498},
issn = {1758-9193},
support = {YJS20230012//Postgraduate Innovation Research and Practice Program of Anhui Medical University/ ; 82471952//National Natural Science Foundation of China/ ; 82371928//National Natural Science Foundation of China/ ; 2308085MH277//Anhui Provincial Natural Science Foundation/ ; 2022AH051135//Scientific Research Key Project of Anhui Province Universities/ ; 2022xkj143//Scientific Research Foundation of Anhui Medical University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Alzheimer Disease/metabolism/microbiology/diagnostic imaging/pathology ; Male ; Aged ; Female ; *Cognitive Dysfunction/metabolism/microbiology/diagnostic imaging ; *Feces/microbiology ; *Magnetic Resonance Imaging/methods ; Brain/metabolism/diagnostic imaging/pathology ; Cognition/physiology ; Dysbiosis/metabolism ; Metabolomics/methods ; Aged, 80 and over ; Middle Aged ; Metabolome ; Multiomics ; },
abstract = {BACKGROUND: Gut microbiota dysbiosis is linked to Alzheimer's disease (AD), but our understanding of the molecular and neuropathological bases underlying such association remains fragmentary.

METHODS: Using 16S rDNA amplicon sequencing, untargeted metabolomics, and multi-modal magnetic resonance imaging, we examined group differences in gut microbiome, fecal metabolome, neuroimaging measures, and cognitive variables across 30 patients with AD, 75 individuals with mild cognitive impairment (MCI), and 61 healthy controls (HC). Furthermore, we assessed the associations between these multi-omics changes using correlation and mediation analyses.

RESULTS: There were significant group differences in gut microbial composition, which were driven by 8 microbial taxa (e.g., Staphylococcus and Bacillus) exhibiting a progressive increase in relative abundance from HC to MCI to AD, and 2 taxa (e.g., Anaerostipes) showing a gradual decrease. 26 fecal metabolites (e.g., Arachidonic, Adrenic, and Lithocholic acids) exhibited a progressive increase from HC to MCI to AD. We also observed progressive gray matter atrophy in broadly distributed gray matter regions and gradual micro-structural integrity damage in widespread white matter tracts along the AD continuum. Integration of these multi-omics changes revealed significant associations between microbiota, metabolites, neuroimaging, and cognition. More importantly, we identified two potential mediation pathways: (1) microbiota → metabolites → neuroimaging → cognition, and (2) microbiota → metabolites → cognition.

CONCLUSION: Aside from elucidating the underlying mechanism whereby gut microbiota dysbiosis is linked to AD, our findings may contribute to groundwork for future interventions targeting the microbiota-metabolites-brain-cognition pathways as a therapeutic strategy in the AD continuum.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Alzheimer Disease/metabolism/microbiology/diagnostic imaging/pathology
Male
Aged
Female
*Cognitive Dysfunction/metabolism/microbiology/diagnostic imaging
*Feces/microbiology
*Magnetic Resonance Imaging/methods
Brain/metabolism/diagnostic imaging/pathology
Cognition/physiology
Dysbiosis/metabolism
Metabolomics/methods
Aged, 80 and over
Middle Aged
Metabolome
Multiomics

@article {pmid39893452,
year = {2025},
author = {Pilmer, L and Woolley, L and Lymbery, A and Dam, C and Elizur, A and Foysal, MJ and Partridge, G},
title = {Exploring single cell microbial protein as a sustainable fishmeal alternative in yellowtail kingfish (Seriola lalandi) diets: impacts on health and gut microbiome.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {16},
pmid = {39893452},
issn = {1674-9782},
support = {2017-030//Fisheries Research and Development Corporation/ ; },
abstract = {BACKGROUND: With the global expansion of aquaculture and the increasing demand for fish meal, identifying appropriate and sustainable alternative protein sources for aquafeeds has become essential. Single-cell protein (SCP), derived from methanotrophic bacteria, presents a promising alternative by converting methane into protein, potentially addressing both the need for alternative protein sources and reducing industrial greenhouse gas emissions. This study aimed to evaluate the effects of different levels of SCP inclusion (0%, 25%, 50%, and 75% fish meal replacement) on the health, gene expression, and gut microbiome of yellowtail kingfish (YTK, Seriola lalandi) following a 35-day growth trial.

RESULTS: The study found that SCP inclusion at the highest level of fishmeal replacement (75%) induced a mild inflammatory response in the hindgut of the fish. However, micromorphological assessments of the hindgut, serum biochemistry, and gene expression analyses revealed no significant detrimental effects from SCP replacement. Notably, there were indications of improved lipid digestibility with SCP. Furthermore, SCP inclusion significantly enhanced microbial richness and altered the composition of the gut microbiome, introducing beneficial bacterial taxa that may contribute to improved gut health and resilience.

CONCLUSIONS: This study highlights SCP as a viable and sustainable alternative to fish meal in YTK diets. The findings suggest that SCP can be included in YTK diets without adverse health effects at moderate levels and may even offer benefits in terms of lipid digestibility and gut microbiome diversity. These results contribute to the advancement of more sustainable aquaculture practices.},
}

@article {pmid39893273,
year = {2025},
author = {Coelho, C and Martins, LO and Tiago, I},
title = {Isolation of lignocellulosic biomass-degrading bacteria from Porcellio dilatatus gut-enriched cultures.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {35},
pmid = {39893273},
issn = {1432-0614},
support = {SFRH/BD/148270/2019//Fundação para a Ciência e a Tecnologia/ ; IF/01061/2014/CP1223/CT0004//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {*Lignin/metabolism ; Animals ; *Bacteria/metabolism/classification/isolation & purification/genetics ; *Gastrointestinal Microbiome ; *Biomass ; Biodegradation, Environmental ; Isopoda/microbiology/metabolism ; Chitin/metabolism ; Microbial Consortia ; },
abstract = {The lignocellulosic biomass (LCB) is an attractive, sustainable, and environmentally friendly alternative to fossil sources to produce biofuel, biomaterials, and biochemicals. However, its recalcitrant and heterogenous structure challenges its biodegradation and valorization. The gut microbiome of soil invertebrate species has emerged as a rich source of LCB-degrading bacteria and enzymes in terrestrial ecosystems. The primary objective of this investigation was to identify the bacterial communities within the Porcellio dilatatus gut (Crustacea: Isopods), to obtain enriched cultures, and to identify bacterial isolates with LCB-degrading activity. A total of 112 enriched cultures were screened, all exhibiting xylanolytic activity. Among them, 94 displayed cellulolytic activity, 30 showed chitinolytic activity, and 21 demonstrated ligninolytic activity. Four enriched cultures were selected, and 128 bacteria with cellulolytic, xylanolytic, chitinolytic, or ligninolytic activity were isolated and taxonomically classified. The obtained results reinforce the potential of bacterial communities within the digestive tract of soil invertebrates as a valuable source of lignocellulose-degrading microorganisms. Thirty-one isolates underwent in-depth enzymatic characterization, and five were selected and functionally evaluated. An artificial bacterial consortium was constructed to assess the potential benefits of using consortia to achieve enhanced LCB degradation. The positive results of this proof-of-concept artificial consortium (PdG-AC) can be used in future applications and is a valuable tool for enzymatic and microbial consortia engineering by, e.g., changing growth conditions for enhanced LCB-degrading abilities. KEY POINTS: • The gut microbiome of Porcellio dilatatus was characterized. • Porcellio dilatatus gut hosts many lignocellulose-degrading bacteria. • Developed an artificial bacterial consortium for lignocellulose degradation.},
}

