@article {pmid41365136,
year = {2025},
author = {Chang, G and Zhang, J and Fang, X and Zhang, S and Lu, H and Jiang, Y and Zhu, J},
title = {Environmental microorganisms as heterogeneous sources and shapers of the fermentation microbiome in Zhejiang rosy vinegar.},
journal = {International journal of food microbiology},
volume = {447},
number = {},
pages = {111554},
doi = {10.1016/j.ijfoodmicro.2025.111554},
pmid = {41365136},
issn = {1879-3460},
abstract = {Zhejiang rosy vinegar (ZRV) fermentation is a complex, spontaneous open-system process, where microbial communities are key to its unique characteristics. However, the precise influence of the brewing workshop environment on these dynamic microbial communities remains underexplored, hindering consistent product quality. Here, we characterized the environmental and fermentation microbial communities across three factories using high-throughput sequencing (16S rRNA and ITS), qPCR, and advanced ecological network analyses. Our results establish that the brewing environment acts as a critical, heterogeneous, and factory-specific microbial reservoir, and provides the primary inoculum for fermentation initiation. Our findings revealed significant inter-factory differences in environmental microbial loads and community structures. For instance, the SX environment was characterized by a unique composition, including the notable presence of Monascus on jar lids. Source tracking confirmed this environmental "seeding" significantly shapes initial fermentation communities, with contributions from floor and jar surfaces. During fermentation, bacterial communities consistently shifted (LAB decrease, Acetobacter increase), but fungal successions varied notably by factory. Specifically, the natural fermentation at the SX factory fostered a distinct fungal community trajectory, characterized by a unique decrease in Saccharomyces and the emergence of Monascus as the dominant genus in later stages. This trajectory was directly linked to its distinct environmental fungal populations and their pronounced influence from the initial solid-state phase. While internal selective pressures eventually govern community structure, environmental conditions profoundly dictate overall microbial diversity and succession. A core microbiome (Bacillus, Sphingomonas, Cryptococcus, Monascus), consistently present in both environmental and fermentation niches, served as key microbial bridges. Our results provide a vital basis for optimizing ZRV production by strategically managing the environmental microbiome to enhance quality and consistency.},
}

@article {pmid41365103,
year = {2025},
author = {Salas, A and Navarro, L and Martinón-Torres, F and Gómez-Carballa, A},
title = {Beyond behavioral studies: Exploring the multi-omics impact of music on human health.: Comment on Can arts-based interventions improve health? A conceptual and methodological critique by Martin Skov and Marcos Nadal.},
journal = {Physics of life reviews},
volume = {56},
number = {},
pages = {91-93},
doi = {10.1016/j.plrev.2025.09.002},
pmid = {41365103},
issn = {1873-1457},
}

@article {pmid41365070,
year = {2025},
author = {Zhou, Y and Zhang, XX and Wang, D and Zhao, M and Sun, L and Huang, W and Xie, Z},
title = {Microbial acetyl-CoA synthesis as an emerging metabolic and regulatory hub in plant-microbe interactions.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128413},
doi = {10.1016/j.micres.2025.128413},
pmid = {41365070},
issn = {1618-0623},
abstract = {Acetyl-CoA synthetase (ACS) is a well-characterized enzyme that catalyzes the ATP-dependent ligation of acetate and coenzyme A to produce acetyl-CoA, a central metabolite coordinating energy metabolism, carbon flux distribution, and post-translational protein modification. Recently, ACS has emerged as a metabolic nexus with broad implications for plant-microbe interactions in agriculture. Beyond its canonical role in primary metabolism, ACS governs diverse physiological processes in beneficial plant-associated microorganisms, including rhizosphere colonization, stress adaptation, secondary metabolite biosynthesis, and morphological development-all of which enhance plant growth and resilience. In contrast, in phytopathogens, ACS is closely related to the expression of virulence factors. Thus, ACS exerts a dual influence, shaping both mutualistic and antagonistic microbial lifestyles in planta. This review synthesizes recent advances in the structural and catalytic diversity of ACS, delineates its ecological and functional roles in agriculturally relevant microorganisms, and explores the environmental and host-derived signals that regulates its expression and activity. Particular attention is given to the interplay between ACS-mediated carbon metabolism and protein acetylation, which together modulate microbial physiology and plant-associated behaviors. ACS is thereby positioned as a strategic metabolic hub, providing a framework for future research at the interface of microbial metabolism, environmental adaptation, and plant health.},
}

@article {pmid41364914,
year = {2025},
author = {Kujawska, M and Hall, LJ},
title = {Microbe-Diet Interactions and Personalized Nutrition.},
journal = {Annual review of food science and technology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-food-111523-121845},
pmid = {41364914},
issn = {1941-1421},
abstract = {Nutrition plays a fundamental role in shaping human health across the life course, influencing both host physiology and the composition and function of the gut microbiota. In turn, the gut microbiota modulates the effects of dietary intake, creating complex bidirectional interactions with profound implications for metabolic health. Although the concept of personalized nutrition offering tailored dietary advice based on observable traits, environmental factors, and genotype has gained prominence, growing evidence supports the promise of precision nutrition that also considers individual microbiome profiles. This approach is particularly relevant for addressing diet-related conditions such as obesity and type 2 diabetes, where interindividual variability in response to the same diet is well documented. Advances in high-throughput sequencing, metabolomics, and machine learning are driving predictive models that can forecast personalized dietary outcomes. However, methodological heterogeneity, lack of consistency, and limited representation of diverse populations in current studies present significant barriers. Ethical challenges, including data privacy and equitable access to personalized nutrition tools, also warrant urgent attention. To realize the full potential of microbiome-informed nutrition, greater harmonization of research methods, robust validation across large and diverse cohorts, and an interdisciplinary framework are essential.},
}

@article {pmid41364878,
year = {2025},
author = {Yoon, SE and Kang, W and Cho, J and Cho, HJ and Chalita, M and Oh, HS and Hyun, DW and Han, S and Kim, H and Sung, H and Lee, JY and Park, B and Ryu, KJ and Kim, HY and Cho, D and Kim, WS and Kim, SJ},
title = {Microbiome and metabolite biomarkers of CAR T-cell therapy outcomes in relapsed/refractory diffuse large B cell lymphoma.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2025016858},
pmid = {41364878},
issn = {2473-9537},
abstract = {CD19 CAR T-cell therapy has revolutionized treatment for relapsed/refractory diffuse large B-cell lymphoma (RR-DLBCL), but challenges like post-treatment failure and immune-related adverse events (AEs) persist. This study explores the gut microbiome as a predictive biomarker for CAR T-cell therapy outcomes and toxicity. Stool and serum samples from RR-DLBCL patients were analyzed at apheresis (47 samples) and one month post-infusion (32 samples) using whole-genome sequencing metagenomics. When compared with healthy controls and newly diagnosed DLBCL, RR-DLBCL showed significant gut dysbiosis, characterized by increased Proteobacteria and Enterobacteriaceae. Responders to treatment had higher levels of Bacteroides fragilis, while non-responders exhibited higher levels of Faecalibacterium prausnitzii. Functional metagenomic analysis suggested enrichment of inosine biosynthesis pathways in responders, and elevated serum inosine demonstrated an exploratory association with improved progression-free survival. Distinct microbial taxa and serum fatty acid profiles were also linked to CAR T-cell-related AEs, with higher acetate and butyrate levels in patients without AEs, and increased isovalerate in those with AEs. These findings indicate that gut microbiome features-particularly Bacteroides fragilis and inosine metabolism-may serve as candidate biomarkers for CAR T-cell therapy outcomes and toxicity. However, given the exploratory nature of these analyses and the limited cohort size, results should be interpreted cautiously. Larger, prospective studies will be required to validate these observations and to assess the potential of microbiome-based strategies to optimize CAR T-cell therapy in RR-DLBCL.},
}

@article {pmid41364769,
year = {2025},
author = {Ratner, HK and Duong, BD and Miao, P and Bertolli, SK and Shen, BA and Mitchell, U and Gallagher, LA and Radey, MC and Peterson, SB and Mougous, JD},
title = {An electron transport complex required in the gut sensitizes Bacteroides to a pore-forming type VI secretion toxin.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {50},
pages = {e2523503122},
doi = {10.1073/pnas.2523503122},
pmid = {41364769},
issn = {1091-6490},
support = {Investigator Award//HHMI (HHMI)/ ; },
mesh = {*Type VI Secretion Systems/metabolism ; *Gastrointestinal Microbiome ; *Bacteroides/metabolism/genetics ; *Bacterial Proteins/metabolism/genetics ; Humans ; *Bacterial Toxins/metabolism ; Electron Transport ; },
abstract = {Data suggest that antagonism between bacteria is prevalent within the gut microbiome. Such antagonism could have profound consequences on the fitness of species; however, the susceptibility determinants to even the most pervasive antagonistic factors in this ecosystem remain incompletely understood. Here, we screened for genetic factors that impact the susceptibility of Bacteroides to type VI secretion system (T6SS)-delivered toxins. This revealed that the Bte2 family of pore-forming toxins, which are widespread in B. fragilis and other human gut-associated Bacteroidales, strictly requires the H[+]/Na[+]-translocating ferredoxin:NAD[+] reductase (Rnf) electron transport chain within target cells in order to intoxicate. In Bacteroides, the precise metabolic role of the conserved Rnf pathway has not been defined. We establish that the Rnf complex is important for redox balancing within cells utilizing sugars derived from dietary fiber and is critical for fitness in vivo. Surprisingly, we find that while the intact Rnf membrane complex is required for Bte2 intoxication, Rnf-catalyzed electron transport is dispensable. We propose that the Rnf complex facilitates Bte2 membrane insertion, leading to intoxication via membrane depolarization. Our data suggest that T6SS toxins may avoid collateral damage within a complex ecosystem by recognizing discriminatory features of competitor species.},
}

*Type VI Secretion Systems/metabolism
*Gastrointestinal Microbiome
*Bacteroides/metabolism/genetics
*Bacterial Proteins/metabolism/genetics
Humans
*Bacterial Toxins/metabolism
Electron Transport

@article {pmid41364767,
year = {2025},
author = {Wang, N and Westermann, LM and Li, M and Li, CY and Murphy, ARJ and Gu, Z and Silvano, E and Blindauer, CA and Lidbury, IDEA and Zhang, YZ and Scanlan, DJ and Chen, Y},
title = {Structural basis and evolutionary pathways of glycerol-1-phosphate transport in marine bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {50},
pages = {e2524546122},
doi = {10.1073/pnas.2524546122},
pmid = {41364767},
issn = {1091-6490},
support = {726116//EC | European Research Council (ERC)/ ; 32330001//NSF of china/ ; 883551//EC | European Research Council (ERC)/ ; },
mesh = {Phylogeny ; *Glycerophosphates/metabolism/chemistry ; Evolution, Molecular ; *Bacterial Proteins/metabolism/genetics/chemistry ; Biological Transport ; *Bacteria/metabolism/genetics ; *Aquatic Organisms/metabolism ; Seawater/microbiology ; Membrane Transport Proteins/metabolism/genetics/chemistry ; },
abstract = {All cells use lipid membranes to maintain cellular integrity and function, though Archaea utilize lipids composed of glycerol-1-phosphate (G1P), while Bacteria and Eukaryotes use glycerol-3-phosphate (G3P). Given that Archaea contribute significantly to global marine biomass, accounting for 0.3 gigatonnes (Gt) of carbon in the oceans, we aimed to uncover how archaeal G1P is recycled by marine microorganisms. Through a multidisciplinary approach combining microbiology, biochemistry, and structural biology, we identified a G1P transporter in marine bacteria, which we named GpxB. Phylogenetic analysis revealed that GpxB belongs to the organic phosphonate transporter (PhnT) family and is widely distributed in the marine microbiome, found in approximately 5 to 10% of microbial cells in surface marine waters. Strikingly, we also identified a second G1P transporter, UgpB, that is known to transport G3P and belongs to the carbohydrate uptake transporter-1 (CUT1) family, in the model bacterium Phaeobacter sp. MED193. To explore the evolutionary pathways that led to the formation of G1P binding sites in both the PhnT and CUT1 families, we determined the structures of GpxB and UgpB bound to G1P and G3P. Using structure-guided mutagenesis and a comparative analysis of the binding pockets within the PhnT and CUT1 families, we traced their evolutionary trajectories, highlighting the distinct strategies through which G1P-binding sites developed in these two protein families.},
}

Phylogeny
*Glycerophosphates/metabolism/chemistry
Evolution, Molecular
*Bacterial Proteins/metabolism/genetics/chemistry
Biological Transport
*Bacteria/metabolism/genetics
*Aquatic Organisms/metabolism
Seawater/microbiology
Membrane Transport Proteins/metabolism/genetics/chemistry

@article {pmid41364520,
year = {2025},
author = {Verbitsky, M and Khosla, P and Bivona, D and Khan, A and Gupta, Y and Park, H and Shen, TH and Ghotra, A and Xu, K and Ghavami, IA and Krithivasan, P and Martino, J and Sezin, T and Lim, TY and Kolupaeva, V and Limdi, NA and Luo, Y and Hakonarson, H and Sanna-Cherchi, S and Kiryluk, K and Mendelsohn, CL and Uhlemann, AC and Barasch, J and Gharavi, AG},
title = {Urobiota analysis and genome-wide association study in pediatric recurrent urinary tract infections and vesicoureteral reflux.},
journal = {JCI insight},
volume = {},
number = {},
pages = {},
doi = {10.1172/jci.insight.199689},
pmid = {41364520},
issn = {2379-3708},
abstract = {Urinary tract infections (UTIs) are the most common severe bacterial infections in young children, often associated with vesicoureteral reflux (VUR). To explore host genetic-microbiota interactions and their clinical implications, we analyzed the urinary microbiota (urobiota) and conducted genome-wide association studies (GWAS) for bacterial abundance traits in pediatric UTI and VUR patients from the RIVUR and CUTIE cohorts. We identified four urobiota community types based on relative abundance, characterized by the genera Enterococcus, Prevotella, Pseudomonas, and Escherichia/Shigella, and their associations with VUR, age, and toilet training. Children with VUR exhibited decreased microbial diversity and increased abundance of genera that included opportunistic pathogens, suggesting a disrupted urobiota. We detected genome-wide significant genetic associations with urinary bacterial relative abundances, in or near candidate genes including CXCL12, ABCC1, and ROBO1, which are implicated in urinary tract development and response to infection. We showed that Cxcl12 is induced 12 hours after uropathogenic bacterial infection in mouse bladder. The association with CXCL12 suggests a genetic link between UTI, VUR and cardiovascular phenotypes later in life. These findings provide the first characterization of host genetic influences on the pediatric urobiota in UTI and VUR, offering insights into the interplay between disease, host genetics and the urobiota composition.},
}

@article {pmid41364398,
year = {2025},
author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W},
title = {Strain-level dynamics of Akkermansia muciniphila in the human gut microbiota.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-025-01982-7},
pmid = {41364398},
issn = {2191-0855},
support = {2018YFC1200100//National Key Research and Development Program of China/ ; },
abstract = {Akkermansia muciniphila (Akk), a mucin-degrading bacterium residing in the human gut, plays a pivotal role in intestinal health. This study investigated its temporal dynamics, strain-level diversity, and cross-regional transmission using longitudinal metagenomic data from the Chinese Microbiome Project (CMP). We observed significant fluctuations in Akk relative abundance across 52 time points in 7 healthy individuals, with detection rates of 56.9% (16S rRNA gene sequencing) and 33.3% (whole-genome sequencing, WGS). Notably, "short-term blooms"--rapid increases followed by declines in relative abundance--were identified in multiple subjects. Genomic analysis of 39 Akkermansia metagenome-assembled genomes (MAGs), combined with 89 publicly available strains with complete genome, revealed phylogenetically distinct clusters (average nucleotide identity, ANI < 98% between clusters). Strikingly, individuals harbored different clusters at varying time points (e.g., AmII replaced by AmIb and later AmIa in subject P4), suggesting strain replacement and recurrent colonization. Furthermore, high-similarity strains (ANI > 99%) were shared between individuals with close contact (e.g., cohabiting subjects P2 and P4) and across geographically distant regions (China, South Korea, and the United States), implicating human-mediated or environmental transmission pathways. These findings underscore the dynamic nature of Akk within the gut microbiota and highlight the need to explore factors driving its colonization, strain competition, and ecological dissemination.},
}