*Lignin/metabolism
Animals
*Bacteria/metabolism/classification/isolation & purification/genetics
*Gastrointestinal Microbiome
*Biomass
Biodegradation, Environmental
Isopoda/microbiology/metabolism
Chitin/metabolism
Microbial Consortia

@article {pmid39893166,
year = {2025},
author = {Bourquin, M and Peter, H and Michoud, G and Busi, SB and Kohler, TJ and Robison, AL and Styllas, M and Ezzat, L and Geers, AU and Huss, M and Fodelianakis, S and , and Battin, TJ},
title = {Predicting climate-change impacts on the global glacier-fed stream microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1264},
pmid = {39893166},
issn = {2041-1723},
mesh = {*Microbiota/genetics ; *Ice Cover/microbiology ; *Climate Change ; *Phylogeny ; *Bacteria/genetics/classification ; *Rivers/microbiology ; Metagenome ; Biodiversity ; Ecosystem ; },
abstract = {The shrinkage of glaciers and the vanishing of glacier-fed streams (GFSs) are emblematic of climate change. However, forecasts of how GFS microbiome structure and function will change under projected climate change scenarios are lacking. Combining 2,333 prokaryotic metagenome-assembled genomes with climatic, glaciological, and environmental data collected by the Vanishing Glaciers project from 164 GFSs draining Earth's major mountain ranges, we here predict the future of the GFS microbiome until the end of the century under various climate change scenarios. Our model framework is rooted in a space-for-time substitution design and leverages statistical learning approaches. We predict that declining environmental selection promotes primary production in GFSs, stimulating both bacterial biomass and biodiversity. Concomitantly, predictions suggest that the phylogenetic structure of the GFS microbiome will change and entire bacterial clades are at risk. Furthermore, genomic projections reveal that microbiome functions will shift, with intensified solar energy acquisition pathways, heterotrophy and algal-bacterial interactions. Altogether, we project a 'greener' future of the world's GFSs accompanied by a loss of clades that have adapted to environmental harshness, with consequences for ecosystem functioning.},
}

*Microbiota/genetics
*Ice Cover/microbiology
*Climate Change
*Phylogeny
*Bacteria/genetics/classification
*Rivers/microbiology
Metagenome
Biodiversity
Ecosystem

@article {pmid39893159,
year = {2025},
author = {Sampson, TR and Wallen, ZD and Won, WJ and Standaert, DG and Payami, H and Harms, AS},
title = {Alpha synuclein overexpression can drive microbiome dysbiosis in mice.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {4014},
pmid = {39893159},
issn = {2045-2322},
support = {ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-000375//Aligning Science Across Parkinson's/ ; },
mesh = {Animals ; *alpha-Synuclein/metabolism/genetics ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Mice ; *Mice, Transgenic ; *Parkinson Disease/microbiology/metabolism/genetics ; Disease Models, Animal ; Humans ; Aging ; Male ; },
abstract = {Growing evidence indicates that persons with Parkinson disease (PD), have a unique composition of indigenous gut microbes. Given the long prodromal or pre-diagnosed period, longitudinal studies of the human and rodent gut microbiome before symptomatic onset and for the duration of the disease are currently lacking. PD is partially characterized by the accumulation of the protein α-synuclein (α-syn) into insoluble aggregates, in both the central and enteric nervous systems. As such, several experimental rodent and non-human primate models of α-syn overexpression recapitulate some of the hallmark pathophysiologies of PD. These animal models provide an opportunity to assess how the gut microbiome changes with age under disease-relevant conditions. Here, we used a transgenic mouse strain, which overexpress wild-type human α-syn to test how the gut microbiome composition responds in this model of PD pathology during aging. Using shotgun metagenomics, we find significant, age and genotype-dependent bacterial taxa whose abundance becomes altered with age. We reveal that α-syn overexpression can drive alterations to the gut microbiome composition and suggest that it limits diversity through age. Taxa that were most affected by genotype-age interaction were Lactobacillus and Bifidobacteria. In a mouse model, we showed direct link between alpha synuclein geneotype (hallmark of PD), a dysbiotic and low-diversity gut microbiome, and dysbiotic levels of Bifidobacteria and Lactobacillus (most robust features of PD microbiome). Given emerging data on the potential contributions of the gut microbiome to PD pathologies, our data provide an experimental foundation to understand how the PD-associated microbiome may arise as a trigger or co-pathology to disease.},
}

Animals
*alpha-Synuclein/metabolism/genetics
*Dysbiosis/microbiology
*Gastrointestinal Microbiome
Mice
*Mice, Transgenic
*Parkinson Disease/microbiology/metabolism/genetics
Disease Models, Animal
Humans
Aging
Male

@article {pmid39892949,
year = {2025},
author = {McGann, C and Phyu, R and Bittinger, K and Mukhopadhyay, S},
title = {Role of the Microbiome in Neonatal Infection: Pathogenesis and Implications for Management.},
journal = {Clinics in perinatology},
volume = {52},
number = {1},
pages = {147-166},
doi = {10.1016/j.clp.2024.10.010},
pmid = {39892949},
issn = {1557-9840},
mesh = {Humans ; Infant, Newborn ; *Probiotics/therapeutic use ; *Gastrointestinal Microbiome ; *Anti-Bacterial Agents/therapeutic use ; *Fecal Microbiota Transplantation/methods ; Neonatal Sepsis/microbiology/therapy ; Microbiota ; },
abstract = {The human microbiome refers to the collective genome of microorganisms, including bacteria, fungi, and viruses residing on human body surfaces that are in contact with the environment. Together these communities protect against invasive infections. Conversely, when disrupted, the microbiome can be the source of pathogens causing invasive infection. Interventions to manipulate it via probiotics, antibiotics, and fecal transplantation are available. The risk benefit of these interventions remains unclear. In this review, the authors discuss evidence linking the gut microbiome to neonatal sepsis and also discuss the challenges for translating this knowledge into better clinical care.},
}

Humans
Infant, Newborn
*Probiotics/therapeutic use
*Gastrointestinal Microbiome
*Anti-Bacterial Agents/therapeutic use
*Fecal Microbiota Transplantation/methods
Neonatal Sepsis/microbiology/therapy
Microbiota

@article {pmid39892863,
year = {2025},
author = {Toffoli, M and Campisciano, G and Santin, A and Pegoraro, S and Zito, G and Spedicati, B and Balduit, A and Romano, F and Di Lorenzo, G and Mangogna, A and Tesolin, P and Nardone, GG and Zanotta, N and Sanna, S and Corbu, F and Kishore, U and Ricci, G and Bulla, R and Girotto, G and Agostinis, C},
title = {A possible association between low MBL/lectin pathway functionality and microbiota dysbiosis in endometriosis patients.},
journal = {Life sciences},
volume = {},
number = {},
pages = {123427},
doi = {10.1016/j.lfs.2025.123427},
pmid = {39892863},
issn = {1879-0631},
abstract = {AIMS: Endometriosis (EM) is a chronic inflammatory disorder with multifactorial etiologies (i.e., genetics and environmental factors, hormonal and immunological changes, and microbiome alterations). The complement system is one of the most frequently dysregulated pathways in EM. Mannose-binding lectin (MBL), a carbohydrate pattern recognition molecule, is the first described recognition subcomponent of the complement lectin pathway (LP). Here, we unveiled the interplay among MBL polymorphisms, plasma levels, LP functionality, and microbiota as potential contributors to EM pathogenesis.

MATERIALS AND METHODS: A cohort of 38 EM patients and 20 healthy controls was enrolled and the levels and functionality of the lectin pathway were assessed via ELISA assays. MBL genetic variants and the endometrial and vaginal microbiome were investigated and correlated.

KEY FINDINGS: High MBL levels were related to the disease severity, although not accountable to the MBL2 genotype. MBL and MASP-2 were present in the uterine mucosa but appeared to have no function at the endometriotic lesion. EM patients with LP functional deficit displayed pathogenic bacterial species more frequently in the endometrial microbiome. Moreover, women affected by EM showed a higher frequency of rare gene variants in the estrogen pathway genes, potentially affecting MBL plasma levels.

SIGNIFICANCE: A lower functionality of LP in the uterine mucosa may contribute to an unbalanced bacterial environment that could activate endometrial cells. Not only the genotype and the inflammatory condition, but also the estrogen pathway can cause altered MBL levels, thus contributing to changes in the LP functionality.},
}

@article {pmid39892390,
year = {2025},
author = {Zhang, Y and Luo, K and Peters, BA and Mossavar-Rahmani, Y and Moon, JY and Wang, Y and Daviglus, ML and Van Horn, L and McClain, AC and Cordero, C and Floyd, JS and Yu, B and Walker, RW and Burk, RD and Kaplan, RC and Qi, Q},
title = {Sugar-sweetened beverage intake, gut microbiota, circulating metabolites, and diabetes risk in Hispanic Community Health Study/Study of Latinos.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2024.12.004},
pmid = {39892390},
issn = {1932-7420},
abstract = {No population-based studies examined gut microbiota and related metabolites associated with sugar-sweetened beverage (SSB) intake among US adults. In this cohort of US Hispanic/Latino adults, higher SSB intake was associated with nine gut bacterial species, including lower abundances of several short-chain-fatty-acid producers, previously shown to be altered by fructose and glucose in animal studies, and higher abundances of fructose- and glucose-utilizing Clostridium bolteae and Anaerostipes caccae. Fifty-six serum metabolites were correlated with SSB intake and a gut microbiota score based on these SSB-related species in consistent directions. These metabolites were clustered into several modules, including a glycerophospholipid module, two modules comprising branched-chain amino acid (BCAA) and aromatic amino acid (AAA) derivatives from microbial metabolism, etc. Higher glycerophospholipid and BCAA derivative levels and lower AAA derivative levels were associated with higher incident diabetes risk during follow-up. These findings suggest a potential role of gut microbiota in the association between SSB intake and diabetes.},
}

@article {pmid39892258,
year = {2025},
author = {Contos, P and Gibb, H and Murphy, NP and Jellinek, S and Wood, JL},
title = {Rebuilding microbiomes: Facilitating animal-microbe interactions through ecological restoration and rewilding.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124344},
doi = {10.1016/j.jenvman.2025.124344},
pmid = {39892258},
issn = {1095-8630},
abstract = {Restoring degraded ecosystems is a complex process that involves rebuilding myriad species interactions that make a functioning ecological community. Microorganisms are key to robust ecological restoration - their mutualisms with above-ground communities drive community assembly and increase host fitness. However, microbes are largely ignored during restoration and there is a significant knowledge gap regarding how to restore their interactions with above-ground communities. Here, we tested whether we could enhance interactions between microbes and their invertebrate hosts by reintroducing, or 'rewilding', leaf litter and soil from remnant sites containing species-rich microbial communities, into species poor and geographically isolated revegetated farmland sites. We sequenced both the soil microbiome and the gut microbiome of two dominant invertebrates: native Ecnolagria grandis beetles and introduced Ommatoiulus moreleti millipedes. We sampled 35 months after the initial reintroduction event in remnant (conservation area and source of litter and soil transplant), rewilding transplant (revegetation site with transplant), and control sites (revegetation with no transplant). We found that even ∼20 years after revegetation, restoration sites had distinct microbial communities compared to remnant areas. Although litter and soil transplants failed to increase soil microbial community similarity towards remnant sites, we found marked increases in the diversity and richness of E. grandis microbiomes and a greater degree of overlap with soil microbiomes within rewilding transplant sites relative to control sites. In contrast, there were few changes in O. moreleti microbiomes. Overall, our results suggest rewilding can recover some species interactions during restoration but may not influence all host-microbe systems.},
}

@article {pmid39892243,
year = {2025},
author = {Mootapally, C and Sharma, P and Dash, S and Kumar, M and Sharma, S and Kothari, R and Nathani, N},
title = {Microbial drivers of biogeochemical cycles in deep sediments of the Kathiawar Peninsula Gulfs of India.},
journal = {The Science of the total environment},
volume = {965},
number = {},
pages = {178609},
doi = {10.1016/j.scitotenv.2025.178609},
pmid = {39892243},
issn = {1879-1026},
abstract = {Deep marine sediments are rich in microbial diversity, which holds metabolic repertoire to modulate biogeochemical cycles on a global scale. We undertook the environmental microbiome inhabiting the Gulf of Kathiawar Peninsula as a model system to understand the potential involvement of the deep marine sediment microbial community and as a cohort in the carbon, nitrogen, and sulfur biogeochemical cycles. These gulfs are characterized by dynamic tidal variations, diverse sediment textures, and nutrient-rich waters, driven by coastal processes and the interaction between natural coastal dynamics and anthropogenic inputs that shape its microbial community diversity. Our findings suggest that carbon fixation was carried out by Gamma-proteobacteria with CBB cycle-related genes or by microbial participants with Wood-Ljungdahl pathway-related genes. Microbial communities involved in nitrogen metabolism were observed to be rich and diverse, and most microbial communities potentially contribute to the nitrogen cycle via processing nitrogen oxides. Bacteria belonging to the KSB1 phylum were also found to fix nitrogen. The sulfur cycle was spread throughout, with Verrucomicrobiota phylum being a major contributor. The varying napAB genes, significantly lower in the Gulf of Kutch compared to the Gulf of Cambay and the Arabian Sea, mediated nitrate reduction. Dynamics between these pathways were mutually exclusive, and organic carbon oxidation was widespread across the microbial community. Finally, the proteobacteria phylum was highly versatile and conceivably contributed to biogeochemical flux with exceptionally high abundance and the ability to form metabolic networks to survive. The work highlights the importance of critical zones and microbial diversity therein, which needs further exploration.},
}

@article {pmid39892234,
year = {2025},
author = {Nguyen, TBH and Henri-Sanvoisin, A and Le Floch, G and Picot, A},
title = {Delving into the soil and phytomicrobiome for disease suppression: A case study for the control of Fusarium Head Blight of cereals.},
journal = {The Science of the total environment},
volume = {965},
number = {},
pages = {178655},
doi = {10.1016/j.scitotenv.2025.178655},
pmid = {39892234},
issn = {1879-1026},
abstract = {Fusarium Head Blight is one of the most devastating fungal diseases of cereals worldwide, causing significant yield losses and affecting grain quality. The predominant role of the interactions within the Fusarium communities as well as with members of the phytomicrobiome in disease onset and development has gained increasing attention. Understanding the diversity and dynamics of bacterial and fungal communities across different substrates colonized by Fusarium spp. in wheat fields can provide valuable insights into disease ecology and lead to the discovery of native microorganisms with biocontrol potential. In this study, the bacterial and fungal communities associated with soil, maize residues, and wheat grains, were studied based on metabarcoding sequencing of 16S rRNA and ITS2 regions in six wheat fields over two years and characterized by different levels of FHB disease pressure and mycotoxin contamination. Overall, the diversity and composition of microbial communities were primarily influenced by substrate type followed by geographic origins of fields and sampling time, notably for grains and residues while the soil microbiome was less impacted by environmental fluctuations. Notably, our findings suggest that crop residues function as a transient substrate between soil and wheat microbiomes. In addition, we found several taxa either strongly negatively correlated to Fusarium spp. and/or to levels of Fusarium DNA or mycotoxins in grains or residues, including Cladosporium, Epicoccum, Paenibacillus, Curtobacterium, Pseudomonas, Pantoea, and Sphingomonas, which could be potential antagonistic agents against Fusarium spp. Altogether, these findings provide novel insights into the field microbiome functioning and their complex interactions with the Fusarium communities.},
}