@article {pmid41364342,
year = {2025},
author = {Akhavan, N and Hrynkiewicz, K and Thiem, D and Gardiner, GE and Lawlor, PG and Balakrishnan, S and Guinan, KJ and O'Sullivan, JT and Mangan, M and Stadnicka, K},
title = {In vitro compatibility screening of Bacillus pumilus and Bacillus altitudinis strains with selected candidate prebiotics for in ovo application of synergistic synbiotics.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-025-13624-w},
pmid = {41364342},
issn = {1432-0614},
support = {UMO-2019/35/B/NZ9/03186 OVOBIOM//The National Science Centre in Poland/ ; },
abstract = {Bacillus species have demonstrated beneficial effects on intestinal health, production parameters, and immune function in poultry under both standard and disease-challenged conditions. Previously, we found that several novel ingredients (beta-glucan, vegetable protein hydrolysate, and liquid seaweed extract) demonstrated growth stimulation effects on Bifidobacterium lactis and Lactobacillus plantarum, Here, we extended this approach to examine in vitro synbiotic combinations of five novel marine-derived candidate probiotic Bacillus strains to assess their potential for in ovo applications. Beta-glucan enhanced the growth of all candidate Bacillus probiotic strains compared to a glucose control (p ≤ 0.05), suggesting a broad-spectrum modulatory role over a 24-h period, with variable magnitudes of response observed between strains. Species specificity was also observed, with lentinus stimulating the Bacillus pumilus but not the Bacillus altitudinis strains. A seaweed extract consistently stimulated the growth of one of the B. altitudinis strains (p ≤ 0.05), which, like all of the strains evaluated here, is seaweed-derived. This suggests potential ecological adaptation in substrate utilization. The shared environmental origin may influence substrate specificity and metabolic complementarity between strains and prebiotic candidates. Both B. altitudinis strains also exhibited enhanced growth at almost all time points (p ≤ 0.05) when cultured with vegetable protein hydrolysate. Based on these findings, we evaluated the effect of a potential synbiotic formulation comprising one of the B. altitudinis strains and vegetable protein hydrolysate in chickens, in ovo. The components were administered intra-amniotically at embryonic development day 18.5, utilizing a standard vaccination protocol. The hatchability of the chickens was not affected, thereby demonstrating the established dose as safe and applicable for further investigation. KEY POINTS: • Shared origin of bioactive compounds may enhance probiotic-prebiotic compatibility in vitro • Protein hydrolysate offers a novel alternative to carbohydrate prebiotics • In ovo delivery of Bacillus-based synbiotic formulations offers potential as an early microbiome programming strategy.},
}

@article {pmid41364164,
year = {2025},
author = {Alavi, SE and Ebrahimi Shahmabadi, H and Sharma, LA and Sharma, A},
title = {The Role of the Oral Microbiome in Periodontal Disease: A Systematic Review of Microbial Associations and Therapeutic Implications.},
journal = {Current microbiology},
volume = {83},
number = {1},
pages = {64},
pmid = {41364164},
issn = {1432-0991},
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; *Bacteria/classification/isolation & purification/genetics ; *Periodontal Diseases/microbiology/therapy ; *Periodontitis/microbiology ; },
abstract = {Periodontitis is a chronic inflammatory disease driven by bacterial pathogens. This meta-analysis aimed to quantitatively assess the association between nine bacterial strains and periodontitis across 11 studies. We extracted odds ratios (ORs) and 95% confidence intervals (CIs) from studies evaluating Streptococcus mutans, Lactobacillus, Fusobacterium nucleatum, Prevotella intermedia, Staphylococcus aureus, Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Tannerella forsythia, and Treponema denticola. Heterogeneity was evaluated using Cochran's Q and I[2] tests. We systematically searched PubMed, Scopus, and Web of Science up to March 2024, following PRISMA guidelines, to identify studies investigating the association between oral bacterial species and periodontitis. Porphyromonas gingivalis was identified as a significant risk factor for periodontitis in all eight studies (ORs: 4.17-97, I[2] = 85.99%). Tannerella forsythia (ORs: 2.75-36.88, I[2] = 85.39%) and Treponema denticola (ORs: 3.12-24.5, I[2] = 85.54%) were also significantly associated with periodontitis. Prevotella intermedia showed a significant association in three out of four studies, despite high heterogeneity (I[2] = 79.82%). Fusobacterium nucleatum and Staphylococcus aureus were not found to be significant risk factors. Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola are key bacterial risk factors for periodontitis. The findings highlight the importance of microbial screening in clinical practice, while the heterogeneity suggests the need for standardized research. Future studies should focus on longitudinal assessments and microbial interactions.},
}

Humans
*Microbiota
*Mouth/microbiology
*Bacteria/classification/isolation & purification/genetics
*Periodontal Diseases/microbiology/therapy
*Periodontitis/microbiology

@article {pmid41364123,
year = {2025},
author = {Chervochkina, AS and Aksenov, AS and Ilmast, NV},
title = {Yolk-Sac Stage Bacteriome: Gaps of Knowledge and Demand for Fish Science.},
journal = {Current microbiology},
volume = {83},
number = {1},
pages = {59},
pmid = {41364123},
issn = {1432-0991},
support = {FSRU-2023-004//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Animals ; *Fishes/microbiology/growth & development ; *Bacteria/classification/genetics/isolation & purification ; *Yolk Sac/microbiology/growth & development ; *Gastrointestinal Microbiome ; Probiotics ; Larva/microbiology/growth & development ; },
abstract = {The intestinal microbiome of fish at early stages of ontogeny represents a complex and dynamic ecosystem that is critically important for immune system development, physiological resilience, and growth. The yolk-sac stage is of particular significance, as larvae rely exclusively on endogenous nutrient reserves while being colonized by microbes for the first time. During this period, the foundations of microbiota are established, which subsequently influence the development of the digestive system, barrier functions, and pathogen resistance. Recent studies show that microbial communities at this stage are characterized by low alpha diversity and the dominance of Proteobacteria, Firmicutes, and Bacteroidetes. With the transition to exogenous feeding, there is an increase in taxonomic and functional diversity, along with the emergence of probiotic genera (Bacillus, Lactobacillus, Shewanella) that promote enzymatic activity, immune modulation, and increased survival of larvae. This review systematically compiles data from the past 20 years, encompassing both culture-dependent methods and high-throughput sequencing approaches. It has been demonstrated that despite the limitations of culture-based methods, they remain indispensable for isolating probiotic strains. A comparison of methodologies revealed high variability in protocols, complicating the direct comparison of results. The findings underscore the applied significance of studying microbiota for aquaculture during the yolk-sac stage. The management of microbial communities through probiotics, prebiotics, and environmental regulation presents prospects for enhancing the survival, growth, and resilience of fish larvae.},
}

Animals
*Fishes/microbiology/growth & development
*Bacteria/classification/genetics/isolation & purification
*Yolk Sac/microbiology/growth & development
*Gastrointestinal Microbiome
Probiotics
Larva/microbiology/growth & development

@article {pmid41364074,
year = {2025},
author = {Luckey, D and Marietta, E and Taneja, V},
title = {HLA Transgenic Mice as a Model to Uncover Biomarkers and Therapeutic Strategies for Rheumatoid Arthritis.},
journal = {Current protocols},
volume = {5},
number = {12},
pages = {e70263},
doi = {10.1002/cpz1.70263},
pmid = {41364074},
issn = {2691-1299},
mesh = {Animals ; *Arthritis, Rheumatoid/therapy/immunology/genetics ; *Disease Models, Animal ; Mice ; Mice, Transgenic ; Humans ; Biomarkers/metabolism ; *HLA Antigens/genetics/immunology ; *Arthritis, Experimental/immunology ; Collagen Type II/immunology ; },
abstract = {Rheumatoid arthritis (RA) is a chronic disease involving inflammation of the joints. While the etiology of RA remains unknown, evidence exists for a significant contribution of the major histocompatibility complex (MHC). Environmental factors are also indicated as playing an etiological role. Since it is impossible to define the mechanisms contributing to disease onset and progression in humans, mouse models have been used widely. While many animal models have been generated by immunization with self-proteins to induce arthritis, type II collagen (CII)-induced arthritis is one of the most commonly used models utilized to understand the immunopathology of RA. CII constitutes 80% to 90% of total collagen content of hyaline cartilage found in joints and is a genetically conserved sequestered protein. Immunization with heterologous CII with an adjuvant in mice leads to cellular and humoral responses to heterologous and autoreactive CII-specific responses and collagen-induced arthritis (CIA). Mice immunized with CII develop inflammatory arthritis that shares many similarities in clinical, serological, and radiological features with RA in humans. However, selecting an antigen for inducing arthritis and the mouse strain are important, as not all strains are susceptible to CIA. A critical difference between RA and CIA is that in mice that lack the expression of human MHC II, the development of CIA is linked to the H2A locus, which is the homologue of HLA-DQ, while most human studies have linked RA susceptibility with HLA-DR alleles. Mice expressing HLA-DQ and HLA-DR molecules have been used to understand the role of MHC genes in susceptibility to RA. The protocols for inducing CIA in the HLA expressing transgenic mice described in this article can be used to understand how the different HLA molecules confer susceptibility to RA. © 2025 Wiley Periodicals LLC. Basic Protocol 1: Use of mouse strains and humanized mice for modeling rheumatoid arthritis Basic Protocol 2: Use of humanized mice for therapeutic protocols.},
}

Animals
*Arthritis, Rheumatoid/therapy/immunology/genetics
*Disease Models, Animal
Mice
Mice, Transgenic
Humans
Biomarkers/metabolism
*HLA Antigens/genetics/immunology
*Arthritis, Experimental/immunology
Collagen Type II/immunology

@article {pmid41364072,
year = {2025},
author = {Bartman, S and Dawdy, M and Wang, Y and Akens, M and Whyne, C and Nam, D},
title = {A possible treatment for fragility fractures of the pelvis? The impact of probiotic treatment on pelvic bone microstructure and strength in osteoporotic rats.},
journal = {Journal of orthopaedic trauma},
volume = {},
number = {},
pages = {},
doi = {10.1097/BOT.0000000000003138},
pmid = {41364072},
issn = {1531-2291},
abstract = {OBJECTIVES: Healing remains a clinical challenge in non-operatively treated fragility fractures of the pelvis (FFPs). Modifying gut microbiota has been found to impact cytokine pathways involved in bone formation and resorption. This study examined the impact of probiotic treatment pre- and post-unilateral pubic rami fracture on bone microstructure and load-to-failure of healing fractured and intact (unfractured) contralateral hemi-pelvises.

METHODS: Twenty-one 6-month-old female Sprague Dawley rats were bilaterally ovariectomized and housed for 3 months to establish an osteoporotic phenotype. At 9-months old, stable unilateral fractures of the superior and inferior pubic rami of the left hemi-pelvis (Type 1a FFP) were created. Prior to fracture creation, rats were randomly separated into control (phosphate buffered saline (PBS) administered for 12-weeks), pre-fracture treatment (probiotics administered for 12-weeks starting 6-weeks pre-fracture), and post-fracture treatment (probiotics administered for 6-weeks post-fracture) groups. At 6-weeks post-fracture, rats were sacrificed, and their pelvises were harvested, µCT imaged, and evaluated via microstructural analysis and biomechanical testing.

RESULTS: On the intact hemi-pelvises, the pre-fracture treatment group (n=5) had significantly higher bone volume (BV) (p=0.050), bone volume fraction (BV/TV) (p=0.019), bone mineral density (BMD) (p=0.019), and tissue mineral density (TMD) (p=0.014) when compared to those in the post-fracture treatment group (n=7). The intact hemi-pelvises of the pre-fracture treatment group also had significantly increased trabecular thickness (TbTh) (p=0.021) when compared to those in the control group (n=6). On the fractured hemi-pelvises, the pre-fracture group had increased total volume (TV) (p=0.020), BV (p=0.011), and BV/TV (p=0.026) when compared to the control group (n=4). While load-to-failure was correlated with microstructural parameters (BV/TV (r=0.42, p=0.015), trabecular number (TbN) (r=0.42, p=0.014), BMD (r=0.55, p=0.0008), TMD (r=0.40, p=0.019) and trabecular spacing (TbS) (r=-0.58, p=0.0003), no significant differences in bone strength were found between groups.

CONCLUSIONS: Probiotic treatment was shown to improve bone microstructure in osteoporotic rats, however, efficacy was related to treatment timing and duration. Administration of probiotics for 12-weeks beginning 6-weeks pre-fracture significantly enhanced bone quality in both the healing fractured and intact contralateral hemi-pelvises. This suggests a critical timing threshold exists for probiotic therapy to impact the gut microbiome, facilitating an alteration of the immune response post-fracture and producing positive structural changes in osteoporotic pelvic bone.},
}

@article {pmid41363910,
year = {2025},
author = {Armstrong, MT and Antunes, K and Willis, NB and Meyer, MB and Pierre, JF and Ozturk, G},
title = {Whey Protein Phospholipid Concentrate and Its Fractions as a Diet Intervention Enhance Bone Health and Alter the Gut Microbiome in Weanling Mice.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {23},
pages = {e71260},
doi = {10.1096/fj.202502683R},
pmid = {41363910},
issn = {1530-6860},
support = {N/A//University of Wisconsin-Madison Dairy Innovation Hub/ ; DK007665//HHS | National Institutes of Health (NIH)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Whey Proteins/pharmacology ; Mice ; *Phospholipids/pharmacology ; Male ; Bone Density/drug effects ; *Bone Development/drug effects ; Weaning ; Mice, Inbred C57BL ; *Bone and Bones/drug effects/metabolism ; },
abstract = {Early post-weaning growth is a critical window for bone development, and diet plays a central role in establishing peak bone mass in early life. Whey protein phospholipid concentrate (WPPC), a co-product of whey protein isolate manufacturing, is enriched in bioactive lipids and proteins that may support bone development and calcium homeostasis. This study aimed to investigate the effects of WPPC and its protein- and lipid-enriched fractions on bone development, gene expression, and gut microbiota in weanling mice. WPPC was fractionated using temperature-dependent centrifugation, microfiltration, and ultrafiltration, yielding lipid- and protein-rich components that were used to supplement isocaloric diets. Mice were fed either lipid fraction (Fat), protein fraction (Protein), or whole WPPC (WPPC) (10% by kcal; ~8.7% w/w) for 12 weeks. Compared to controls, the Protein and WPPC groups exhibited significantly increased femur length (4.44% and 4.01%, respectively), while the Fat group showed significantly higher bone mineral density (6.15%). Quantitative PCR of jejunal tissues revealed upregulation of calcium transporter genes (Cldn2, Cldn12, and Pmca1) in WPPC-fed mice with no changes in vertebral bone markers of osteocyte differentiation. Circulating iFGF23 levels also remained unchanged, suggesting limited endocrine involvement. Gut microbiota analysis via 16S rRNA sequencing showed diet-specific shifts, including increased Akkermansia and Streptococcus in the WPPC group and elevated Lactobacillaceae in the Protein and Fat groups. These findings demonstrate that WPPC and its enriched macronutrient fractions promote skeletal development and modulate calcium uptake and gut microbial composition, supporting their potential as functional ingredients for bone health applications in early life.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Whey Proteins/pharmacology
Mice
*Phospholipids/pharmacology
Male
Bone Density/drug effects
*Bone Development/drug effects
Weaning
Mice, Inbred C57BL
*Bone and Bones/drug effects/metabolism

@article {pmid41363768,
year = {2025},
author = {Basting, CM and Klatt, NR},
title = {Dissecting the Impact of the Gut Microbiome on HIV Reservoir Dynamics.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf560},
pmid = {41363768},
issn = {1537-6613},
}

@article {pmid41363709,
year = {2025},
author = {Tanwar, H and Gnanasekaran, JM and Ganesh, N and Zhou, C and Plotkin, A and Baima, G and Costalonga, M and Zhou, F and Feng, H and Jani, P and Raufman, JP and Thumbigere-Math, V},
title = {Dextran sodium sulfate confounds causal role of periodontitis in inflammatory bowel disease.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70045},
pmid = {41363709},
issn = {1943-3670},
support = {//University of Maryland School of Dentistry/ ; },
abstract = {BACKGROUND: Emerging evidence supports a bidirectional link between periodontitis and inflammatory bowel disease (IBD). To investigate this relationship, experimental models commonly use dextran sodium sulfate (DSS) to induce colitis. However, DSS is presumed to selectively affect the colon, and its potential off-target effects on the oral cavity remain poorly understood. We examined whether DSS disrupts oral health, potentially confounding oral-gut axis research.

METHODS: C57BL/6 mice received 2% DSS in drinking water for 8 days, followed by 2 days of untreated water. Colitis severity was assessed by weight loss, colon length, histopathology, and quantitative real-time-polymerase chain reaction (qRT-PCR). Oral health was evaluated via micro-computed tomography (micro-CT) analysis of alveolar bone, gingival histology, cytokine expression, and 16S rRNA sequencing of the oral microbiome.

RESULTS: DSS induced hallmark features of colitis, including weight loss, colon shortening, epithelial crypt damage, and mucosal inflammation. Strikingly, DSS also induced significant oral pathology, including alveolar bone loss, gingival epithelial hyperplasia, inflammatory infiltration, and upregulated gingival pro-inflammatory cytokines (interleukin [IL] -6, IL-17, tumor necrosis factor-alpha [TNF-α]). DSS further altered the oral microbiota causing reduced alpha-diversity and a dysbiotic shift, with enrichment of Streptococcus danieliae and depletion of commensals such as Lactobacillus murinus and Clostridium ASF502. These microbial changes were accompanied by upregulated pathways involved in carbohydrate metabolism, oxidative stress response, and environmental sensing.