@article {pmid39892168,
year = {2025},
author = {Zha, H and Li, S and Zhuge, A and Shen, J and Yao, Y and Chang, K and Li, L},
title = {Hazard assessment of airborne and foodborne biodegradable polyhydroxyalkanoates microplastics and non-biodegradable polypropylene microplastics.},
journal = {Environment international},
volume = {196},
number = {},
pages = {109311},
doi = {10.1016/j.envint.2025.109311},
pmid = {39892168},
issn = {1873-6750},
abstract = {Microplastics (MP) are ubiquitous in the environment, and are toxic to various living organisms. Proper application of biodegradable plastics may alleviate the hazards of conventional non-biodegradable plastics. In the current study, multi-omics analyses were performed to compare the biodegradable polyhydroxyalkanoates (PHA) and non-biodegradable polypropylene (PP) MP for their toxicity on mouse liver and lung. Airborne PHA MP induced nasal microbiome dysbiosis, pulmonary microbiome alteration, pulmonary and serum metabolome disruption, and hepatic transcriptome disturbances, resulting in mild pulmonary toxicity. By contrast, airborne PP MP caused greater alterations in nasal and pulmonary microbiome, pulmonary and serum metabolome, and hepatic transcriptome, resulting in pulmonary and hepatic toxicity. Both foodborne PHA and PP MP caused intestinal microbiome dysbiosis, while foodborne PHA MP caused slighter intestinal and serum metabolome disruption, hepatic transcriptome disturbances and hepatotoxicity (e.g., lower serum aspartate aminotransferase and alanine aminotransferase) compared to foodborne PP MP. Some potential differential biomarkers were determined between PP and PHA MP exposures, i.e., nasal Allobaculum and pulmonary Alloprevotella for airborne PHA; nasal Lactobacillus and pulmonary Acinetobacter for airborne PP; intestinal Faecalibacterium for foodborne PHA; and intestinal unclassified_Erysipelatoclostridiaceae for foodborne PP. The results show that PHA MP can induce less pulmonary and hepatic toxicity compared to PP MP, suggesting PHA is a potential substitution for PP. The findings can benefit the hazard assessment of airborne and foodborne PHA and PP MP.},
}

@article {pmid39892121,
year = {2025},
author = {Scairati, R and Auriemma, RS and Del Vecchio, G and Di Meglio, S and Pirchio, R and Graziadio, C and Pivonello, R and Colao, A},
title = {Diabetes mellitus, vaginal microbiome and sexual function: Outcomes in postmenopausal women.},
journal = {Maturitas},
volume = {194},
number = {},
pages = {108210},
doi = {10.1016/j.maturitas.2025.108210},
pmid = {39892121},
issn = {1873-4111},
abstract = {Diabetes mellitus is a chronic disease and a public health challenge worldwide, associated with numerous complications, including genitourinary infections and sexual dysfunction in women, particularly in menopause. The vaginal microbiome, which comprises beneficial and pathogenic bacteria, their genomes, and the surrounding environment, plays a crucial role in maintaining genitourinary health. Chronic hyperglycemia disrupts immune functions, exacerbates oxidative stress, and alters the vaginal microbiome, increasing the risk of genitourinary infections. Recent advances in microbial analysis, including 16S rRNA sequencing, have provided insights into the complex composition of the vaginal microbiome and its dysbiosis in diabetes mellitus. Some glucose-lowering drugs, such as sodium-glucose cotransporter 2 inhibitors, may increase the risk of genitourinary infections. Additionally, psychological distress, hormonal imbalances, and diabetes-related genitourinary symptoms contribute to sexual dysfunction in diabetic women. Healthcare for diabetic women requires a multidisciplinary approach, including not only glycemic control but also vaginal and sexual health assessment. A holistic approach is essential to advance personalized strategies, including medications and psychological support.},
}

@article {pmid39892071,
year = {2025},
author = {Amirbekov, A and Vrchovecká, S and Říha, J and Wacławek, S and Ševců, A and Hrabák, P},
title = {Synergistic effect of Alnus glutinosa saplings and rhizosphere microorganisms on organochlorine pesticides remediation in contaminated soil.},
journal = {Chemosphere},
volume = {373},
number = {},
pages = {144174},
doi = {10.1016/j.chemosphere.2025.144174},
pmid = {39892071},
issn = {1879-1298},
abstract = {The widespread use of hexachlorocyclohexanes (HCH) as pesticides has raised environmental concerns due to their persistence and toxicity. Addressing the pressing need for effective bioremediation strategies, this study explores the effects of α-, β-, δ-, and ε-HCH isomers on the growth, hormonal changes, physiological parameters and bioaccumulation in Alnus glutinosa saplings (1-year-old and 2-year-old) and bacterial communities in polluted soil. A. glutinosa saplings not only withstanded HCH exposure but also enhanced the remediation efficiency by 6.8-24.4%, suggesting an acceleration of pollutant breakdown likely mediated by root exudates positively affecting the soil microbiome. Interestingly, 1-year-old saplings demonstrated greater remediation efficiency post-pruning than unpruned 2-year-old saplings, despite the latter having a larger root biomass. The hormonal analysis indicated that HCH presence led to a reduction in abscisic acid (ABA) and an increase in jasmonic acid (JA), with the magnitude of changes being age-dependent. Salicylic acid (SA) levels increased 1-year-old and decreased in 2-year-old saplings under HCH stress. Moreover, a higher presence of lin-degrading genes in the rhizosphere of treated saplings compared to controls confirmed ongoing biodegradation processes. The outcomes help to better understand the processes involved in degradation of persistent pesticides in soil. The mechanism of in-plant isomerization and the identification of metabolites should be the focus of future research.},
}

@article {pmid39891374,
year = {2025},
author = {Mohamed-Ahmed, R and Robinson, D},
title = {Up-and-coming pharmacotherapeutic options for treating patients with refractory overactive bladder.},
journal = {Expert opinion on pharmacotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14656566.2025.2458577},
pmid = {39891374},
issn = {1744-7666},
abstract = {INTRODUCTION: Overactive bladder (OAB) is a prevalent disorder with a significant impact on quality of life. The pathophysiology of OAB is multifactorial and the majority of patients will require treatment with multiple therapies across the course of their disease. First line treatments include bladder retraining, fluid advice and pelvic floor muscle training. Following this, patients may be offered treatment with anticholinergic and β3 agonist medications. Anticholinergics are known to have high rates of discontinuation due to side effects and there are concerns regarding anticholinergic load and its impact on cognitive function in older adults.

AREAS COVERED: This paper aims to discuss the current and emerging treatment options available for patients who suffer from OAB.

EXPERT OPINION: The management of OAB in the clinical setting remains challenging. The goal of newer pharmacotherapies in OAB would be treatment that provides long term symptomatic relief with minimal side effects and an improved quality of life. The future of OAB research is promising and should consider the implications of the gut-bladder axis, regenerative medicine, biomarkers and the role of digital health.},
}

@article {pmid39891234,
year = {2025},
author = {Noble, AS and Abbaszadeh, J and Lee, CK},
title = {Host selection is not a universal driver of phyllosphere community assembly among ecologically similar native New Zealand plant species.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {35},
pmid = {39891234},
issn = {2049-2618},
mesh = {New Zealand ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; Plants/microbiology/classification ; Phylogeny ; },
abstract = {BACKGROUND: A growing body of evidence demonstrates that host-associated microbial communities of plant leaf surfaces (i.e. the phyllosphere) can influence host functional traits. However, it remains unclear whether host selection is a universal driver of phyllosphere community assembly. We targeted mānuka (Leptospermum scoparium) and three neighbouring non-mānuka plant species along an 1800-m transect in a New Zealand native bush to conduct a hypothesis-driven investigation of the relative influence of host species identity and stochastic dispersal on the composition of natural phyllosphere bacterial communities.

RESULTS: We detected significant correlations between host species identity and mānuka phyllosphere communities that are consistent with a dominant role of host selection in the assembly of the mānuka phyllosphere microbiome. In contrast, the phyllosphere community compositions of neighbouring, ecologically similar native plants were highly variable, suggesting that stochastic processes, such as dispersal, had a stronger influence on the phyllosphere microbiomes of those non-mānuka plants compared to the phyllosphere microbiome of mānuka. Furthermore, the distribution of phyllosphere taxa among plant species was congruent with a scenario in which microorganisms had dispersed from mānuka to non-mānuka phyllosphere microbiomes.

CONCLUSIONS: We conclude that host selection of phyllosphere communities is not and should not be presumed to be a universal trait across plant species. The specificity of the mānuka phyllosphere microbiome suggests the presence of functionally significant bacteria that are under direct, possibly chemically mediated, selection by the host. Furthermore, we propose that phyllosphere microbiomes under strong host selection, such as that of mānuka, may act as a source of microorganisms for the phyllosphere microbiomes of neighbouring plants. Video Abstract.},
}

New Zealand
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Plant Leaves/microbiology
RNA, Ribosomal, 16S/genetics
Plants/microbiology/classification
Phylogeny

@article {pmid39891232,
year = {2025},
author = {Wulczynski, M and Brooks, SPJ and Green, J and Matias, F and Kalmokoff, M and Green-Johnson, JM and Clarke, ST},
title = {Environmental enrichment with nylon gnaw sticks introduces variation in Sprague Dawley rat immune and lower gastrointestinal parameters with differences between sexes.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {12},
pmid = {39891232},
issn = {2524-4671},
support = {SPJB//A-base funding at Health Canada/ ; RGPIN-2017-05237//Natural Sciences and Engineering Research Council of Canada Grant/ ; },
abstract = {BACKGROUND: Environmental enrichment (EE) is commonly included as an important component of animal housing to promote well being of laboratory animals; however, much remains to be learned about the impact of chewable forms of EE on experimental outcomes in the context of nutritional and microbiome-related studies, and whether outcomes differ between sexes. In the present study, nylon chew bones (gnaw sticks, GS) were evaluated for their effects on fermentation profiles, microbial community structure, and cytokine profiles of gastrointestinal and systemic tissues in pair-housed female and male Sprague Dawley (SD) rats.

RESULTS: Food consumption and weight gain were not significantly altered by access to GS. Cecal short-chain fatty acid and branched-chain fatty acid profiles significantly differed between sexes in rats with access to GS, and alpha diversity of the microbiome decreased in females provided GS. Sex-related tissue cytokine profiles also significantly differed between rats with and without access to GS.

CONCLUSIONS: These findings indicate that including GS can influence microbiota and immune-related parameters, in a sex dependent manner. This shows that environmental enrichment strategies need to be clearly reported in publications to properly evaluate and compare experimental results, especially with respect to the use of chewable EE in the context of studies examining diet, microbiome and immune parameters.},
}

@article {pmid39891205,
year = {2025},
author = {Huang, D and Liao, J and Balcazar, JL and Ye, M and Wu, R and Wang, D and Alvarez, PJJ and Yu, P},
title = {Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {34},
pmid = {39891205},
issn = {2049-2618},
support = {42177113//National Natural Science Foundation of China/ ; 42277418//National Natural Science Foundation of China/ ; Y2022084//the Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; 2022YFC3704700//National Key Research and Development Program of China/ ; },
mesh = {*Chromium/pharmacology ; *Soil Microbiology ; *Stress, Physiological ; *Bacteria/genetics/classification/drug effects ; *Microbiota/drug effects ; Soil Pollutants ; Metagenomics/methods ; Viruses/genetics/drug effects/classification ; Soil/chemistry ; },
abstract = {BACKGROUND: The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress.

RESULTS: Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that antiviral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities.

CONCLUSIONS: Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation. Video Abstract.},
}

*Chromium/pharmacology
*Soil Microbiology
*Stress, Physiological
*Bacteria/genetics/classification/drug effects
*Microbiota/drug effects
Soil Pollutants
Metagenomics/methods
Viruses/genetics/drug effects/classification
Soil/chemistry

@article {pmid39891202,
year = {2025},
author = {Ma, S and Chen, Q and Zheng, Y and Ren, T and He, R and Cheng, L and Zou, P and Jing, C and Zhang, C and Li, Y},
title = {A tale for two roles: Root-secreted methyl ferulate inhibits P. nicotianae and enriches the rhizosphere Bacillus against black shank disease in tobacco.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {33},
pmid = {39891202},
issn = {2049-2618},
mesh = {*Plant Diseases/microbiology/prevention & control ; *Rhizosphere ; *Plant Roots/microbiology ; *Nicotiana/microbiology ; *Bacillus/metabolism/genetics ; Soil Microbiology ; Disease Resistance ; },
abstract = {BACKGROUND: Root exudates serve as chemical signaling molecules that regulate rhizosphere interactions and control soil-borne diseases. The interactions between plants and the soil microbiome play dynamic and crucial roles in regulating the resistance of plants to biotic stress. However, the specific roles of many root exudates in plant pathogens remain unclear. The root exudate methyl ferulate, a naturally occurring and relatively non-toxic antifungal agent, has been applied to control postharvest pathogens and preserve foodstuffs and has not been used in plant disease control.

RESULTS: This study investigated the role of the root exudate methyl ferulate in controlling tobacco black shank disease. We observed that methyl ferulate was secreted in greater quantities in the tobacco resistant cultivar Gexin 3 following inoculation with P. nicotianae than in the susceptible cultivar Xiaohuangjin 1025. Our findings also revealed that methyl ferulate strongly inhibited P. nicotianae (EC50 = 67.51 µg/mL), effectively controlling tobacco black shank disease by impairing NADH dehydrogenase function (the activity decreased by 50%). Furthermore, methyl ferulate recruited disease-suppressive rhizosphere microbes, such as Bacillus (the relative abundance of these microbes increases from 4.69% to 13.79%), thereby increasing disease resistance. The overexpression of caffeic acid O-methyltransferase NtCOMT10 resulted in increased methyl ferulate secretion (increased to 221.09% compared with that of the wild-type), concomitant improvement in the disease suppression of tobacco black shank disease (disease index decreased from 20% to less than 10%) and enrichment of beneficial microbes. In addition, methyl ferulate exerted antagonistic effects on other phytopathogens, such as B. cinerea, P. aphanidermatum, P. sojae, C. lagenarium and F. oxysporum.