CONCLUSION: DSS induces periodontal inflammation and oral dysbiosis, independent of colitis. These findings expose a critical confounder in oral-gut axis models and highlight the need to include DSS-only or periodontitis-only controls and alternative models to accurately distinguish systemic effects of DSS from true oral-gut interactions.

PLAIN LANGUAGE SUMMARY: This study shows that dextran sodium sulfate (DSS), a chemical used to model gut inflammation in mice, also causes gum disease-like changes-including bone loss, inflammation, and changes in oral bacteria. These findings reveal that DSS alone can affect the mouth and may confound studies investigating links between gum disease and inflammatory bowel disease, highlighting the need for better-controlled models.},
}

@article {pmid41363662,
year = {2025},
author = {Liu, B and Li, W and Zhao, R and Klauer, RR and Hansen, A and Miller, N and Chen, Y and Blenner, MA and Tang, YJ},
title = {Leveraging Retrieval-Augmented Generation to Accelerate Discoveries on Mealworm Larvae and Plastic Degradation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c14258},
pmid = {41363662},
issn = {1520-5851},
abstract = {Large language models (LLMs) are transforming broad research areas, yet concerns about their trustworthiness remain. This study explored the use of Retrieval-Augmented Generation (RAG) to improve LLMs' knowledge extraction in the field of mealworm-mediated plastic degradation. We integrated publications up to June 2024 (75 papers) to evaluate the model performance using a curated data set of 100 queries. GraphRAG, LightRAG, and a traditional RAG were examined with five LLM models (GPT-4o, GPT-5, Deepseek-V3.1, Qwen-plus, and Llama-3.3). Our results reveal that LightRAG improved LLMs the most in information extraction. Specifically, for quantitative information extraction, the best performing RAG + LLM pipeline achieves over 92% accuracy. Meanwhile, for open-ended queries, LightRAG + Llama answers the questions with the best balance of precision and information coverage. Moreover, empirical results validated the answers about the mealworm gut microbiome composition and plastic deconstruction patterns through the LightRAG + Llama pipeline. In designing plastic biodegradation experiments, the original LLMs outperformed RAG-trained LLMs. The expandable nature of RAG enables timely updates to the knowledge base. This study demonstrates a reliable application of advanced LLMs in the emerging environmental science field. Our findings identify challenges, such as conflict handling, and guide future research in scientific artificial intelligence.},
}

@article {pmid41363528,
year = {2025},
author = {Huang, PC and Ngo, CQ and Dewalt, A and Kolomiets, MV and Edwards, JA},
title = {A Broadly Distributed Rhizobacterium, Roseateles chitinivorans P500, Promotes Growth and Systemic Resistance via Jasmonic Acid-Dependent Oxylipin Signaling in Grasses.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {},
doi = {10.1094/MPMI-10-25-0142-FI},
pmid = {41363528},
issn = {0894-0282},
abstract = {Harnessing root-associated microbiomes to promote beneficial microbial compositions could offer a sustainable strategy to increase crop resilience. Major challenges impeding this strategy are the lack of understanding of which native members of the microbiome benefit the host and molecular signaling events underlying these benefits. In this study, we isolated a strain of Roseateles chitinivorans, RcP500, corresponding to the most abundant bacterial taxon in the switchgrass root microbiome. Inoculation of roots with RcP500 promoted growth and induced systemic resistance (ISR) to Bipolaris leaf spot of switchgrass and closely related Panicum hallii. R. chitinivorans is also highly abundant in rhizosphere and root microbiomes of maize and rice and enhanced growth of these two plant species. Furthermore, RcP500 elicited ISR in maize against anthracnose leaf blight and southern corn leaf blight. Bioassays and root metabolite profiling in maize wild-type (WT) and jasmonic acid (JA)-deficient opr7opr8 mutant plants revealed the requirement of JA-dependent processes in RcP500-elicited synthesis of the JA precursor, 12-OPDA (cis-(+)-12-oxo-phytodienoic acid) and an α-ketol, 9,10-KODA (9-hydroxy-10-oxo-12(Z)-octadecadienoic acid), two oxylipins previously implicated in ISR signaling. Xylem sap transfusion of RcP500 colonized plants to naïve receiver plants corroborated the role of JA in promoting these signaling intermediates. While root JA synthesis was downregulated upon RcP500 colonization, gibberellic acid was induced, suggesting a potential mechanism behind simultaneous growth promotion and ISR triggered by this bacterium. Overall, this study identified a novel rhizobacterium with a broad host range that promotes growth and systemic resistance across multiple plant species in a JA-dependent, ketol-driven manner.},
}

@article {pmid41363457,
year = {2025},
author = {Koetsier, RA and Reitz, ZL and Belzer, C and Chevrette, MG and Handelsman, J and Zhu, Y and van der Hooft, JJJ and Medema, MH},
title = {Using cross-species co-expression to predict metabolic interactions in microbiomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0132125},
doi = {10.1128/msystems.01321-25},
pmid = {41363457},
issn = {2379-5077},
abstract = {In microbial ecosystems, metabolic interactions are key determinants of species' relative abundance and activity. Given the immense number of possible interactions in microbial communities, their experimental characterization is best guided by testable hypotheses generated through computational predictions. However, widely adopted software tools-such as those utilizing microbial co-occurrence-typically fail to highlight the pathways underlying these interactions. Bridging this gap will require methods that utilize microbial activity data to infer putative target pathways for experimental validation. In this study, we explored a novel approach by applying cross-species co-expression to predict interactions from microbial co-culture RNA-sequencing data. Specifically, we investigated the extent to which co-expression between genes and pathways of different bacterial species can predict competition, cross-feeding, and specialized metabolic interactions. Our analysis of the Mucin and Diet-based Minimal Microbiome (MDb-MM) data yielded results consistent with previous findings and demonstrated the method's potential to identify pathways that are subject to resource competition. Our analysis of the Hitchhikers of the Rhizosphere (THOR) data showed links between related specialized functions, for instance, between antibiotic and multidrug efflux system expression. Additionally, siderophore co-expression and further evidence suggested that increased siderophore production of the Pseudomonas koreensis koreenceine BGC deletion-mutant drives siderophore production in the other community members. In summary, our findings confirm the feasibility of using cross-species co-expression to predict pathways potentially involved in microbe-microbe interactions. We anticipate that the approach will also facilitate the discovery of novel gene functions through their association with other species' metabolic pathways, for example, those involved in antibiotic response.IMPORTANCEAn improved mechanistic understanding of microbial interactions can guide targeted interventions or inform the rational design of microbial communities to optimize them for applications such as pathogen control, food fermentation, and various biochemical processes. Existing methodologies for inferring the mechanisms behind microbial interactions often rely on complex model-building and are, therefore, sensitive to the introduction of biases from the incorporated existing knowledge and model-building assumptions. We highlight the microbial interaction prediction potential of cross-species co-expression analysis, which contrasts with these methods by its data-driven nature. We describe the utility of cross-species co-expression for various types of interactions and thereby inform future studies on use-cases of the approach and the opportunities and pitfalls that can be expected in its application.},
}

@article {pmid41363449,
year = {2025},
author = {Meyer, KM and Lindow, SE},
title = {Microbial dispersal from surrounding vegetation influences phyllosphere microbiome assembly of corn and soybean.},
journal = {mBio},
volume = {},
number = {},
pages = {e0333525},
doi = {10.1128/mbio.03335-25},
pmid = {41363449},
issn = {2150-7511},
abstract = {Non-crop plants surrounding agricultural fields provide numerous ecological services to crops but have rarely been considered a source of microorganisms during the early stages of crop growth. In this study, we test whether crops in close proximity to surrounding woodland habitat fragments develop a denser microbiome that more closely resembles the microbiome composition of the surrounding vegetation than plants farther away. We sampled epiphytic bacteria from corn and soybean plants weekly for 4 (corn) and 3 (soybean) weeks during early development using a spatially explicit design, and on the final time point, we sampled additional cohorts of younger leaves. To contextualize the source strength of the surrounding vegetation, we also sampled soil at each sampling location. Both crop species exhibited a microbiome density gradient and a decay of microbiome similarity to the surrounding vegetation over a distance of 100 m from the vegetation at many time points. Phyllosphere microbiome similarity to the soil tended to increase into the field interior. The strength of host microbiome filtering also depended on the proximity to the surrounding vegetation, with intermediate to most distant locations exhibiting the highest values of host filtering. Last, the microbiomes of younger leaves tended to more closely resemble those of the older surrounding conspecific leaves than the soil or surrounding woodland vegetation. Overall, our study demonstrates that dispersal of bacteria from nearby leaves can shape the abundance and composition of developing crop phyllosphere microbiomes and highlights the diminishing role that soil plays when plant sources are closer or more abundant.IMPORTANCEA central concern in microbial ecology is understanding the sources of microbial colonists and how proximity to such sources impacts community assembly. This area of research is especially important for plants during early stages of development, where the arrival of leaf-specialized bacteria plays an influential role in priming plant immunity and consequently promoting disease resistance. In this study, we test the effect of dispersal from surrounding vegetation on the phyllosphere assembly of corn and soybean using a time series over the early stages of growth. Our work demonstrates that at these early developmental stages, non-crop vegetation surrounding croplands acts as a meaningful source of phyllosphere microorganisms. We further show that the influence of soil on the phyllosphere depends on host proximity to surrounding vegetation and that microbiomes of young leaves emerging on more mature plants tend to be more influenced by older surrounding crop leaves than soil or non-crop leaves.},
}

@article {pmid41363330,
year = {2025},
author = {Licata, AG and Zoppi, M and Dossena, C and Rossignoli, F and Rizzo, D and Bergamaschi, L and Nigro, O and Chiaravalli, S and Massimino, M and De Cecco, L},
title = {A QIIME2-based workflow for multi-amplicon 16S rRNA profiling.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0083625},
doi = {10.1128/mra.00836-25},
pmid = {41363330},
issn = {2576-098X},
abstract = {We present an open-source QIIME2 pipeline for 16S multi-amplicon sequencing. Benchmarked against proprietary software with a mock community, our workflow demonstrates comparable sequencing depth and taxonomic accuracy (F1-Score=0.875). The multi-region approach outperforms single amplicons, validating our pipeline as a robust alternative for semiconductor-based sequencing data.},
}

@article {pmid41363094,
year = {2025},
author = {Fu, W and Li, P and Sun, C and Sun, B and Kong, Z and Zhu, Y and Tian, H and Guo, Q and Lai, H},
title = {Lysobacter Orchestrates Plant-Microbiome Crosstalk to Enhance Tomato Fruit Quality.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c09587},
pmid = {41363094},
issn = {1520-5118},
abstract = {Lysobacter can promote plant growth and induce disease resistance, but its potential contribution to fruit quality remains understudied. This study investigated the role of Lysobacter fragariae P25 in regulating tomato fruit quality through integrated metabolomics, transcriptomics, and metatranscriptomics. We found that P25 inoculation modified fruit flavor and nutrition by increasing the accumulation of soluble sugars, unsaturated fatty acids, and essential amino acids and decreasing the tomatidine content. Fruit color and functional quality were enhanced upon inoculation with higher levels of flavonoids, lycopene, vitamins, and phenolic acids. The inoculated soil showed greater fertility and biological activity coupled to heightened microbial diversity and recruitment of potentially beneficial taxa in the rhizosphere, shifting community functions and networks toward healthier patterns. Cross-kingdom interactions between microbial genes and fruit metabolites were identified, linking rhizosphere microbiomes to fruit quality. Our results demonstrate P25-mediated plant-microbiome crosstalk in tomatoes, which drives metabolic reprogramming and consequently enhances the overall fruit quality.},
}

@article {pmid41362927,
year = {2025},
author = {Sun, D and Hua, Z and Xiao, Y and He, D and Wu, H and Lin, X and Chen, Q and Li, Z and Hou, Y},
title = {Bidirectional microbial regulation by tyrosine metabolism enhances palmatine-mediated colitis protection.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2596405},
doi = {10.1080/19490976.2025.2596405},
pmid = {41362927},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Berberine Alkaloids/pharmacology ; *Tyrosine/metabolism ; *Colitis/microbiology/prevention & control/chemically induced/drug therapy ; Mice, Inbred C57BL ; Cresols/metabolism ; Dysbiosis ; Disease Models, Animal ; Th17 Cells/immunology/drug effects ; Male ; Dextran Sulfate ; },
abstract = {Gut microbiota dysbiosis and intestinal immune dysfunction contribute to the disease pathogenesis of ulcerative colitis (UC), therapeutic strategies aim to reshape microbial balance and reduce inflammation. It is unclear that how this bidirectional regulation between microbe-immune system is achieved and what is a possible nexus point for this regulation. Here, we demonstrated that palmatine (PAL) alleviates colitis by modulating interference competition between two microbes through the mediation of microbial tyrosine metabolites. Specifically, PAL directly inhibits B. acidifaciens while indirectly promoting the growth of B. stercorirosoris in mice with DSS-induced colitis. Notably, p-cresol (PC), a crucial microbial metabolite produced by B. acidifaciens, exacerbates colitis by promoting Th17 cells activation and inhibiting the growth of B. stercorirosoris. Furthermore, the immediate reduction in p-hydroxyphenylacetic acid, which is metabolized by B. stercorirosoris, contributes to the aggravation of colitis. Mechanistically, PC significantly inhibited the glycolysis of B. stercorirosoris, with downregulation of gene expression associated with glycolysis. In addition, we found that the inhibitory function of PC was offset by the addition of large amounts of polysaccharide and glucose in the medium of B. stercorirosoris. In summary, this study uncovers the mechanism by which palmatine‒microbiome‒host crosstalk cooperatively alleviate colitis through PC-mediated the bidirectional regulation. These findings propose that microbial metabolites function as regulators of microbiota‒host interactions, offering potential interventions for the treatment or prevention of dysbiosis-driven diseases.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Berberine Alkaloids/pharmacology
*Tyrosine/metabolism
*Colitis/microbiology/prevention & control/chemically induced/drug therapy
Mice, Inbred C57BL
Cresols/metabolism
Dysbiosis
Disease Models, Animal
Th17 Cells/immunology/drug effects
Male
Dextran Sulfate

@article {pmid41362921,
year = {2025},
author = {Müller, P and Schmidtchen, V and de la Cuesta-Zuluaga, J and Pérez Jiménez, L and Gekeler, C and Mateus, A and Maier, L},
title = {Antagonistic drug interactions protect commensal Bacteroidaceae from macrolides via an RND-type efflux pump.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2596806},
doi = {10.1080/19490976.2025.2596806},
pmid = {41362921},
issn = {1949-0984},
mesh = {*Macrolides/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/drug effects ; *Bacteroidetes/drug effects/genetics/metabolism ; *Bacterial Proteins/metabolism/genetics ; Drug Resistance, Bacterial ; *Membrane Transport Proteins/metabolism/genetics ; Drug Interactions ; },
abstract = {Antibiotics are essential to modern medicine, but their broad-spectrum activity can unintentionally disrupt the gut microbiota. This collateral damage may be alleviated by antagonistic drug interactions, in which specific compounds used in combination therapies selectively protect beneficial gut microbes from antibiotic activity. Using efflux pump inhibitors, transcriptomic and proteomic analyses, and targeted gene deletions, we show that a variety of non-antibiotic pharmaceuticals-from diverse therapeutic classes and at sub-inhibitory concentrations-can protect multiple Bacteroidales species from macrolide antibiotics. In Bacteroidaceae, this protection is mediated by a resistance-nodulation-division (RND)-type efflux pump, which is induced by the non-antibiotic drug but not by macrolides alone. Notably, protection persists even after the non-antibiotic drug is removed, and prolonged exposure results in stable macrolide resistance that is dependent on the RND-type efflux pump. Our findings illustrate how non-antibiotic drugs can inadvertently activate otherwise silent detoxification systems in gut microbes, uncovering resistance mechanisms that arise without antibiotic selection or gene transfer. While this can be harnessed to protect the microbiome during antibiotic therapy, it also reveals hidden resistance phenotypes that may escape detection in standard antimicrobial resistance assays.},
}

*Macrolides/pharmacology
*Anti-Bacterial Agents/pharmacology
Gastrointestinal Microbiome/drug effects
*Bacteroidetes/drug effects/genetics/metabolism
*Bacterial Proteins/metabolism/genetics
Drug Resistance, Bacterial
*Membrane Transport Proteins/metabolism/genetics
Drug Interactions

@article {pmid41362820,
year = {2026},
author = {Lanton, T and Eidelshtein, D and Rachmilewitz, J and Abramovitch, R and Pappo, O and Udi, S and Baraghithy, S and Tam, J and Perles, S and Williams, E and Elgavish, S and Ruppo, S and Benyamini, H and Mor, U and Elinav, E and Schmidt-Arras, D and Rehman, A and Rosenstiel, P and Giannou, A and Huber, S and Rose-John, S and Galun, E and Axelrod, JH},
title = {Blockade of Interleukin-6 Trans-signaling in the Presence of Certain Gut Microbiota Induces Mature-onset Obesity in Mice.},
journal = {Gastro hep advances},
volume = {5},
number = {2},
pages = {100819},
pmid = {41362820},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Interleukin-6 (IL-6) performs multiple roles in regulating metabolic pathways in both mice and man. Here, we examined the age-dependent metabolic phenotype of SGP mice-mice overexpressing sgp130, a factor that specifically blocks IL-6 trans-signaling-that were housed in distant vivaria.