CONCLUSIONS: Our findings indicated that methyl ferulate, a component of root exudates regulated by NtCOMT10, can inhibit phytopathogens and enrich rhizosphere Bacillus against plant disease. The great dual effect of methyl ferulate on the control of phytopathogens and its low cost enable a novel potential avenue for controlling soil-borne fungal diseases. This study provides ingenious insights into controlling soil-borne diseases through beneficial root exudates. Video Abstract.},
}

*Plant Diseases/microbiology/prevention & control
*Rhizosphere
*Plant Roots/microbiology
*Nicotiana/microbiology
*Bacillus/metabolism/genetics
Soil Microbiology
Disease Resistance

@article {pmid39891198,
year = {2025},
author = {Berdeja, MP and Reynolds, NK and Pawlowska, T and Heuvel, JEV},
title = {Commercial bioinoculants improve colonization but do not alter the arbuscular mycorrhizal fungal community of greenhouse-grown grapevine roots.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {15},
pmid = {39891198},
issn = {2524-6372},
abstract = {BACKGROUND: Arbuscular mycorrhizal fungi (AMF) are beneficial root symbionts contributing to improved plant growth and development and resistance to abiotic and biotic stresses. Commercial bioinoculants containing AMF are widely considered as an alternative to agrochemicals in vineyards. However, their effects on grapevine plants grown in soil containing native communities of AMF are still poorly understood. In a greenhouse experiment, we evaluated the influence of five different bioinoculants on the composition of native AMF communities of young Cabernet Sauvignon vines grown in a non-sterile soil. Root colonization, leaf nitrogen concentration, plant biomass and root morphology were assessed, and AMF communities of inoculated and non-inoculated grapevine roots were profiled using high-throughput sequencing.

RESULTS: Contrary to our predictions, no differences in the microbiome of plants exposed to native AMF communities versus commercial AMF bioinoculants + native AMF communities were detected in roots. However, inoculation induced positive changes in root traits as well as increased AMF colonization, plant biomass, and leaf nitrogen. Most of these desirable functional traits were positively correlated with the relative abundance of operational taxonomic units identified as Glomus, Rhizophagus and Claroideoglomus genera.

CONCLUSION: These results suggest synergistic interactions between commercial AMF bioinoculants and native AMF communities of roots to promote grapevine growth. Long-term studies with further genomics, metabolomics and physiological research are needed to provide a deeper understanding of the symbiotic interaction among grapevine roots, bioinoculants and natural AMF communities and their role to promote plant adaptation to current environmental concerns.},
}

@article {pmid39891167,
year = {2025},
author = {Marangon, E and Rädecker, N and Li, JYQ and Terzin, M and Buerger, P and Webster, NS and Bourne, DG and Laffy, PW},
title = {Destabilization of mutualistic interactions shapes the early heat stress response of the coral holobiont.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {31},
pmid = {39891167},
issn = {2049-2618},
mesh = {*Anthozoa/microbiology/physiology ; *Symbiosis ; Animals ; *Heat-Shock Response/physiology ; *Dinoflagellida/physiology/genetics ; RNA, Ribosomal, 16S/genetics ; Coral Reefs ; Microbiota/physiology ; Hot Temperature ; Bacteria/classification/genetics/metabolism ; },
abstract = {BACKGROUND: The stability of the symbiotic relationship between coral and their dinoflagellate algae (Symbiodiniaceae) is disrupted by ocean warming. Although the coral thermal response depends on the complex interactions between host, Symbiodiniaceae and prokaryotes, the mechanisms underlying the initial destabilization of these symbioses are poorly understood.

RESULTS: In a 2-month manipulative experiment, we exposed the coral Porites lutea to gradually increasing temperatures corresponding to 0-8 degree heating weeks (DHW) and assessed the response of the coral holobiont using coral and Symbiodiniaceae transcriptomics, microbial 16S rRNA gene sequencing and physiological measurements. From early stages of heat stress (< 1 DHW), the increase in metabolic turnover shifted the holobiont to a net heterotrophic state in which algal-derived nutrients were insufficient to meet host energy demands, resulting in reduced holobiont performance at 1 DHW. We postulate the altered nutrient cycling also affected the coral-associated microbial community, with the relative abundance of Endozoicomonas bacteria declining under increasing heat stress. Integration of holobiont stress responses correlated this decline to an increase in expression of a host ADP-ribosylation factor, suggesting that Symbiodiniaceae and Endozoicomonas may underlie similar endosymbiotic regulatory processes.

CONCLUSIONS: The thermotolerance of coral holobionts therefore is influenced by the nutritional status of its members and their interactions, and this identified metabolic interdependency highlights the importance of applying an integrative approach to guide coral reef conservation efforts. Video Abstract.},
}

*Anthozoa/microbiology/physiology
*Symbiosis
Animals
*Heat-Shock Response/physiology
*Dinoflagellida/physiology/genetics
RNA, Ribosomal, 16S/genetics
Coral Reefs
Microbiota/physiology
Hot Temperature
Bacteria/classification/genetics/metabolism

@article {pmid39891011,
year = {2025},
author = {Bakshani, CR and Ojuri, TO and Pilgaard, B and Holck, J and McInnes, R and Kozak, RP and Zakhour, M and Çakaj, S and Kerouedan, M and Newton, E and Bolam, DN and Crouch, LI},
title = {Carbohydrate-active enzymes from Akkermansia muciniphila break down mucin O-glycans to completion.},
journal = {Nature microbiology},
volume = {10},
number = {2},
pages = {585-598},
pmid = {39891011},
issn = {2058-5276},
support = {224240/Z/21/Z//Wellcome Trust (Wellcome)/ ; BB/M029018/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; SBF0061175/AMS_/Academy of Medical Sciences/United Kingdom ; },
mesh = {*Akkermansia/enzymology/metabolism ; Humans ; *Polysaccharides/metabolism ; *Mucins/metabolism ; *Gastrointestinal Microbiome/physiology ; Glycoside Hydrolases/metabolism/chemistry ; Milk, Human/chemistry ; Polysaccharide-Lyases/metabolism/chemistry ; Bacterial Proteins/metabolism/chemistry/genetics ; },
abstract = {Akkermansia muciniphila is a human microbial symbiont residing in the mucosal layer of the large intestine. Its main carbon source is the highly heterogeneous mucin glycoprotein, and it uses an array of carbohydrate-active enzymes and sulfatases to access this complex energy source. Here we describe the biochemical characterization of 54 glycoside hydrolases, 11 sulfatases and 1 polysaccharide lyase from A. muciniphila to provide a holistic understanding of their carbohydrate-degrading activities. This was achieved using a variety of liquid chromatography techniques, mass spectrometry, enzyme kinetics and thin-layer chromatography. These results are supported with A. muciniphila growth and whole-cell assays. We find that these enzymes can act synergistically to degrade the O-glycans on the mucin polypeptide to completion, down to the core N-acetylgalactosaime. In addition, these enzymes can break down human breast milk oligosaccharide, ganglioside and globoside glycan structures, showing their capacity to target a variety of host glycans. These data provide a resource to understand the full degradative capability of the gut microbiome member A. muciniphila.},
}

*Akkermansia/enzymology/metabolism
Humans
*Polysaccharides/metabolism
*Mucins/metabolism
*Gastrointestinal Microbiome/physiology
Glycoside Hydrolases/metabolism/chemistry
Milk, Human/chemistry
Polysaccharide-Lyases/metabolism/chemistry
Bacterial Proteins/metabolism/chemistry/genetics

@article {pmid39890997,
year = {2025},
author = {Marter, P and Freese, HM and Ringel, V and Brinkmann, H and Pradella, S and Rohde, M and Jarek, M and Spröer, C and Wagner-Döbler, I and Overmann, J and Bunk, B and Petersen, J},
title = {Superior Resolution Profiling of the Coleofasciculus Microbiome by Amplicon Sequencing of the Complete 16S rRNA Gene and ITS Region.},
journal = {Environmental microbiology reports},
volume = {17},
number = {1},
pages = {e70066},
pmid = {39890997},
issn = {1758-2229},
support = {34509606-TRR 51//Deutsche Forschungsgemeinschaft/ ; //Collaborative Research Center Roseobacter (TRR51)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Cyanobacteria/genetics/classification/isolation & purification ; Sequence Analysis, DNA ; Phylogeny ; DNA, Ribosomal Spacer/genetics ; DNA, Bacterial/genetics ; Bacteria/genetics/classification/isolation & purification ; Metagenomics ; },
abstract = {The filamentous cyanobacterium Coleofasciculus chthonoplastes is the key primary producer of marine microbial mats. We elucidated the microbiomes of 32 non-axenic Coleofasciculus isolates using PacBio-based amplicon sequencing of the complete 16S rRNA gene and the internally transcribed spacer (16S-ITS). The length of authentic amplicon sequence variants (ASVs) ranged from 1827 to 3044 nucleotides (median: 2267 nt). The results, which were complemented by metagenome analyses and cultivation approaches, revealed the presence of more than 70 associated heterotrophs in the culture of Coleofasciculus sp. WW12. The great bacterial diversity in the cyanosphere is dominated by Pseudomonadota (59%) and Bacteroidota (23%). Allelic ribosomal operon variants were detected in 18 Coleofasciculus strains and our analyses proposed the presence of at least four different species. A comparative analysis of cyanobacterial microbiomes documented complementary advantages of amplicon sequencing versus metagenomics with an individual strength of the 16S-ITS approach in terms of (i) ribosomal target sequence quality, (ii) contaminant detection and (iii) identification of rare bacteria. The characterisation of the Coleofasciculus microbiome showed that long-read amplicon sequencing of the 16S-ITS region is the method of choice for rapid profiling of non-axenic cyanobacteria. Its superior resolution allows a reliable differentiation of even very closely related strains.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Cyanobacteria/genetics/classification/isolation & purification
Sequence Analysis, DNA
Phylogeny
DNA, Ribosomal Spacer/genetics
DNA, Bacterial/genetics
Bacteria/genetics/classification/isolation & purification
Metagenomics

@article {pmid39890778,
year = {2025},
author = {Zhu, B and Bai, Y and Yeo, YY and Lu, X and Rovira-Clavé, X and Chen, H and Yeung, J and Nkosi, D and Glickman, J and Delgado-Gonzalez, A and Gerber, GK and Angelo, M and Shalek, AK and Nolan, GP and Jiang, S},
title = {A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1230},
pmid = {39890778},
issn = {2041-1723},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Colitis/microbiology ; Mice ; *Proteomics ; *Mice, Inbred C57BL ; Intestinal Mucosa/microbiology/metabolism ; Glycomics/methods ; Disease Models, Animal ; Cellular Microenvironment ; Intestines/microbiology ; Transcriptome ; Host Microbial Interactions/immunology ; Multiomics ; },
abstract = {The intricate interactions between the host immune system and its microbiome constituents undergo dynamic shifts in response to perturbations to the intestinal tissue environment. Our ability to study these events on the systems level is significantly limited by in situ approaches capable of generating simultaneous insights from both host and microbial communities. Here, we introduce Microbiome Cartography (MicroCart), a framework for simultaneous in situ probing of host and microbiome across multiple spatial modalities. We demonstrate MicroCart by investigating gut host and microbiome changes in a murine colitis model, using spatial proteomics, transcriptomics, and glycomics. Our findings reveal a global but systematic transformation in tissue immune responses, encompassing tissue-level remodeling in response to host immune and epithelial cell state perturbations, bacterial population shifts, localized inflammatory responses, and metabolic process alterations during colitis. MicroCart enables a deep investigation of the intricate interplay between the host tissue and its microbiome with spatial multi-omics.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Colitis/microbiology
Mice
*Proteomics
*Mice, Inbred C57BL
Intestinal Mucosa/microbiology/metabolism
Glycomics/methods
Disease Models, Animal
Cellular Microenvironment
Intestines/microbiology
Transcriptome
Host Microbial Interactions/immunology
Multiomics

@article {pmid39890664,
year = {2025},
author = {Zhou, Y and Jiang, P and Ding, Y and Zhang, Y and Yang, S and Liu, X and Cao, C and Luo, G and Ou, L},
title = {Deciphering the Distinct Associations of Rhizospheric and Endospheric Microbiomes with Capsicum Plant Pathological Status.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {1},
pmid = {39890664},
issn = {1432-184X},
support = {2023YFD1201502//National Key Research and Development Program of China/ ; 42107262//National Natural Science Foundation of China/ ; CARS-24-A05//China Agriculture Research System of MOF and MARA/ ; },
mesh = {*Capsicum/microbiology/growth & development ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; Endophytes/isolation & purification/classification/physiology/genetics ; Plant Diseases/microbiology ; Plant Roots/microbiology ; Fungi/classification/genetics/isolation & purification/physiology ; },
abstract = {Exploring endospheric and rhizospheric microbiomes and their associations can help us to understand the pathological status of capsicum (Capsicum annuum L.) for implementing appropriate management strategies. To elucidate the differences among plants with distinct pathological status in the communities and functions of the endospheric and rhizospheric microbiomes, the samples of healthy and diseased capsicum plants, along with their rhizosphere soils, were collected from a long-term cultivation field. The results indicated a higher bacterial richness in the healthy rhizosphere than in the diseased rhizosphere (P < 0.05), with rhizospheric bacterial diversity surpassing endospheric bacterial diversity. The community assemblies of both the endospheric and rhizospheric microbiomes were driven by a combination of stochastic and deterministic processes, with the stochastic processes playing a primary role. The majority of co-enriched taxa in the healthy endophyte and rhizosphere mainly belonged to bacterial Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal Ascomycota. Most of the bacterial indicators, primarily Alphaproteobacteria and Actinobacteria, were enriched in the healthy rhizosphere, but not in the diseased rhizosphere. In addition, most of the fungal indicators were enriched in both the healthy and diseased endosphere. The diseased endophyte constituted a less complex and stable microbial community than the healthy endophyte, and meanwhile, the diseased rhizosphere exhibited a higher complexity but lower stability than the healthy rhizosphere. Notably, only a microbial function, namely biosynthesis of other secondary metabolites, was higher in the healthy endophytes than in the diseased endophyte. These findings indicated the distinct responses of rhizospheric and endospheric microbiomes to capsicum pathological status, and in particular, provided a new insight into leveraging soil and plant microbial resources to enhance agriculture production.},
}

*Capsicum/microbiology/growth & development
*Rhizosphere
*Microbiota
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
Endophytes/isolation & purification/classification/physiology/genetics
Plant Diseases/microbiology
Plant Roots/microbiology
Fungi/classification/genetics/isolation & purification/physiology