METHODS: Transgenic SGP mice engineered to block IL-6 trans-signaling and wild-type littermates were raised in a Jerusalem animal facility to up to 14 months of age and assessed for weight gain, body composition, and metabolic determinants of energy expenditure in young versus aged mice. Proteomic and RNA-seq analyses were performed on liver samples as a function of age and genotype.

RESULTS: At ∼6 months of age, weight gain, body fat accumulation, hepatosteatosis, hyperglycemia, and macrophage recruitment to adipose tissue emerged and progressed with age in SGP mice maintained in the Jerusalem animal facility, but not in 3 other vivaria. IL-6/sIL-6R blockade strongly reduced signal transducer and activator of transcription 3 phosphorylation in the liver, and hepatocyte-targeted ablation of signal transducer and activator of transcription 3 recapitulated the IL-6 trans-signaling blockade phenotype. Multiomics analyses of mouse livers revealed age- and genotype-related changes in gene expression profiles attributable to bacterial byproducts. Depletion of the gut microbiota by antibiotic treatment from the age of 6 months reversed the obese phenotype in transgenic mice, confirming the crucial role of the microbiome in the phenotype. Accordingly, the microbiome of mice from the Jerusalem animal facility differed significantly from that of mice from animal facilities in Kiel and Hamburg, Germany, where the same mice did not develop a metabolic phenotype.

CONCLUSION: These findings reveal the crucial functions of IL-6 trans-signaling in preventing mature-onset body fat accumulation induced by certain intestinal microbiota.},
}

@article {pmid41362765,
year = {2025},
author = {Luo, J and Yang, J and Li, S and Liu, J and Qin, X and Li, L and Liu, W and Xing, H},
title = {Tumor-resident microbiota in gynecologic malignancies: Molecular mechanisms, clinical correlations, and translational potential.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113729},
pmid = {41362765},
issn = {2589-0042},
abstract = {Intratumoral microbiota refers to the microbial communities, including bacteria, fungi, and viruses, residing within tumor tissues and forming part of the tumor microenvironment. Evidence shows that it significantly influences solid tumors like colorectal and breast cancer. Advances in sequencing have revealed the specific distribution of these microbes in gynecologic malignancies. Their dynamic composition is closely linked to tumor initiation, progression, and response to therapy, providing new insights for precision medicine. This review examines their molecular mechanisms and clinical relevance, focusing on impacts on diagnosis (e.g., microbial biomarkers), personalized treatment (e.g., modulation of chemotherapy/immunotherapy efficacy), and prognosis (e.g., recurrence risk prediction). It also discusses the translational potential and clinical application challenges of targeting microbiota, aiming to provide new strategies for precision medicine in gynecologic oncology.},
}

@article {pmid41362728,
year = {2026},
author = {Li, Q and Xia, S and Zhang, X and Liu, Y and Xiao, X and Yang, J},
title = {Gut Microbiota-Driven Pathways Linking Chronic Stress to Tumor Progression.},
journal = {International journal of biological sciences},
volume = {22},
number = {1},
pages = {258-279},
pmid = {41362728},
issn = {1449-2288},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Neoplasms/microbiology/metabolism/pathology ; Dysbiosis/microbiology ; Disease Progression ; Animals ; },
abstract = {Chronic stress is increasingly recognized as a critical factor influencing tumor progression, but its underlying mechanisms remain incompletely understood. This review examines the role of gut microbiota as a critical mediator linking chronic stress to tumor progression. Recent evidence suggests that chronic stress triggers gut dysbiosis, characterized by reduced microbial diversity, depletion of beneficial bacteria, and enrichment of potentially harmful species. We summarize the mechanisms by which chronic stress regulates gut microbial dysbiosis, including stress-related hormone signaling, intestinal inflammation, mucosal barrier disruption, and altered gut motility. Additionally, we examine how stress-induced dysbiosis contributes to tumor progression through immune suppression, metabolic reprogramming, enhanced tumor stemness, and potentially through barrier dysfunction, and chronic inflammation. We further discuss potential therapeutic interventions, including specific probiotics, prebiotics and other strategies that may help suppress tumor development by modulating the stress-microbiota-cancer axis. In conclusion, these emerging insights provide a foundation for novel therapeutic strategies that target the stress-microbiome-cancer axis, which may help suppress tumor progression and complement conventional cancer treatments to improve clinical outcomes in cancer patients.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Neoplasms/microbiology/metabolism/pathology
Dysbiosis/microbiology
Disease Progression
Animals

@article {pmid41362644,
year = {2025},
author = {Wu, H and Sun, D and Fang, S and Pan, Q and Yue, C},
title = {Genetically Predicted Causal Risk Factors for Preeclampsia: A Comprehensive Mendelian Randomization Study.},
journal = {International journal of women's health},
volume = {17},
number = {},
pages = {5105-5116},
pmid = {41362644},
issn = {1179-1411},
abstract = {BACKGROUND: Preeclampsia is a complex hypertensive disorder of pregnancy, significantly impacting maternal and fetal health worldwide. Despite extensive research, its pathogenesis, involving inflammatory, immune, microbiological, and metabolic factors, requires comprehensive elucidation.

METHODS: This study applied Mendelian randomization (MR) to investigate causal relationships between multi-omics traits and the risk of preeclampsia. The genome-wide association studies (GWAS) datasets used consisted of immune cells (N = 3757), inflammatory factors (N = 14,824), gut microbiota (N = 7738), circulating metabolites (N1 = 7824, N2 = 8299), plasma proteins (N = 3301), and preeclampsia (7212 cases, 194,266 controls). The inverse variance-weighted method was used in the main analysis, and the weighted median, weighted mode, and MR Egger regression were used in sensitivity analyses.

RESULTS: Our analysis identified 81 potential causal factors for preeclampsia. Among the most novel and clinically significant findings were several druggable plasma proteins, including Astacin-like metalloendopeptidase (ASTL) and Baculoviral IAP repeat-containing protein 3 (BIRC3), which exhibited strong causal evidence. Furthermore, we identified specific gut microbiota genera, notably Bifidobacterium, as potential protective factors. We also validated the causal roles of key metabolic disturbances, like cysteine and guanidinoacetate, and dysfunctions in specific immune cell populations, particularly regulatory T and B cells.

CONCLUSION: These findings highlight the intricate interplay of immune, inflammatory, microbiological, metabolic, and protein factors in preeclampsia, suggesting novel diagnostic and therapeutic targets. Further research is warranted to explore these associations in detail.},
}

@article {pmid41362618,
year = {2025},
author = {Ma, Y and Chen, X and Li, J and Ma, J},
title = {Atopobium vaginae advances endometrial cancer growth via macrophage function in mouse models.},
journal = {iScience},
volume = {28},
number = {12},
pages = {113820},
pmid = {41362618},
issn = {2589-0042},
abstract = {The female genital tract microbiome is essential for health. This study investigated the endometrial microbiota in endometrial cancer (EC) patients and explored their role in disease progression. We collected samples from patients with benign uterine conditions, endometrial hyperplasia, and EC. Microbial diversity was analyzed using 16S sequencing. The effects of Atopobium vaginae on macrophage phagocytosis, polarization, and EC progression were examined in vitro and in vivo. Atopobium vaginae was significantly upregulated in EC and hyperplasia patients, correlating with increased levels of inflammatory cytokines IL-6 and IL-10. Experiments demonstrated that Atopobium vaginae inhibited macrophage phagocytosis, promoted M2 polarization, and increased tumor size, thereby advancing EC progression. Our findings highlight Atopobium vaginae as a key factor in EC progression by regulating macrophage function and inflammatory cytokines. The study provides new insights into EC pathogenesis and reveals potential therapeutic avenues.},
}

@article {pmid41362405,
year = {2025},
author = {Jena, S and Lawore, D and Green, LN and Brubaker, DK},
title = {Characterizing species-specific metabolic signatures in vaginal microbiota across planktonic and biofilm states.},
journal = {Biofilm},
volume = {10},
number = {},
pages = {100330},
pmid = {41362405},
issn = {2590-2075},
abstract = {Bacterial vaginosis (BV) affects about 29 % of U.S. women, with higher rates in some groups and up to 50-69 % recurrence within a year. It increases the risk of STIs, pregnancy complications, and can cause significant discomfort and reduced quality of life. Prior studies mapped vaginal metabolomes, but individual microbial metabolite signatures remain poorly understood. Given that biofilms exhibit distinct metabolic requirements compared to planktonic cultures, analyzing biofilm vs. planktonic culture metabolites with their unique metabolic needs may uncover novel treatment targets. This study provides a comprehensive metabolomic comparison of key vaginal microbes-Lactobacillus crispatus, Gardnerella vaginalis, and Lactobacillus iners under both planktonic and biofilm conditions. Our analysis showed that metabolite production and consumption vary by microbe and growth mode. G. vaginalis formed biofilms in multiple media, with limited shared metabolic pathways between its biofilm types, indicating unique metabolic processes. Despite L. crispatus suspension and biofilm cultures sharing 142 consumed and 104 produced metabolites, the biofilm culture demonstrated a remarkable metabolic shift. Comparing all three species, we observed convergence in nutrient utilization, but divergence in metabolic outputs reflecting growth-specific adaptations, highlighting the importance of considering microbial state in vaginal microbiome studies.},
}

@article {pmid41362323,
year = {2025},
author = {Zhang, X and Zhu, L and Han, Y and Wang, K and Ji, N and Fan, J and Zhou, Y and Yao, X and Li, B and Lu, S and Guan, L},
title = {Comparative analysis of metabolite and microbial community dynamics during spontaneous fermentation of Lonicera caerulea berries.},
journal = {Food chemistry: X},
volume = {32},
number = {},
pages = {103301},
pmid = {41362323},
issn = {2590-1575},
abstract = {Spontaneous fermentation of Lonicera caerulea berries was monitored using integrated widely targeted metabolomics and high-throughput microbiome sequencing to elucidate the dynamic changes in metabolites and microbial communities. Throughout fermentation, 90 non-volatile metabolites and 52 volatile compounds were identified with variable importance in projection (VIP) ≥ 1 and p ≤ 0.05. The evolution of distinct flavor profiles of the fermented L. caerulea berries was attributed to significant changes in the transformation and accumulation of organic acids, lipids, saccharides, phenolic compounds, and amino acids. Metabolic pathway analysis indicated that linoleic acid and phenylalanine metabolism were dominant in the early fermentation stage, whereas aminoacyl-tRNA biosynthesis, cyanoamino acid metabolism, and arginine biosynthesis prevailed in the later phase. Fungal communities were prevalent throughout fermentation. Early fermentation was dominated by Valsa, Actinobacillus, Mortierella, and Ascomycota, and late fermentation was Gluconobacter and Wickerhamomyces enrichment. Notably, strong and significant correlations (|r| > 0.8, p < 0.05) were observed between specific microorganisms, such as Wickerhamomyces and Gluconobacter, and key metabolites, including glucose-6-phosphate, methionine, leucine, isoleucine, and glutamic acid. These findings offer fundamental insights into the biochemical mechanisms of spontaneous fermentation of L. caerulea and provide a scientific basis for developing controlled fermentation strategies to improve the quality of fruit-based foods.},
}

@article {pmid41362317,
year = {2025},
author = {Pajuelo, E and Romano-Rodríguez, E and Mateos-Naranjo, E and Flores-Duarte, NJ and Rodríguez-Llorente, ID and Redondo-Gómez, S},
title = {Halophytes as holobionts: disentangling the contribution of plant genotype and environmental factors to the associated microbiome of hydro- and xerohalophytes.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100511},
pmid = {41362317},
issn = {2666-5174},
abstract = {Halophytes are of great interest for their ecosystemic benefits and valuable secondary metabolites. However, they are threatened by factors such as heat waves, drought, increased salinity and pollution, associated with climate change and human activity. In this context, their associated microbial communities are crucial for their survival. Despite that, there are no comparative studies on microbial communities associated with two types of halophytes: hydrohalophytes (plants from humid saline environments) and xerohalophytes (plants from saline arid environments). This study aimed to investigate the factors that determine the structure of microbial communities of three hydrohalophytes of the Southwest Spain (Atlantic coastal), in particular Atriplex portulacoides, Salicornia perennis and Suaeda vera; and three xerohalophytes of Southeast Spain (Mediterranean coast and inland saltmarshes), namely, Atriplex glauca, Anabasis articulata and Halocnemum strobilaceum. Samples were collected in three locations and two seasons (autumn and spring) to analyze how plant genetics and environmental factors influence their microbiota. The analysis was done by sequencing the 16S V3-V4 region in samples of different plant compartments: endophytes, rhizosphere soils and bare soils. The results showed strong attraction of bacteria and archaea to the rhizosphere, although further tight selection limits the number of endophytes. A "core" of endophytes common to both functional halophytes was identified, including the genera Kushneria, Halomonas, Pseudoalteromonas and Zunongwangia, which were considered generalists. In addition, specific genera considered as specialists were found: hydrohalophytes showed affinity for Vibrio, Pseudomonas and Marinomonas, while xerohalophytes harbored Marinilactobacillus, Alkalicoccus, Alkalibacterium and Arthrobacter. Although most endophytes persist across seasons, their relative abundances can change for better adaptation. Clear differences were also encountered among the rhizosphere inhabitants in both functional halophytes: whereas halophilic ammonia oxidizing archaea were prevalent in the rhizosphere of hydrohalophytes, versatile adaptive bacteria were predominant in that of xerohalophytes. These microorganisms play vital roles, including promoting plant growth, participating in the carbon and nitrogen metabolisms, and recycling organic matter. In conclusion, the study determined that the main factors shaping the microbial populations associated to halophytes were: halophyte type > halophyte species > soil characteristics > seasonality.},
}

@article {pmid41362316,
year = {2025},
author = {Ling, X and Yim, CC and Sun, Q and Peng, Y and Zhang, Y and Kam, KW and Young, AL and Ip, P and Tsui, SK and Tham, CC and Pang, CP and Chen, LJ and Yam, JC},
title = {The pediatric ocular surface microbiome in pet-owning households.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100518},
pmid = {41362316},
issn = {2666-5174},
abstract = {INTRODUCTION: Pet exposure is associated with the allergy development in children. The influence of pet exposure on the pediatric ocular surface microbiome (OSM), a potential mediator of ocular immunity, remains uncharacterized. This study investigates OSM alterations in children with household pet contact.

METHODS: In this cross-sectional study, conjunctival swabs from 347 children (aged 5-15 years) in the CUHK Hong Kong Children Eye Study were analyzed. 16S rRNA sequencing (V3-V4 region) was performed, followed by bioinformatic analysis (QIIME2, DADA2, SILVA 138) and functional prediction (PICRUSt2). Alpha/beta diversity, taxonomic composition, and KEGG pathways were compared.

RESULTS: Pet-exposed children had higher alpha diversity (Shannon/Simpson/Observed indexes; P < 0.05) with positive dose-response to contact time. Compositionally, these children showed distinct beta diversity (Bray-Curtis Distance, P = 0.015) and enriched genera (Streptococcus, Actinomyces, Neisseria; LDA Score > 2.0). NF-κB signaling and VEGF signaling were predicted to enrich in pet-exposed children while non-exposed children showed increased macrolide biosynthesis pathways.