@article {pmid39890521,
year = {2025},
author = {Rafie, E and Zugman, M and Pal, SK and Routy, B and Elkrief, A},
title = {What Is the Role of Fecal Microbiota Transplantation in Immunotherapy Trials? Current Perspectives and Future Directions.},
journal = {European urology focus},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.euf.2024.12.009},
pmid = {39890521},
issn = {2405-4569},
abstract = {Immune checkpoint inhibitors (ICIs) are rapidly transforming the treatment landscape of genitourinary and other immunogenic malignancies. Despite these advances, biomarkers for the prediction of ICI response remain to be established. The gut microbiome has been identified as a modulator of immune regulation and a potential regulator of response to ICIs. Fecal microbiota transplantation (FMT) has emerged as a potential novel therapeutic tool to enhance ICI response, as demonstrated in several trials, spanning across genitourinary malignancies as well as others. While safety and clinical potential of FMT have been demonstrated, FMT parameters including optimal treatment regimens, bowel preparation protocols, patient selection, and donor-host compatibility need to be defined. Furthermore, targeted interventions including probiotic supplementation represent promising therapeutic avenues meriting further study.},
}

@article {pmid39890294,
year = {2025},
author = {Baker, JM and Dickson, RP},
title = {The Microbiome and Pulmonary Immune Function.},
journal = {Clinics in chest medicine},
volume = {46},
number = {1},
pages = {77-91},
doi = {10.1016/j.ccm.2024.10.006},
pmid = {39890294},
issn = {1557-8216},
mesh = {Humans ; *Microbiota/immunology/physiology ; *Lung/microbiology/immunology ; Lung Diseases/immunology/microbiology ; },
abstract = {In the last decade, the lung microbiome field has matured into a promising area of translational and clinical research due to emerging evidence indicating a role for respiratory microbiota in lung immunity and pathogenesis. Here, we review recent insights pertaining to the lung microbiome's relationship with pulmonary immune function. We discuss areas of future investigation that will be essential to the development of immunomodulatory therapies targeting the respiratory microbiome.},
}

Humans
*Microbiota/immunology/physiology
*Lung/microbiology/immunology
Lung Diseases/immunology/microbiology

@article {pmid39890144,
year = {2025},
author = {Pogreba Brown, K and Austhof, E and McFadden, CM and Scranton, C and Sun, X and Vujkovic-Cviji, I and Rodriguez, D and Falk, L and Heslin, KM and Arani, G and Obergh, V and Bessey, K and Cooper, K},
title = {Determining the incidence, risk factors and biological drivers of irritable bowel syndrome (IBS) as part of the constellation of postacute sequelae of SARS-CoV-2 infection (PASC) outcomes in the Arizona CoVHORT-GI: a longitudinal cohort study.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e095093},
pmid = {39890144},
issn = {2044-6055},
mesh = {Humans ; *COVID-19/epidemiology ; *Irritable Bowel Syndrome/epidemiology ; Longitudinal Studies ; Arizona/epidemiology ; *Post-Acute COVID-19 Syndrome ; Incidence ; Risk Factors ; *SARS-CoV-2 ; Male ; Female ; Biomarkers/blood ; Adult ; Middle Aged ; Gastrointestinal Microbiome ; },
abstract = {INTRODUCTION: Postacute sequelae of SARS-CoV-2 infection (PASC) are extensive. Also known as long COVID, primary outcomes reported are neurologic, cardiac and respiratory in nature. However, several studies have also reported an increase in gastrointestinal (GI) symptoms and syndromes following COVID-19. This study of PASC will include extensive analyses of GI symptoms, determine if people with pre-existing irritable bowel syndrome (IBS) are at higher risk of developing PASC generally or PASC-GI, and which biomarkers are impacted and to what degree. This R01 study is being funded by the National Institute of Diabetes and Digestive and Kidney Diseases (1R01DK135483-01) from 2023 to 2028.

METHODS AND ANALYSES: This study combines a longitudinal epidemiologic cohort study and in-depth, novel biologic analyses. In collaboration with a pre-existing study, the Arizona CoVID-19 Cohort (CoVHORT)-GI will recruit participants based on the history of COVID infection(s), new or ongoing GI symptoms 3-6 months postinfection, and pre-existing or incident IBS diagnosis to represent five study groups for comparison and analyses. A subset (n=1000) of those recruited will submit both stool and blood samples. Both samples will undergo a novel method to quantitate humoral and mucosal immune responses to host-derived faecal communities in conjunction with magnetic bead-based separation and high-depth shotgun microbial sequencing. Stool samples will also undergo traditional microbiome analyses (diversity and abundance) and faecal calprotectin assays. Additional serum analyses will aim to determine if a proteomics-based signature exists that differentiates a unique biomarker compositional signature discriminating PASC-GI versus no PASC. All laboratory data will be linked with in-depth epidemiologic data on demographics, symptoms and chronic conditions.

ETHICS AND DISSEMINATION: This study involves human participants and was approved by the University of Arizona Institutional Review Board (IRB (#00002332) and has been deemed minimal risk. Participants gave informed consent to participate in the study before taking part. All publications from the study will be shared back to participants along with alternative lay summaries and webinars to communicate key findings. The data management plan has been published and is publicly available online, including protocols for data requests.},
}

Humans
*COVID-19/epidemiology
*Irritable Bowel Syndrome/epidemiology
Longitudinal Studies
Arizona/epidemiology
*Post-Acute COVID-19 Syndrome
Incidence
Risk Factors
*SARS-CoV-2
Male
Female
Biomarkers/blood
Adult
Middle Aged
Gastrointestinal Microbiome

@article {pmid39890137,
year = {2025},
author = {Kennedy, EC and Ross, FC and O'Shea, CA and Lavelle, A and Ross, P and Dempsey, E and Stanton, C and Hawkes, CP},
title = {Observational study protocol: the faecal microbiome in the acute stage of new-onset paediatric type 1 diabetes in an Irish cohort.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e089206},
pmid = {39890137},
issn = {2044-6055},
mesh = {Humans ; *Diabetes Mellitus, Type 1/microbiology ; *Feces/microbiology ; Child ; *Gastrointestinal Microbiome ; Male ; Female ; Prospective Studies ; Ireland ; Child, Preschool ; Adolescent ; Metabolome ; },
abstract = {INTRODUCTION: Type 1 diabetes (T1D) is an autoimmune-mediated disorder caused by the destruction of pancreatic beta cells. Although there is an underlying genetic predisposition to developing T1D, the trigger is multifactorial and likely includes environmental factors. The intestinal microbiome has been identified as one such factor. Previous studies have illustrated differences in the microbiota of people with T1D compared with healthy controls. This study aims to describe the evolution of the microbiome and metabolome during the first year of clinical T1D, or stage 3 T1D diagnosis, and investigate whether there are differences in the microbiome and metabolome of children who present with and without diabetic ketoacidosis. The study will also explore possible associations between the microbiome, metabolome, glycaemic control and beta cell reserve.

METHODS AND ANALYSIS: This prospective cohort study will include children with newly diagnosed T1D and sibling controls (n=100, males and females) and their faecal microbiome will be characterised using shotgun metagenomic sequencing at multiple time points during the first year of diagnosis. We will develop a microbial culture biobank based on culturomic studies of stool samples from the healthy controls that will support future investigation. Metabolomic analysis will aim to identify additional biomarkers which may be involved in disease presentation and progression. Through this initial exploratory study, we aim to identify specific microbial biomarkers which may be used as future interventional targets throughout the various stages of T1D progression.

ETHICS AND DISSEMINATION: This study has been approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals. Study results will be available to patients with T1D and their families, carers, support networks and microbiome societies and other researchers.

TRIAL REGISTRATION NUMBER: The clinicaltrials.gov registration number for this trial is NCT06157736.},
}

Humans
*Diabetes Mellitus, Type 1/microbiology
*Feces/microbiology
Child
*Gastrointestinal Microbiome
Male
Female
Prospective Studies
Ireland
Child, Preschool
Adolescent
Metabolome