CONCLUSION: Pet exposure associates with increased diversity, enrichment of taxa associated with animals and the environment, and NF-κB/VEGF pathway activation in the pediatric OSM. This suggests OSM as a novel mechanism for pet-related immune modulation, potentially influencing ocular surface health and allergy susceptibility.},
}

@article {pmid41361940,
year = {2025},
author = {Zheng, J and Wang, K and He, J and Guan, Y and Wu, Y and Wu, J},
title = {Surface Microbiome Profiling of Dental Elevators Using Third-Generation Sequencing: Implications for Infection Control in Dental Practice.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70178},
doi = {10.1002/mbo3.70178},
pmid = {41361940},
issn = {2045-8827},
support = {//This work was supported by Beijing Natural Science Foundation (7214274) and National Natural Science Foundation of China (52473286)./ ; },
mesh = {Humans ; Biofilms/growth & development ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; *Dental Instruments/microbiology ; Cross Infection/prevention & control/microbiology ; DNA, Bacterial/genetics ; Equipment Contamination ; Infection Control ; Sequence Analysis, DNA ; },
abstract = {This study aimed to characterize the biofilm-forming microbial communities on clinically used dental elevators to assess their potential risks of cross-contamination and nosocomial infections resulting from percutaneous injuries in dental healthcare settings. Over a period of 3 consecutive weeks starting on August 1, 2024, biofilm samples were collected from the tips of 15 dental elevators used on the first five wisdom teeth extraction patients daily. Total DNA was extracted, and specific barcoded primers were synthesized to construct SMRTbell sequencing libraries, which were subsequently sequenced using the PacBio Sequel II platform. The sequencing generated 923,990 circular consensus sequences (CCS), with an average of 61,599 CCS per sample. Taxonomic annotation revealed a diverse microbial community dominated by genera such as Prevotella, Fusobacterium, Streptococcus, and Lactobacillus, alongside unclassified taxa from the Candidatus Saccharibacteria (TM7) group. Alpha and beta diversity analyses demonstrated significant variations in microbial composition across samples, highlighting the heterogeneity of biofilm formation, while strong positive correlations observed between specific bacterial genera, such as Bacillus and Paenibacillus, suggested potential co-colonization patterns. These findings underscore the complexity of microbial contamination on dental instruments and emphasize the need for improved sterilization protocols to mitigate infection risks. Consequently, this study provides valuable insights into the microbiological safety of dental practices and highlights the utility of third-generation sequencing in advancing infection control strategies.},
}

Humans
Biofilms/growth & development
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
*Dental Instruments/microbiology
Cross Infection/prevention & control/microbiology
DNA, Bacterial/genetics
Equipment Contamination
Infection Control
Sequence Analysis, DNA

@article {pmid41361886,
year = {2025},
author = {Liu, Y and Yu, S and Wang, X and Ye, D and Aili, M and Fu, X and Zou, J and Ma, Q},
title = {Integrated salivary microbiome and metabolome profiling reveals ecological and functional alterations in severe early childhood caries.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07541-9},
pmid = {41361886},
issn = {1479-5876},
support = {82170947//National Natural Science Foundation of China/ ; 32400094//National Natural Science Foundation of China/ ; 2025ZNSFSC0771//Natural Science Foundation of Sichuan Province/ ; RD-02-202402//Fundamental Research Funds for the Central Universities, Research and Develop Program, West China Hospital of Stomatology Sichuan University/ ; RCDWJS2023-10//Research Funding from West China School/Hospital of Stomatology Sichuan University/ ; },
abstract = {BACKGROUND: Early childhood caries (ECC), particularly severe early childhood caries (S-ECC), remains a prevalent chronic disease, significantly affecting children's health and quality of life. Despite extensive research, the detailed ecological and metabolic shifts underlying S-ECC pathogenesis are still poorly characterized. Integrating microbial and metabolic profiling of saliva may provide crucial insights and identify novel biomarkers and therapeutic targets.

METHODS: We performed high-throughput 16S rRNA gene sequencing and untargeted metabolomics to comprehensively profile the salivary microbiome and metabolome in children with S-ECC (n = 30) compared to caries-free (CF) controls (n = 30). Differential microbial taxa and metabolites were identified, and their functional implications were explored through KEGG pathway enrichment analysis. Furthermore, integrated correlation analysis was conducted to uncover interactions between key microbial taxa and metabolites.

RESULTS: Microbial community analysis revealed significant ecological alterations in the saliva of children with S-ECC, characterized by enrichment of potentially cariogenic taxa, including Rothia, Lautropia, Lactobacillus, Achromobacter, as well as Streptococcus mutans, Prevotella histicola, and Lachnoanaerobaculum saburreum. Conversely, health-associated genera such as Bergeyella and Acinetobacter were more abundant in CF children. Metabolomics identified a total of 4,325 salivary metabolites, among which 1,226 differed significantly between groups. Notably, metabolites involved in amino acid metabolism pathways-phenylalanine, tyrosine, D-amino acids, aminobenzoate, arginine, and proline-were upregulated in S-ECC saliva. Integrated analysis further revealed strong positive correlations between key cariogenic bacteria (S. mutans, P. histicola, L. saburreum) and multiple metabolites, including succinic acid, 2-piperidone, D-3-phenyllactic acid, 5-aminovaleric acid, L-malic acid, 2-hydroxypalmitic acid, LPE (16:0), vitamin K1 2,3-epoxide, leucylproline, and L-valine.

CONCLUSIONS: Our findings demonstrate distinct ecological and functional signatures in the salivary microbiome and metabolome associated with S-ECC. The identified microbial and metabolic alterations, particularly in amino acid metabolism, provide novel insights into the pathogenesis of S-ECC and highlight potential biomarkers for early detection and targeted intervention. However, the cross-sectional design and single time-point saliva collection limit the ability to assess longitudinal dynamics. Future longitudinal studies are warranted to track microbial and metabolomic changes during disease progression and intervention.},
}

@article {pmid41361854,
year = {2025},
author = {Dawkins, JJ and Gerber, GK},
title = {MMETHANE: interpretable AI for predicting host status from microbial composition and metabolomics data.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02270-z},
pmid = {41361854},
issn = {2049-2618},
support = {MTM2 2025512//National Science Foundation/ ; R35GM149270/GM/NIGMS NIH HHS/United States ; President's Scholar Award//Brigham and Women's Hospital/ ; },
abstract = {BACKGROUND: Metabolite production, consumption, and exchange are intimately involved with host health and disease, as well as being key drivers of host-microbiome interactions. Despite the increasing prevalence of datasets that jointly measure microbiome composition and metabolites, computational tools for linking these data to the status of the host remain limited.

RESULTS: To address these limitations, we developed MMETHANE, a purpose-built deep learning model for predicting host status from paired microbial sequencing and metabolomic data. MMETHANE incorporates prior biological knowledge, including phylogenetic and chemical relationships, and is intrinsically interpretable, outputting an English-language set of rules that explains its decisions. Using a compendium of six datasets with paired microbial composition and metabolomics measurements, we showed that MMETHANE always performed at least on par with existing methods, including blackbox machine learning techniques, and outperformed other methods on 80% of the datasets evaluated. We additionally demonstrated through two cases studies analyzing inflammatory bowel disease gut microbiome datasets that MMETHANE uncovers biologically meaningful links between microbes, metabolites, and disease status.

CONCLUSIONS: MMETHANE is an open-source software package that brings state-of-the-art interpretable AI technologies to the microbiome field, emphasizing usability with simple written explanations of its decisions and biologically relevant visualizations. This robust and accurate tool enables investigation of the interplay between microbes, metabolites, and the host, which is critical for understanding the mechanisms of host-microbial interactions and ultimately improving the diagnosis and treatment of human diseases impacted by the microbiome. Video Abstract.},
}

@article {pmid41361834,
year = {2025},
author = {Compare, D and Fosso, B and Nunziato, M and Sgamato, C and Di Maggio, F and D'Argenio, V and Granata, I and Zamparelli, MS and Lovero, D and Casaburi, G and Rocco, A and Coccoli, P and Pesole, G and Salvatore, F and Nardone, G},
title = {Gut mucosa-associated microbiota signatures in healthy individuals and patients at different stages of liver disease: a pilot study.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {99},
pmid = {41361834},
issn = {1757-4749},
support = {CIRO//Regione Campania/ ; PON03PE_00060_2//Ministero dell'Università e della Ricerca/ ; },
abstract = {BACKGROUND: The gut microbiota plays a key role in the progression of chronic liver disease and the development of hepatocellular carcinoma (HCC). However, findings on microbiota composition in such patients remain inconsistent, likely due to differences in disease aetiology and sample type. The mucosa-associated microbiota (MAM), residing in the intestinal mucin layer, more accurately reflects mucosal health than faecal microbiota, being more stable and less influenced by diet. This study aimed to characterise the ileal and sigmoid MAM in patients with chronic hepatitis C (CHC), liver cirrhosis (LC), and HCC.

METHODS: We performed DNA metabarcoding sequencing of mucosa samples collected from the ileum and sigmoid colon of patients at different stages of liver disease and healthy controls (HC). The predicted functions were analysed via phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) to infer metabolic pathways that can be expressed in the microbiome.

RESULTS: Among 33 participants (20 HCV-related liver disease and 13 healthy controls), MAM α-diversity decreased significantly in advanced disease stages, particularly in LC and HCC, regardless of the metric applied (p ≤ 0.05). β-diversity analyses showed distinct microbial community structures across groups. Both ileal and sigmoid MAM were dominated by Bacteroidetes, Firmicutes, and Proteobacteria, with enrichment of Firmicutes_D, Proteobacteria, and Fusobacteria in LC and HCC. Several genera, including Bulleidia, Pantoea, Clostridium_Q, Rothia, and Streptococcus, were significantly increased in HCC, whereas beneficial taxa such as Akkermansia and Butyricimonas were depleted. Functional predictions indicated enrichment of degradative pathways (e.g., taurine, chitin derivatives, and carbohydrate metabolism) in LC and HCC.

CONCLUSION: Our pilot study suggests that MAM alterations do not directly mirror liver disease progression but show distinct patterns associated with different stages. These associations, more evident in advanced disease, involve bacterial taxa linked to gut integrity, inflammation, and carcinogenesis. This exploratory work lays the groundwork for future studies to validate these findings and investigate their relevance to microbiome-based diagnostics and therapies in HCC.},
}

@article {pmid41361827,
year = {2025},
author = {Tao, M and Wu, T and Li, S and Tan, Y and Zhou, X and Chen, Y and Huang, L and Wang, W and Li, S and Wang, L and Luo, Z and Wang, Y and Ling, K and Liang, Z},
title = {Intratumoral Collinsella aerofaciens exhibits antitumor activity in endometrial carcinoma through activation of the p53 signaling pathway.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07543-7},
pmid = {41361827},
issn = {1479-5876},
support = {2019YFC1005202//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: The intratumoral microbiota plays dual roles in cancer progression and suppression, but its composition and functional mechanisms in endometrial carcinoma (EC) remain incompletely defined. This study aimed to characterize the EC intratumoral microbiome, elucidate microbial spatial localization, and identify bacteria with tumor-suppressive properties.

METHODS: Tumor and adjacent normal tissues from patients with EC were analyzed using 5R 16S rRNA sequencing to profile microbial communities, with fluorescence in situ hybridization (FISH) validating bacterial localization. Spatial transcriptomics (ST), single-cell RNA sequencing (scRNA-seq), and FISH were integrated to map microbiota-niche cell interactions. RNA sequencing was performed on EC cells treated with bacterial supernatant. Fecal microbiota transplantation (FMT) from EC patients to mice was used to assess gut-tumor microbial crosstalk.

RESULTS: Collinsella aerofaciens (C. aerofaciens), Haloamaerobium gallinarum, and Massilia oculi were enriched in adjacent normal tissues, while Bacteroides vulgatus (B. vulgatus) and Delfia tsuruhatensis dominated tumor tissues. Tumors exhibited reduced microbial richness versus normal tissues. C. aerofaciens localized predominantly to smooth muscle cells and modulated the tumor microenvironment, as revealed by FISH and ST-scRNA-seq integration. RNA sequencing suggested that C. aerofaciens suppressed EC progression by activating the p53 signaling pathway. FMT experiments demonstrated gut microbiota-driven remodeling of the tumor microbiome.

CONCLUSIONS: This study identifies C. aerofaciens as a novel tumor-suppressive bacterium in EC, with mechanistic evidence linking its activity to p53 pathway activation. Gut microbiota modulates intratumoral microbial composition, suggesting potential dual-target therapeutic strategies for EC.},
}

@article {pmid41361740,
year = {2025},
author = {Thompson, W and Al-Ahmad, A and Cieplik, F and Hbibi, A and Jakubovics, NS and Scholz, KJ and Teoh, L and Charles-Ayinde, M and Fox, CH},
title = {The IADR Policy Statement on Antimicrobial Resistance.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251388914},
doi = {10.1177/00220345251388914},
pmid = {41361740},
issn = {1544-0591},
abstract = {Antimicrobial resistance (AMR) poses an urgent global health threat, with significant implications for dentistry, which accounts for an estimated 10% of global antibiotic prescriptions. In response, the International Association for Dental, Oral, and Craniofacial Research (IADR) developed a new policy statement recognizing the critical role of oral health professionals and research in addressing AMR. This statement, adopted at the 103rd IADR General Session, highlights the misuse and overuse of antibiotics and antiseptics in dental settings and underscores the role of the oral microbiome as a potential AMR gene reservoir. Drawing on World Health Organization priorities, it outlines key research areas across prevention, diagnosis, treatment, health systems, environmental surveillance, and gender equity. The IADR calls for integrated, evidence-based approaches to antimicrobial stewardship, emphasizing the need for improved diagnostics, context-specific interventions, and cross-sectoral collaboration. This policy reinforces IADR's commitment to advancing science-based solutions to preserve antimicrobial efficacy and promote global oral and public health.},
}

@article {pmid41361574,
year = {2025},
author = {Lee, Y and Yoo, DM and Choi, SH},
title = {Long-term risk of dry eye disease following gastrectomy and colectomy in a nationwide cohort study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31570-5},
pmid = {41361574},
issn = {2045-2322},
support = {No. RS-2023-00211930//the National Research Foundation of Korea(NRF) grant funded by the Korean government(MSIT)/ ; },
abstract = {Dry eye disease (DED) is a complex symptomatic disorder characterized by a multifactorial etiology. Among those factors, the gut microbiome is one of the emerging factors related to dry eye disease (DED). But the relationship between gastrointestinal (GI) surgery, one of the obvious factors that alters gut microbiome, and DED has not been studied. This study evaluated the incidence of DED after gastrectomy and colectomy. The Korean National Health Insurance Service-National Sample Cohort (2002-2019) was used. A total of 2346 patients who underwent gastrectomy and 3086 who underwent colectomy, and 1:4 matched controls were included. Cox proportional hazards models with overlap weighting were used to estimate adjusted hazard ratios (HRs). Gastrectomy was significantly associated with increased DED risk (adjusted HR: 1.09; 95% CI 1.02-1.16; p = 0.007), while colectomy was not significantly associated with DED (HR: 1.00; 95% CI 0.94-1.07). In subgroup analysis, total gastrectomy showed a stronger association than subtotal gastrectomy (HR: 1.40; 95% CI 1.29-1.52). Gastrectomy, particularly total gastrectomy, is associated with ea higher incidence of dry eye disease. Colectomy showed no such association. These findings suggest the importance of ocular monitoring after gastric surgery.},
}

@article {pmid41361503,
year = {2025},
author = {Lebeuf-Taylor, E and Meltzer, A and Lubrano, S and Cottenie, K and Griesser, M},
title = {Passive environmental and group-level processes drive gut microbiome composition in a wild corvid.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-025-00496-8},
pmid = {41361503},
issn = {2524-4671},
support = {Vanier Canada Graduate Scholarship//Natural Sciences and Engineering Research Council of Canada/ ; Discovery Grant//Natural Sciences and Engineering Research Council of Canada/ ; EXC 2117 L21-04//Deutsche Forschungsgemeinschaft/ ; },
}

@article {pmid41361489,
year = {2025},
author = {Zhao, SY and Hausbeck, J and Coon, KL},
title = {Historical mosquito colonization dynamics are associated with patterns of microbial community assembly in aboveground aquatic habitats.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00831-1},
pmid = {41361489},
issn = {2524-6372},
support = {DGE-1747503//Directorate for STEM Education/ ; 5T32AI007414-27//National Institute of Allergy and Infectious Diseases/ ; 2019368//Directorate for Biological Sciences/ ; 2018-67012-2991//National Institute of Food and Agriculture/ ; },
abstract = {Mosquito larvae develop in aquatic habitats that harbor highly variable communities of bacteria and other microorganisms, which have been well demonstrated to shape individual fitness outcomes in laboratory settings. However, relatively little is known about how this microbial variation contributes to or is influenced by mosquito population dynamics in the field. To investigate potential associations between mosquito population dynamics and microbial community assembly, we characterized bacterial communities in naturally occurring larval habitats with variable historical mosquito productivity using amplicon sequencing. We then applied a null model approach to quantify the relative importance of selection, dispersal, and drift processes in bacterial community assembly. Habitat microbiota clustered into two distinct biotypes: Biotype 1 communities were dominated by Proteobacteria, while Biotype 2 communities were dominated by Cyanobacteria. Both biotypes were shaped by a combination of selection and neutral (i.e., dispersal and drift) processes. However, selection played a more prominent role in habitats with Biotype 1 communities, whereas drift was more influential in Biotype 2 habitats. Variation partitioning further identified historical mosquito productivity and the spatial aggregation of sites with similar productivity histories as key drivers of selection. These findings suggest that mosquito population dynamics are associated with differences in microbial community structure, potentially through feedbacks between mosquito activity and habitat conditions. This study lays the foundation for future work to disentangle causal relationships and to integrate patterns of microbiota diversity and mosquito occurrence into vectorial capacity models for improved prediction of mosquito-borne disease transmission dynamics in the field.},
}

@article {pmid41361482,
year = {2025},
author = {Shang, T and Zhang, R and Liu, Y and Shi, S},
title = {Intestinal oxygen and microbiota crosstalk: implications for pathogenesis of gastrointestinal diseases and emerging therapeutic strategies.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {100},
pmid = {41361482},
issn = {1757-4749},
support = {82474008, 82173902 and 82104274//National Natural Science Foundation of China/ ; },
abstract = {The gut microbiota and its hypoxic host environment play a critical role in human health. Despite its importance, the mechanisms maintaining homeostasis and the characteristics defining dysbiosis remain largely undefined. In particular, the regulation of intestinal oxygen (IO) levels emerges as a critical factor in maintaining microbial balance. Host-driven factors, including epithelial oxygen consumption, mucosal perfusion, and luminal gas diffusion, establish a hypoxic gradient essential for the stable colonization by obligate anaerobes. Disruptions to this gradient, leading to pathological hyperoxia, are associated with overgrowth of facultative anaerobic bacteria and contribute to gastrointestinal diseases like ulcerative colitis, colorectal cancer, and irritable bowel syndrome. Emerging therapeutic approaches focus on modulating IO homeostasis to address dysbiosis. Compounds like sodium tungstate inhibit microbial respiratory pathways, while PPAR-γ agonists enhance mitochondrial efficiency in colonic epithelial cells, thereby restoring proper hypoxia. Dietary interventions and probiotic therapies also hold promise by promoting local anaerobic conditions and enhancing barrier functions, thus supporting the restoration of a healthy microbial community. This review highlights the role of IO in shaping host-microbe interactions, focusing on how host IO levels influence microbial homeostasis. We evaluate the potential for IO modulation to improve gut microbiota structure and explore its impact on microbial metabolism and disease pathogenesis. Additionally, we discuss the promise of dietary, probiotic, and pharmacological interventions in restoring the host's control over the IO microenvironment and microbiota, aiming to prevent and treat related diseases.},
}

@article {pmid41361374,
year = {2025},
author = {Kim, I and Jung, DR and Jung, Y and Ha, JH and Lee, EK and Kim, JM and Kim, JY and Cho, YS and Shin, JH},
title = {Complete genome sequence of Heyndrickxia oleronia EISK28 isolated from human facial skin.},
journal = {BMC genomic data},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12863-025-01388-1},
pmid = {41361374},
issn = {2730-6844},
support = {RS-2023-KH140949//Korea Health Industry Development Institute/Republic of Korea ; },
abstract = {OBJECTIVES: Heyndrickxia oleronia is a Gram-positive, rod-shaped bacterium originally isolated from termites but has gained clinical importance due to its association with Demodex mites and rosacea, a chronic inflammatory skin disease. Despite its clinical relevance, genomic resources from human-associated environments remain limited, with existing reference genomes derived from ecologically distant sources. This study aimed to provide the first complete genome sequence of H. oleronia EISK28 isolated from human facial skin to support future research on its role in skin health and disease.

DATA DESCRIPTION: H. oleronia EISK28 was isolated from human facial skin and sequenced using Oxford Nanopore long-read technology. De novo assembly resulted in a single complete circular chromosome of 5,118,808 bp with 164× coverage depth. Structural annotation identified 5,143 genes comprising 4,958 CDSs, 36 rRNAs, 144 tRNAs, 5 non-coding RNAs, and 65 pseudo genes. Functional annotation assigned the predicted CDSs to 22 of 25 COG categories and identified 93 carbohydrate-active enzymes. Secondary metabolite analysis revealed three biosynthetic gene clusters, and genome-based antibiotic resistance profiling predicted 11 resistance genes, while phenotypic testing confirmed resistance to ampicillin and penicillin. Mobile genetic element screening detected 34 insertion sequences, 2 prophages, and 16 genomic islands but no association with antibiotic resistance genes.},
}

@article {pmid41361302,
year = {2025},
author = {Alemu, BK and Wang, CC and Poon, LC and Wang, Y},
title = {Maternal probiotics intake during pregnancy and exclusive colostrum breastfeeding are associated with a reduced risk of neonatal jaundice.},
journal = {BMC medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12916-025-04516-x},
pmid = {41361302},
issn = {1741-7015},
abstract = {BACKGROUND: Neonatal jaundice (NJ), characterized by significantly increased bilirubin levels, is a prevalent global neonatal condition affecting 60-80% of newborns. It imposes long-term adverse effects on neurodevelopment and overall health. Current clinical treatments, such as phototherapy, primarily focus on symptom management, whereas the preventive strategies for NJ remain largely lacking. Infant breastfeeding is associated with NJ. However, whether maternal probiotics use and infant colostrum feeding may reduce the NJ risk has yet to be determined and warrants further investigation in large-scale cohorts. Therefore, this study aimed to evaluate whether they have any preventive effect.

METHODS: We investigated the relationship of maternal probiotic intake and baby feeding type with NJ onset using the CHILD cohort, a prospective birth cohort recruited 3624 mothers and 3542 paired infants. Probiotic intake during pregnancy and its patterns (increased, maintained, or decreased compared to preconception) were obtained via questionnaires. The NJ conditions (yes/no) and feeding modes (exclusive colostrum, formula-only, or mixed feeding) were collected from hospital birth records. Bivariate and multivariable logistic regressions were employed to evaluate the risk using adjusted odds ratio (AOR) with 95% confidence intervals (CI) after adjustment for confounders. P < 0.05 indicates statistical significance.

RESULTS: A total of 2596 healthy controls and 433 NJ cases with complete data were included from the CHILD cohort for analysis. Interestingly, probiotic intake during pregnancy was associated with a remarkably reduced odds of NJ (AOR 0.78 (0.61, 0.98), P = 0.041) compared to participants who never used probiotics. Neonates with exclusive colostrum feeding also had a significantly lower incidence of NJ than other feeding modes (AOR 0.34 with (95%CI) (0.27,0.44), P < 0.001). Further stratification analysis on probiotic intake showed that mothers who increased (AOR 0.53 (0.32, 0.89), P = 0.016) or maintained (AOR 0.44 (0.24, 0.80), P < 0.007) probiotic intake during pregnancy had a lower risk of NJ compared to those who decreased intake.

CONCLUSIONS: This cohort-based evidence highlights that maternal probiotic intake and exclusive colostrum feeding are important modifiable factors associated with reduced NJ risk.},
}

@article {pmid41361265,
year = {2025},
author = {Wang, C and Wang, C and Chen, S and Shi, K and Yu, J and Ding, Y and Yue, Y and Hua, Y and Wang, H and Chen, J},
title = {Global landscape of antibiotic resistance genes in the human gut microbiome metagenome-assembled genomes.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04586-0},
pmid = {41361265},
issn = {1471-2180},
support = {No.202524//the Scientific Research Program of the Bozhou University/ ; No. W2412100//International Cooperation and Exchanges NSFC-ASRT/ ; No. 42276137//National Natural Science Foundation of China/ ; No. 2022YFC2804205//National Key Research and Development Program of China/ ; No. 2022YFC2804104//National Key Research and Development Program of China/ ; },
}

@article {pmid41361135,
year = {2025},
author = {Konturek, PC and Ghopreal, T and Dieterich, W and Zopf, Y},
title = {[Gut-lung axis from a gastroenterological perspective].},
journal = {MMW Fortschritte der Medizin},
volume = {167},
number = {Suppl 6},
pages = {22-26},
doi = {10.1007/s15006-025-5477-3},
pmid = {41361135},
issn = {1613-3560},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/immunology ; Dysbiosis/immunology/therapy ; *Lung/microbiology/immunology ; Fecal Microbiota Transplantation ; *Lung Diseases/microbiology/immunology ; Lung Neoplasms/immunology ; Probiotics/therapeutic use ; },
abstract = {BACKGROUND: The microbiome is unique to each individual. It plays a key role in numerous physiological processes in the body. Intestinal dysbiosis is associated with various diseases.

METHOD: This work provides an overview of the current state of knowledge regarding the role of microbiota in the lungs and the gut-lung axis.

RESULTS AND CONCLUSIONS: Numerous studies have demonstrated a link between respiratory diseases and an altered lung microbiome. Dysbiosis of the gut microbiota influences the lung's immune response via gut-lung axis. Changes in the lung microbiome due to various environmental factors, such as smoking, particulate matter, or air pollution, contribute to lung cancer development. The composition of the gut microbiome influences the response to therapy with immune checkpoint inhibitors. Modulation of the gut microbiota through fecal microbiota transplantation (FMT), diet, prebiotics, probiotics, and synbiotics can positively influence the response to immunotherapy.},
}

Humans
*Gastrointestinal Microbiome/physiology/immunology
Dysbiosis/immunology/therapy
*Lung/microbiology/immunology
Fecal Microbiota Transplantation
*Lung Diseases/microbiology/immunology
Lung Neoplasms/immunology
Probiotics/therapeutic use

@article {pmid41361024,
year = {2025},
author = {Chilloux, J and Brial, F and Everard, A and Smyth, D and Andrikopoulos, P and Zhang, L and Plovier, H and Myridakis, A and Hoyles, L and Moreno-Navarrete, JM and Luque, JL and Casagrande, V and Menghini, R and Ahmetaj-Shala, B and Blancher, C and Martinez-Gili, L and Gencer, S and Fearnside, JF and Barton, RH and Neves, AL and Rothwell, AR and Gérard, C and Calderari, S and Williamson, MJ and Fuchs, JE and Govada, L and Boulangé, CL and Patel, S and Scott, J and Thursz, M and Chayen, N and Glen, RC and Gooderham, NJ and Nicholson, JK and Federici, M and Fernández-Real, JM and Gauguier, D and Liu, PP and Cani, PD and Dumas, ME},
title = {Inhibition of IRAK4 by microbial trimethylamine blunts metabolic inflammation and ameliorates glycemic control.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {41361024},
issn = {2522-5812},
support = {MR/M501797/1//RCUK | Medical Research Council (MRC)/ ; MR/W022532/1//RCUK | Medical Research Council (MRC)/ ; MR/Y010051/1//RCUK | Medical Research Council (MRC)/ ; MR/L01632X/1//RCUK | Medical Research Council (MRC)/ ; MR/Y001028/1//RCUK | Medical Research Council (MRC)/ ; MR/K020919/1//RCUK | Medical Research Council (MRC)/ ; ANR-10-LABX-46//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-16-IDEX-0004-ULNE//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-18-IBHU-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; Agreement 20001891/NP0025517//Région Hauts-de-France/ ; 20002845//Région Hauts-de-France/ ; METACARDIS HEALTH-F4-2012-305312//European Commission (EC)/ ; METACARDIS HEALTH-F4-2012-305312//European Commission (EC)/ ; Imperial Biomedical Research Centre//DH | National Institute for Health Research (NIHR)/ ; Imperial Biomedical Research Centre//DH | National Institute for Health Research (NIHR)/ ; T.0115.24//Fonds De La Recherche Scientifique - FNRS (Belgian National Fund for Scientific Research)/ ; WELBIO X.1517.24//Fonds De La Recherche Scientifique - FNRS (Belgian National Fund for Scientific Research)/ ; FRFS-WELBIO: WELBIO-CR-2022A-02P//Fonds De La Recherche Scientifique - FNRS (Belgian National Fund for Scientific Research)/ ; EOS: program no. 40007505//Fonds De La Recherche Scientifique - FNRS (Belgian National Fund for Scientific Research)/ ; 06678//Wellcome Trust (Wellcome)/ ; 06678//Wellcome Trust (Wellcome)/ ; 06678//Wellcome Trust (Wellcome)/ ; 057733/WT_/Wellcome Trust/United Kingdom ; MOP-49413//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; MOP-142471//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; },
abstract = {The global type 2 diabetes epidemic is a major health crisis. Although the microbiome has roles in the onset of insulin resistance (IR), low-grade inflammation and diabetes, the microbial compounds controlling these processes remain to be discovered. Here, we show that the microbial metabolite trimethylamine (TMA) decouples inflammation and IR from diet-induced obesity by inhibiting interleukin-1 receptor-associated kinase 4 (IRAK4), a central kinase in the Toll-like receptor pathway sensing danger signals. TMA blunts TLR4 signalling in primary human hepatocytes and peripheral blood monocytic cells and rescues mouse survival after lipopolysaccharide-induced septic shock. Genetic deletion and chemical inhibition of IRAK4 result in metabolic and immune improvements in high-fat diets. Remarkably, our results suggest that TMA-unlike its liver co-metabolite trimethylamine N-oxide, which is associated with cardiovascular disease-improves immune tone and glycemic control in diet-induced obesity. Altogether, this study supports the emerging role of the kinome in the microbial-mammalian chemical crosstalk.},
}

@article {pmid41360964,
year = {2025},
author = {Karimzadeh, F and Heidari, R and Lamooki, FM and Soureshjani, EH and Aziz, S and Mirzaei, SA},
title = {Design of a multi-epitope vaccine against intestinal parasites associated with colorectal cancer using immunoinformatics approaches.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31713-8},
pmid = {41360964},
issn = {2045-2322},
support = {SKUMS-7837//Shahrekord University of Medical Sciences/ ; },
abstract = {The increasing prevalence of gastrointestinal infections caused by Cryptosporidium parvum and Schistosoma mansoni, coupled with the lack of definitive treatments, underscores the need for vaccine development to prevent infection-related cancers. Using experimentally validated epitopes for vaccine development enhances confidence in inducing strong and durable immune responses compared to predicted epitopes, which require lab validation. In this study, we employed a unique computational strategy using 197 experimentally validated epitopes of C. parvum and S. mansoni obtained from the IEDB database. After applying homology filters against human proteome and microbiome sequences and conducting HLA population coverage analysis, we chose seven cytotoxic T lymphocyte (CTL), seven helper T cell (HTL), and five B-cell epitopes. These were combined with an RpfE adjuvant and appropriate linkers to design a highly immunogenic chimeric antigen with broad global coverage, optimized for stability, solubility, and manufacturability. Molecular docking revealed strong binding affinities of CTL and HTL epitopes to their respective HLA alleles. Immune simulations demonstrated the multi-epitope antigen's ability to elicit both innate and adaptive immune responses. Docking of the vaccine construct with immune receptors (TLR2-TLR1 and TLR4-MD2) yielded significant scores of - 179.8 ± 4.5 and - 191.5 ± 3.4 kcal/mol, respectively. Molecular dynamics simulations verified the structural stability of vaccine-receptor complexes, while binding free energy calculations reinforced their strong affinities. Finally, in silico cloning validated the vaccine's potential for efficient E. coli expression. These computational findings support the construct as a promising vaccine candidate against C. parvum and S. mansoni, warranting further experimental validation.},
}

@article {pmid41360945,
year = {2025},
author = {Mukhopadhyay, M},
title = {Cracking the cancer microbiome.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41592-025-02953-3},
pmid = {41360945},
issn = {1548-7105},
}

@article {pmid41360901,
year = {2025},
author = {Lima, J and McNeilly, TN and Auffret, MD and Steele, P and Frew, D and Martínez-Álvaro, M and Dewhurst, RJ and Watson, M and Roehe, R},
title = {Rumen microbiome profiles of dairy cattle are affected by the presence of, and vaccination against, the abomasal parasitic nematode Ostertagia ostertagi.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30604-2},
pmid = {41360901},
issn = {2045-2322},
support = {BB/N016742/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N01720X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 10045515//Innovate UK/ ; },
abstract = {Ostertagia ostertagi is a highly prevalent nematode that affects grazing cattle and impacts performance and welfare by reducing appetite and hindering weight gain. Despite its economic significance, the influence of the abomasal parasite O. ostertagi on the rumen microbiome remains unexplored. We examined the effects of subclinical O. ostertagi infection and vaccination on the rumen microbiome at taxonomic and functional levels. In an experimental trial, calves treated with vaccine or adjuvant-only were orally challenged with O. ostertagi larvae daily for 25 days; 4 groups of animals (UNF: unvaccinated, unchallenged; VAC: vaccinated, challenged; CHE: unvaccinated, challenged, high cumulative faecal egg counts (cFEC), and CLE: unvaccinated, challenged, low cFEC) were selected for whole shotgun metagenomic sequencing. Using a rigorous permutation test based on partial least squares discriminant analyses, we identified 36 (91), 38 (31), 21 (57), 41 (64) and 29 (57) microbial genera (genes) that distinguished VAC, CHE and CLE from UNF, CHE from CLE, and CHE from VAC, respectively. The subclinical infection reshaped the rumen microbiome; enrichment of opportunistic pathogens such as Listeria, and depletion of Filifactor in infected animals were identified as potential biomarkers for host immune response, whereas Actinomyces and Microspora were potential biomarkers of resistance to infection. Microbial biochemical pathways like acetogenesis (e.g., Elusimicrobium, nrfA), pectin and hemicellulose degradation (e.g., Sphaerochaeta), and phosphorus and sulphur metabolism (e.g., Candidatus Accumulibacter and Desulfatibacillum) were also affected by parasitism. Both infection and vaccination altered methanogens, methanotrophs and the methane metabolism pathway, highlighted by distinct gene clustering patterns between infected and uninfected animals. Clustering patterns of infected and vaccinated animals exhibited some similarities, which may reflect immune system modulation of the ruminal microbiome as a result of an abomasal infection. This study unveils critical changes in the rumen microbiome due to the infection by and vaccination against the abomasal parasite O. ostertagi. Our results highlight the importance of monitoring microbial dynamics in the development of effective anthelmintic treatments and vaccines.},
}

@article {pmid41360872,
year = {2025},
author = {Cheatham, SM and Rehman, Z and Arastonejad, M and Kane, R and Ahmad, N and Luffman, N and Harada, H and Zhang, Y and Tyc, KM and Gewirtz, DA and Akbarali, HI},
title = {Butyrate prevents chemotherapy-induced gastrointestinal toxicity and microbial dysbiosis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30385-8},
pmid = {41360872},
issn = {2045-2322},
support = {P30 DA033934/NH/NIH HHS/United States ; T32DA007927/NH/NIH HHS/United States ; P30CA016059/NH/NIH HHS/United States ; P30DA0339324/NH/NIH HHS/United States ; },
abstract = {Chemotherapy-induced gastrointestinal toxicity is a significant dose-limiting complication for cancer treatment. Disruption of the gastrointestinal (GI) epithelial barrier function by several chemotherapeutic agents results in development of mucositis and diarrhea. Thus, maintaining barrier integrity may be of therapeutic benefit. Recent studies have shown the beneficial effects of the microbial metabolite butyrate, a short chain fatty acid (SCFA), on epithelial barrier integrity. In this current study, we tested the effect of oral butyrate on irinotecan-induced gastrointestinal (GI) toxicity in mice. Irinotecan dose-dependently reduced body weight, increased fecal water content and increased gastrointestinal motility. Acetylcholine induced contractions were markedly increased in colons of irinotecan treated mice as were nicotine-induced inward currents in isolated ileum myenteric neurons. Loperamide reduced GI motility of irinotecan treated mice, however tolerance developed with chronic use, consistent with clinical findings of loperamide refractory diarrhea in patients. Oral butyrate improved epithelial permeability and prevented irinotecan-induced increase in β-glucuronidase activity in fecal samples. Irinotecan treatment produced a significant shift in the β diversity of the fecal microbiome that was mitigated by butyrate. The microbial dysbiosis was associated with increases in the mucin degrading bacteria Akkermansia muciniphilia and the hydrogen sulfide producing Desulfovibrio sp10575755 that was reduced with butyrate treatment.},
}

@article {pmid41360562,
year = {2026},
author = {He, Q and Li, X and Liu, C and Liu, Z and Zhou, S and Li, Y and Ma, T},
title = {Application and research progress of dietary fiber-based fat substitutes in food systems.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 2},
pages = {117876},
doi = {10.1016/j.foodres.2025.117876},
pmid = {41360562},
issn = {1873-7145},
mesh = {*Dietary Fiber/analysis ; *Fat Substitutes/chemistry ; Humans ; Emulsions ; Food Handling ; Nutritive Value ; Dietary Fats ; },
abstract = {The rising global burden of diet-related noncommunicable diseases has accelerated the development of low-fat foods that retain desirable sensory and functional properties. Dietary fibers, leveraging their unique water-holding capacity, gelling behavior, and tunable rheology, have emerged as versatile fat replacers across diverse food matrices. This review synthesizes recent advances in the design and application of dietary-fiber-based fat substitutes, categorizing them into two primary classes: Abbas et al. (2024) (1) fat-free mimetics (hydrogels and particulate systems) and (Akal, 2023 (2)) fat-based substitutes (fiber-stabilized emulsions, emulsion gels, and oleogels). Key strategies to enhance fiber functionality, including chemical, enzymatic, and physical modifications for hydrophobicity enhancement, and synergistic composites with proteins or lipids, are critically evaluated. Representative applications in meat products, dairy systems, baked goods, and spreads are analyzed, emphasizing improvements in texture, water/fat retention, oxidative stability, and nutritional profiles. Persistent challenges include replicating the crispness and melt behavior of full-fat analogs, ensuring the safety of modified fibers, balancing essential fatty acids and fat-soluble vitamins, and optimizing gastrointestinal tolerance. Future directions encompass multi-component mimetics (e.g., protein-fiber complexes and polysaccharide-lipid hybrids), sustainable modification technologies (enzymatic/physical treatments), and precision replacement strategies guided by nutritional genomics and microbiome science. Interdisciplinary collaboration and supportive policy frameworks will be pivotal in advancing dietary-fiber-based fat substitutes toward a new paradigm of 'healthy, palatable, and safe' low-fat foods.},
}

*Dietary Fiber/analysis
*Fat Substitutes/chemistry
Humans
Emulsions
Food Handling
Nutritive Value
Dietary Fats

@article {pmid41360553,
year = {2026},
author = {Du, S and Zhang, X and Zhang, M and Lin, T and Liu, B and Jing, M and Zhao, J and Chen, L},
title = {Comparative analysis of Tibetan human milk fat globule membrane proteins across lactation stages.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 2},
pages = {117862},
doi = {10.1016/j.foodres.2025.117862},
pmid = {41360553},
issn = {1873-7145},
mesh = {Humans ; *Milk, Human/chemistry ; *Glycoproteins/analysis/metabolism ; *Glycolipids/analysis/metabolism ; Female ; *Lipid Droplets ; *Lactation ; Colostrum/chemistry ; Proteomics/methods ; Infant ; Tibet ; *Membrane Proteins/analysis ; Feces/microbiology ; Adult ; Infant, Newborn ; Gastrointestinal Microbiome ; Milk Proteins/analysis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Milk fat globule membrane (MFGM) proteins are significant nutrients contained in human milk. However, information on MFGM proteins in Tibetan human milk remains limited. This study analyzed and compared MFGM proteins in human colostrum (HC), human transitional milk (HT), and human mature milk (HM) from Tibetan lactating mothers using label-free quantitative proteomics. We identified 2977 proteins in HC, HT, and HM, of which 215 were differentially expressed proteins (DEPs). In addition, the uniquely expressed proteins (UEPs) in HC, HT, and HM were also identified. We used bioinformatics to analyze these DEPs and UEPs and revealed the relationships between MFGM proteins, as well as their functions and pathways of action. The 16S rRNA was conducted on infant fecal samples, which reveals correlations between human milk MFGM proteins and the infant gut microbiome. This study enhances the understanding of MFGM proteins in human milk and provides new insights for improving infant formulas and developing specific products, especially for populations in high-altitude regions.},
}

Humans
*Milk, Human/chemistry
*Glycoproteins/analysis/metabolism
*Glycolipids/analysis/metabolism
Female
*Lipid Droplets
*Lactation
Colostrum/chemistry
Proteomics/methods
Infant
Tibet
*Membrane Proteins/analysis
Feces/microbiology
Adult
Infant, Newborn
Gastrointestinal Microbiome
Milk Proteins/analysis
RNA, Ribosomal, 16S/genetics

@article {pmid41360535,
year = {2026},
author = {Wang, H and Luo, Y and Zhang, Y and Xiong, Y and Bian, G and Feng, B},
title = {Flavor quality during fermentation of the specialty product proso millet (Panicum miliaceum L.) thick wine: Insights from microbiome and metabolomics analyses.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 2},
pages = {117835},
doi = {10.1016/j.foodres.2025.117835},
pmid = {41360535},
issn = {1873-7145},
mesh = {*Fermentation ; *Wine/analysis/microbiology ; *Taste ; *Microbiota ; *Metabolomics/methods ; Odorants/analysis ; Lactobacillus/metabolism ; Volatile Organic Compounds/analysis ; Hydrogen-Ion Concentration ; Bacteria/metabolism/classification ; Lactic Acid/analysis ; },
abstract = {Proso millet (PM) thick wine is a fermented, health-promoting traditional Chinese rice wine; however, little is known about the succession and functional roles of microbiota during its fermentation. In this study, we examined the correlations between microbial communities, physicochemical properties, and flavor components during PM fermentation. The results showed that the decreasing pH and increasing total acid and lactic acid levels were associated with the metabolism of dominant bacteria, particularly Lactobacillus. The aroma of PM thick wine is characterized primarily by fruity, sweet, apple, and green, with terpenoids, esters, and aldehydes identified as the main volatile differential metabolites contributing to aroma during fermentation. In the early fermentation stages, Lactobacillus, Bacillus, and Enterobacter were the predominant bacterial genera, whereas Lactobacillus became dominant in the later stages as the microbial community shifted toward greater acid tolerance. Correlation analysis indicated that Lactobacillus promoted the production of terpenoids and acids, while the remaining nine dominant bacterial genera promoted aldehyde production in PM thick wine. These findings provide theoretical guidance for further studies on flavor regulation in PM thick wine at the microbial community level and via microbial augmentation.},
}

*Fermentation
*Wine/analysis/microbiology
*Taste
*Microbiota
*Metabolomics/methods
Odorants/analysis
Lactobacillus/metabolism
Volatile Organic Compounds/analysis
Hydrogen-Ion Concentration
Bacteria/metabolism/classification
Lactic Acid/analysis

@article {pmid41360533,
year = {2026},
author = {Chen, L and Yang, J and Wang, Y and Xiao, X and Zhang, H and Hou, X and Liu, D and Du, H},
title = {Artemisia argyi folium as a traditional and safe dietary additive ameliorates metabolic syndrome via gut microbiota and its metabolites.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 2},
pages = {117830},
doi = {10.1016/j.foodres.2025.117830},
pmid = {41360533},
issn = {1873-7145},
mesh = {*Artemisia/chemistry ; *Metabolic Syndrome/drug therapy ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Plant Extracts/pharmacology/chemistry ; Male ; Mice ; *Food Additives/pharmacology ; Polyphenols ; Plant Leaves/chemistry ; },
abstract = {Artemisia argyi, a globally recognized plant widely used in medicine and food, has become an important and popular food additive in Asia and other parts of the world. However, its edible safety has always been controversial. Herein, we aimed to evaluate the safety and health benefits of A. argyi as a dietary additive. Fresh and dried A. argyi water extracts (FAA and DAA, respectively) were prepared by simulating two processing methods for edible tender A. argyi. And chemical composition analysis showed that both FAA and DAA were rich in nutritional and functional components, including polysaccharides, proteins, and polyphenols. UHPLC-TQ-MS analysis showed that tender A. argyi mainly contained 11 polyphenol components (mainly flavonoids and phenolic acids). Then, an acute toxicity study, based on the maximum limit method, showed that single administrations of FAA and DAA at doses of 40 and 133 g/kg, respectively (crude drug dosage), induced no signs of poisoning and no mortality. In a sub-chronic toxicity study, FAA and DAA treated at 3.42 and 6.83 g/kg (crude drug dosage) induced no significant toxic reactions, hematological abnormalities, or impairments in organ structure and function. Serum metabolomic analysis revealed the presence of only 46 and 52 differential metabolites in the FAA and DAA groups, respectively. Functional enrichment analysis revealed that tender A. argyi did not induce toxicity by altering metabolism from an overall perspective; however, it may have induced beneficial effects by regulating lipid metabolism. Furthermore, dual consideration of chemical abundance and network pharmacological analyses indicated that eupatilin was the most promising active ingredient among the polyphenols for treating metabolic syndrome. In mice with metabolic syndrome, eupatilin reversed changes in body weight, reduced blood glucose levels, and improved dysregulated lipid metabolism and intestinal barrier damage. Mechanistically, the gut microbiome analysis showed 9 differential genera were significantly restored after eupatilin intervention. And metabolomic analysis showed that 4 key differential metabolites were identified from the feces of Eup-treated mice. In addition, integrated analysis revealed that eupatilin mainly promoted L-phenylalanine metabolism by increasing the abundance of Akkermansia and decreasing the abundance of Helicobacter and Rikenella. Briefly, these findings systematically elucidated the safety of tender A. argyi as a dietary additive and its health benefits in metabolic syndrome via gut microbiota and metabolites. Importantly, this study will provide essential scientific support for the dual application of A. argyi in medicine and nutrition.},
}

*Artemisia/chemistry
*Metabolic Syndrome/drug therapy
*Gastrointestinal Microbiome/drug effects
Animals
*Plant Extracts/pharmacology/chemistry
Male
Mice
*Food Additives/pharmacology
Polyphenols
Plant Leaves/chemistry

@article {pmid41360358,
year = {2025},
author = {Wang, N and Tang, Y},
title = {Rebalancing the inflammatory niche in allergic rhinitis ".},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {120776},
doi = {10.1016/j.cca.2025.120776},
pmid = {41360358},
issn = {1873-3492},
abstract = {Allergic rhinitis (AR) may be driven in part by cross-talk between resident microbiota, microbe-derived small molecules, and tissue-resident group 2 innate lymphoid cells (ILC2s). In this review we focus on defined signaling axes by which Traditional Chinese Medicine (TCM) can influence that network: (1) microbially produced short-chain fatty acids (SCFAs), particularly butyrate, suppress ILC2 proliferation and type-2 cytokine output primarily via HDAC inhibition that downregulates the lineage transcription factor GATA3; receptor-dependent effects via the SCFA sensors FFAR3 (GPR41), FFAR2 (GPR43), and GPR109A (HCAR2) also occur in some cell types and tissues, and can engage β-arrestin/ERK or AMPK-linked pathways depending on cell context. In purified ILC2s, ex-vivo reductions in GATA3 and IL-13/IL-5 are observed at low micromolar to several hundred micromolar butyrate (human ILC2 ≈ 10 μM; murine ex-vivo ILC2 ≈ 200 μM), while viability is generally preserved below ~1 mM, indicating a physiologically plausible dose window for metabolite-driven modulation; (2) microbially modified secondary bile acids alter mucosal immune tone and epithelial function via FXR and TGR5 signaling; and (3) microbial tryptophan metabolites (indoles) act as aryl hydrocarbon receptor (AhR) ligands that preserve epithelial integrity and shape ILC3/ILC2 balance. We review preclinical and emerging clinical data suggesting that selected TCM formulas and phytochemicals (e.g., Gegen Qinlian Decoction, Astragalus polysaccharides, berberine, baicalin/baicalein, glycyrrhizin) are associated with (a) remodeling of gut and airway microbial communities and increases in SCFA or beneficial bile/indole pools in preclinical and some human studies, (b) measurable rises in systemic or luminal SCFAs in several models and limited human cohorts, and (c) direct attenuation of epithelial alarmin (TSLP/IL-33) signaling in cellular and animal models. Where human data exist, causality remains unproven and further mechanistic clinical investigation is required. Together these actions provide testable, mechanism-based routes to suppress ILC2 activation and restore mucosal homeostasis in AR. We explicitly link TCM-driven microbiome/metabolome changes to canonical molecular mediators (HDAC, GPR41/43, FXR/TGR5, AhR, TSLP/IL-33, HMGB1) to facilitate mechanistic trial design that measures taxa → metabolite → receptor/epithelial → ILC2 causal chains.},
}

@article {pmid41360332,
year = {2025},
author = {Yu, Y and Jin, Y and Zhou, Y and Cui, Z and Xin, Y and Liu, H and Zhao, J and Elsabahy, M and Su, M and Gao, H},
title = {Nanoprodrug targeting tumor-associated intracellular bacteria enhances colorectal cancer immunotherapy.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {114512},
doi = {10.1016/j.jconrel.2025.114512},
pmid = {41360332},
issn = {1873-4995},
abstract = {The tumor-associated intracellular microbiota influences cancer progression by fostering an immunosuppressive tumor microenvironment. Targeting pro-tumor intracellular bacteria may represent a promising strategy for cancer immunotherapy. Herein, we reveal that Fusobacterium nucleatum (F. nucleatum) is preferentially enriched within M2-polarized macrophages in both human colorectal cancer (CRC) specimens and cellular models. Notably, its intracellular presence correlates significantly with reduced CD8[+] T cell infiltration, highlighting its immunosuppressive function. To disarm this microbial shield, we develop infection-specific ciprofloxacin (CIP) prodrug nanoparticles (MTCP-NPs) conjugated to an M2 macrophage-targeting peptide (IL4Rpep-1) via a cathepsin B (CTSB)-cleavable linker (FRRG) to selectively kill intramacrophage F. nucleatum. MTCP-NPs undergo IL4 receptor-mediated endocytosis in F. nucleatum-infected macrophages, where intracellular CTSB triggers CIP release to eliminate F. nucleatum and suppress indoleamine 2,3-dioxygenase (IDO) secretion. In F. nucleatum-infected CRC models, MTCP-NPs clear intracellular bacteria, alleviate immunosuppression by downregulating IDO and reducing MDSCs to mobilize CD8[+] T cell immunity. Furthermore, this treatment modulates the gut microbiota by reprogramming tryptophan metabolism. When combined with anti-PD-L1 therapy, MTCP-NPs amplify anti-tumor efficacy and prolong survival while promoting the generation of memory-like T cells associated with sustained immune responses. This strategy establishes a unique microbiome-immunotherapy framework by targeting tumor-associated intracellular bacteria to unleash T cell responses.},
}

@article {pmid41360158,
year = {2025},
author = {Wang, D and Zeng, J},
title = {Microbiome analysis reveals the adverse effects of diarrhea on the gut microbiota of yaks.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108218},
doi = {10.1016/j.micpath.2025.108218},
pmid = {41360158},
issn = {1096-1208},
abstract = {Diarrhea exhibits a extremely high prevalence among yak calves, significantly affecting the development of the yak industry and resulting in substantial economic losses. Gut microbiota has been demonstrated to be closely related to various diseases, particularly gastrointestinal disorders. However, to date, no studies have specifically explored the relationship between diarrhea in yak calves and gut microbiota. Therefore, this study aims to characterize the alterations of gut microbiota in yak calves during diarrhea. Results indicated that the diversity and abundance of the gut bacterial community in diarrheic yak calves were significantly reduced. In contrast, the gut fungal community remains relatively stable during diarrhea, with no significant changes observed in its diversity and abundance. Although diarrhea does not affect the composition of the dominant phyla of intestinal bacteria and fungi, the abundance of some microbial taxa has experienced significant changes. Specifically, diarrhea resulted in a marked increase in 2 phyla and 14 genera, while a significant decrease was observed in 5 phyla and 137 genera in gut bacterial community. Additionally, 30 genera in the gut fungal community exhibited significant increases, whereas 12 genera demonstrated significant decreases during diarrhea. Notably, we also identified significant alterations in intestinal function during diarrhea, including cytoskeleton and carbohydrate transport, etc. Taken together, this research indicated that diarrhea significantly affects the gut microbiota in yak calves, with more pronounced changes observed in the gut bacterial community. Furthermore, this research also represents a crucial exploration of the composition and alterations of gut microbiota in diarrheic yak calves, which will help prevent and control diarrhea in yaks inhabiting high-altitude regions and promote the development of the yak industry.},
}

@article {pmid41359366,
year = {2025},
author = {Cheah, S and Burke, J and Bruinsma, FJ and Evans, M and Tsimiklis, H and Hodge, AM and Lynch, BM and Giles, GG and Sinha, R and Southey, MC and Milne, RL},
title = {Faecal sample collection for gut microbiome research in a prospective cohort: a pilot study within the Australian Breakthrough Cancer Study.},
journal = {Cancer research communications},
volume = {},
number = {},
pages = {},
doi = {10.1158/2767-9764.CRC-25-0445},
pmid = {41359366},
issn = {2767-9764},
abstract = {Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home faecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomised into four groups defined by faecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted in and, of those, 88% returned a sample. Of those asked to provide a faecal sample via faecal occult blood test card (FOBT) and complete a short "day of sample" questionnaire (dosQ), 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home faecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items.},
}

@article {pmid41359046,
year = {2025},
author = {Dalby, KL and Horsley, H and Spratt, D and Khasriya, R},
title = {The Vaginal Microbiome and Recurrent and Chronic Urinary Tract Infection.},
journal = {International urogynecology journal},
volume = {},
number = {},
pages = {},
pmid = {41359046},
issn = {1433-3023},
abstract = {INTRODUCTION AND HYPOTHESIS: The vaginal and urinary microbiomes are closely linked, yet the role of this relationship in recurrent and chronic urinary tract infections (UTIs) remains uncertain. Research into genitourinary ecology and UTI has largely focused on acute infections and reproductive age groups, leaving a gap in understanding the role of the microbiome in recurrent and chronic cases. This review is aimed at presenting that disruptions within vaginal microbiota contribute to UTI chronicity in menopausal women, highlighting the potential for microbiome-targeted interventions in this high-risk group.

METHODS: A comprehensive literature review was conducted, with search terms including cystitis, urogenital, antibiotic, infection, and bladder, vaginal microbiome, vaginal ecology, topical oestrogen, atrophy, genitourinary syndrome of menopause, vulvo-vaginal atrophy (VVA), bacterial vaginosis and lactobacillus. Relevant articles were screened, critiqued, and synthesised based on key themes.

RESULTS: Lactobacillus spp. appears to be the key component of a healthy vaginal microbiome. Decreased vaginal Lactobacillus abundance, seen with vaginal dysbioses and the menopause, correlates with an increased presence of urinary pathogens, increasing susceptibility to UTI. This review demonstrates that interventions to optimise vaginal ecology could reduce UTI burden. These approaches offer non-antibiotic treatment strategies, lowering antimicrobial resistance risk. However, studies frequently exclude those with chronic and recurrent infections, underscoring the necessity for more research targeting this group.

CONCLUSIONS: This review highlights the link between disrupted vaginal ecology and recurrent and chronic UTI, and the need for expanded research into microbiome-targeted treatments. A paucity of studies researching recurrent and chronic UTI cohorts limits the evidence base for clinical generalisation, meaning that more focussed studies are needed to improve understanding and clinical management.},
}

@article {pmid41359024,
year = {2025},
author = {Qian, K and Du, M and Tan, S and Ding, M and Song, M and Lu, M and Qi, C and Cheng, L and Zhang, X},
title = {gutMSNP: a comprehensive database for human gut microbial single-nucleotide polymorphisms.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1205},
pmid = {41359024},
issn = {1362-4962},
support = {62222104//National Natural Science Foundation of China/ ; 62172130//National Natural Science Foundation of China/ ; 62222104//National Natural Science Foundation of China/ ; },
abstract = {gutMSNP (https://bio-computing.hrbmu.edu.cn/gutMSNP/home) is a user-friendly database designed to provide a systematic and comprehensive resource for single-nucleotide polymorphisms (SNPs) in the human gut microbiome. Given that even a single SNP in gut microbial genomes can profoundly modulate microbial pathogenicity and thereby impact host health, a large-scale, standardized SNP repository is indispensable for elucidating microbial functions and the molecular mechanisms underpinning microbiota-driven disorders. The current release of gutMSNP includes: (i) 164 015 783 SNPs identified across human gut microbial genomes and categorized into three coverage confidence levels; (ii) 364 species-level and 8251 gene-level microbial records, each exhibiting phenotype-specific SNP distribution patterns; (iii) 8146 representative reference genomes of human gut microbes; and (iv) an online tool for capturing SNPs. The database enables users to search for SNPs in microbial species of interest along with detailed functional and positional annotations, explore phenotype-specific SNP distribution patterns in selected species and their associated genes, download reference genomes for downstream analyses, and detect as well as annotate SNPs in user-uploaded microbial genome files. With its massive SNP dataset, versatile query capabilities, and integrated analytical tools, gutMSNP will serve as a fundamental resource for SNP-based investigations in the human gut microbiome.},
}

@article {pmid41358834,
year = {2025},
author = {Zhang, Q and Wang, Y and Zhang, H and Xu, G and Xu, S and Yang, G},
title = {Blubber Thickening Driven by UCP1 Inactivation: Insights from a Cetacean-Like Transgenic Mouse Model.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70047},
pmid = {41358834},
issn = {1749-4877},
abstract = {Cetaceans possess thick blubber, a specialized adipose tissue essential for thermal insulation, a streamlined body form, energy storage, and buoyancy. However, the mechanisms that underpin this adaptation are not yet fully understood. Here, we found that uncoupling protein 1 (UCP1) of cetaceans has undergone significant evolutionary relaxation. A transgenic mouse model with cetacean-like UCP1 inactivation revealed a pronounced obesity phenotype, including expanded brown adipose tissue (BAT) and increased white adipose tissue (WAT) adipocyte hyperplasia. Histological, metabolic, and physiological assessments showed reduced lipolysis, impaired glucose metabolism, and upregulated lipid metabolism pathways in BAT. Additionally, gut microbiome analysis indicated an increased Firmicutes/Bacteroidetes ratio, suggesting enhanced energy absorption and weight gain. Comparison with traditional UCP1-KO mice further revealed that the unique mutations in cetacean UCP1 could be the molecular basis for observed fat accumulation phenotype. Our findings provide novel insights into the evolutionary mechanisms underlying blubber thickening in the secondary aquatic adaptation of cetaceans.},
}

@article {pmid41358730,
year = {2025},
author = {Yan, H and Zhang, Y and Zhang, Z and Zhao, Z and Zhang, L and Ju, F},
title = {Soil pH and nitrate shape deterministic assembly of microbial communities in agricultural soils via Nitrososphaeria.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0206725},
doi = {10.1128/aem.02067-25},
pmid = {41358730},
issn = {1098-5336},
abstract = {UNLABELLED: Understanding the assembly mechanisms of soil microbial communities is critical for maintaining nitrogen cycling in agricultural ecosystems, which underpins soil fertility and sustains crop productivity. While environmental filtering and biotic interactions shape these communities, our understanding of how functional taxa interact with soil properties across extensive agricultural landscapes remains limited. Here, we investigated the influence of environmental factors on the Chinese agricultural soil microbiome, integrating assessments of microbiota diversity, composition, and assembly process. The results indicated that soil pH and moisture were among the strongest abiotic factors explaining the agricultural soil microbiota compositional variation at a continental scale, surpassing the examined geographical and climatic effects. Stochastic processes dominated the assembly of microbial communities in large-scale agricultural soils, whereas the relative importance of deterministic processes increased with rising pH from acidic to alkaline soils. Phylogenetic turnover, as indicated by the beta nearest taxon index (βNTI), revealed determinism peaked under nitrogen-limited conditions but weakened with moderate precipitation, suggesting that both extreme aridity and rainfall amplify environmental filtering. We also found that divergent environmental preferences were displayed by ammonia-oxidizing microorganisms, including four archaeal genera belonging to the Nitrososphaeria class. Their significant correlations with βNTI as well as soil pH, nitrate, and moisture suggested that soil properties likely influenced prokaryotic community assembly primarily through modulating these functional taxa. This study highlights the vital role of ammonia-oxidizing-related soil properties in shaping the functional groups and assembly mechanisms of soil microbial communities, while enhancing our understanding of how ecological niche modifications by ammonia-oxidizers influence community interactions and nutrient dynamics in agricultural soils.

IMPORTANCE: Agricultural soil microbiomes are essential for element cycling, fertility maintenance, and crop productivity, yet how key functional taxa interact with environmental factors to shape community assembly remains poorly understood. In this transcontinental study spanning diverse vegetation types, we demonstrate that ammonia-oxidizing archaea mediate soil microbial community assembly in response to pH and nitrate levels, with evidence of nonlinear threshold effects driven by nitrate. These findings underscore the pivotal role of keystone taxa in structuring soil biodiversity and ecological functions. Our study offers valuable insights into microbially mediated carbon and nitrogen cycling under climate change and supports crop-specific soil management strategies for sustainable agriculture.},
}

@article {pmid41358671,
year = {2025},
author = {Ngwese, MM and Adegbite, BR and Zinsou, JF and Fitzstevens, JL and Schmidt, VT and Moure, PAN and Maloum, MN and Tyakht, AV and Huus, KE and Youngblut, ND and Kremsner, PG and Adegnika, AA and Ley, RE},
title = {Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2587966},
doi = {10.1080/19490976.2025.2587966},
pmid = {41358671},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Feces/parasitology/microbiology ; Animals ; Gabon/epidemiology ; Female ; Male ; Child ; *Helminthiasis/parasitology/epidemiology/microbiology ; Metagenomics ; *Helminths/isolation & purification/classification/genetics ; Child, Preschool ; Rural Population ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Ascaris lumbricoides/isolation & purification ; Strongyloides stercoralis/isolation & purification ; Necator americanus/isolation & purification ; Trichuris/isolation & purification ; Biodiversity ; },
abstract = {Soil-transmitted helminths (STH) are common in (sub)tropical regions and primarily affect impoverished populations. These parasites reside in the gut, where they interact with both the microbiota and host immunity. Clinical STH detection is laborious and often not performed within the context of gut microbiome studies. Here, we present a proof-of-concept study assessing whether fecal metagenome data could be used to assess STH infection, and to relate STH infection to microbiome features. We leveraged 310 gut metagenomes obtained from mother-child pairs in two different locations in Gabon: one rural and one semi-urban, and assessed the presence of four STH species (Ascaris lumbricoides, Strongyloides stercoralis, Trichuris trichiura, and Necator americanus) using qPCR. Sequence data were used to characterize the microbiomes and to detect these parasites. Metagenomic read mapping and genome coverage metrics closely matched qPCR detection patterns. Within-location analyses revealed that parasite species richness was associated with microbiome diversity and taxonomic composition, with the strongest associations observed in children from the rural site. Applying this approach to published data from five additional African cohorts identified context-specific parasite-microbiome associations, as well as a modest but reproducible association between microbiome alpha diversity and parasite infection. These findings highlight the potential of shotgun metagenomics for concurrent parasite detection and microbiome profiling across diverse geographic and demographic contexts.},
}

Humans
*Gastrointestinal Microbiome/genetics
Feces/parasitology/microbiology
Animals
Gabon/epidemiology
Female
Male
Child
*Helminthiasis/parasitology/epidemiology/microbiology
Metagenomics
*Helminths/isolation & purification/classification/genetics
Child, Preschool
Rural Population
Bacteria/classification/genetics/isolation & purification
Metagenome
Ascaris lumbricoides/isolation & purification
Strongyloides stercoralis/isolation & purification
Necator americanus/isolation & purification
Trichuris/isolation & purification
Biodiversity

@article {pmid41358650,
year = {2025},
author = {Lee, I and Kim, BS and Suk, KT and Lee, SS},
title = {Corrigendum to: Gut Microbiome-Based Strategies for the Control of Carbapenem-Resistant Enterobacteriaceae.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e35005},
doi = {10.4014/jmb.2025.3512.C01},
pmid = {41358650},
issn = {1738-8872},
}

@article {pmid41358462,
year = {2025},
author = {Nema, A and Dhar, D and Ramireddy, VSR and Priyam, K and Agarwal, S and Srivastava, SK},
title = {A Small Pill-Like Ingestible Microdevice for Site-Specific Microbiome Sampling in the Upper GI Tract.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e10289},
doi = {10.1002/smll.202510289},
pmid = {41358462},
issn = {1613-6829},
support = {IIRPSG-2024-01-00486//Indian Council of Medical Research/ ; },
abstract = {The gut microbiota varies along the length and cross-section of the gastrointestinal (GI) tract, influencing diseases. Direct sampling from the upper GI tract remains challenging due to anatomical constraints and low-volume genomic sequencing. Here, we report an ingestible, pill-like microdevice (7 × 2.7 mm) that enables in vivo microbiome and biomarker sampling in Sprague-Dawley rats - demonstrating, for the first time, successful autonomous pyloric transit of a microdevice via oral gavage. The device comprises an enteric-coated gelatin cap that protects it in gastric pH (1-1.5) and disintegrates at intestinal pH (3-5), allowing luminal fluid via an inlet connected to activation and sampling chambers. A polyacrylate hydrogel in the activation chamber swells to seal the inlet to prevent cross-contamination. In vivo studies (n = 5) confirmed successful pyloric transit in 4/5 rats without tissue injury or inflammation. Each retrieved device yielded 13.48 ± 4.66 ng genomic DNA, enabling 16S rRNA sequencing of site-specific microbiota distinct from fecal profiles. Concurrent detection of intestinal alkaline phosphatase (≈6.5 µg mL[-1]) confirmed dual microbiome-protein biomarker capability. We demonstrate species-level microbiota identification via nanopore sequencing using an orally ingestible platform technology for longitudinal gut microbiome profiling, paving way for studies in large animals and humans.},
}

@article {pmid41358163,
year = {2025},
author = {Schulte-Hillen, R and Giesler, JK and Mock, T and Belshaw, N and John, U and Harder, T and Kühne, N and Neuhaus, S and Wohlrab, S},
title = {Genotype and culture condition effects on single-cell diatom microbiomes: enhanced detection of low-abundance taxa with CRISPR-Cas9.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf194},
pmid = {41358163},
issn = {2730-6151},
abstract = {Primary production in aquatic systems is governed by interactions between microalgae and their associated bacteria. Most of our knowledge about algal microbiomes stems from natural mixed communities or isolated algal monocultures, which therefore does neither address the role of genotypic diversity among the algal host cells nor do they reveal how this host diversity impacts the assembly process of associated bacteria. To overcome this knowledge gap, we developed a single-cell 16S sequencing approach in combination with CRISPR-Cas9 guided depletion of host 16S contaminations from the chloroplast. The validity of this novel method was tested by comparing bacterial communities of 144 single-cells across three genotypes of the Arctic marine diatom Thalassiosira gravida grown under different environmental conditions. From these, 62 single-cells were additionally sequenced after CRISPR-Cas9 treatment. Due to the improved sequencing depth, bacterial richness associated with individual diatom cells was increased by up to 56%. By applying this CRISPR-Cas9 treatment we not only revealed intraspecific host-genotype associations but also low-abundance bacterial taxa that were not detected by standard 16S rRNA gene metabarcoding. Thus, the CRISPR-Cas9 assisted single-cell approach developed in this study advances our understanding on how the intraspecific diversity among algal hosts impacts the assembly process of their associated bacteria. This knowledge is essential to understand the co-evolution and adaptation of species in algal microbiomes.},
}

@article {pmid41358162,
year = {2025},
author = {Nicolas-Asselineau, L and Speth, DR and Zeller, LM and Woodcroft, BJ and Singleton, CM and Liu, L and Dueholm, MKD and Milucka, J},
title = {Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf209},
pmid = {41358162},
issn = {2730-6151},
abstract = {Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in wastewater treatment, such as denitrification, are performed by a diverse community of prokaryotic and eukaryotic microbes. However, the diversity of the microbiome and the potential role of the different microbial taxa in some wastewater treatment plant setups is not fully understood. We aimed to investigate the presence and diversity of denitrifying bacteria of the candidate family Azoamicaceae that form obligate symbioses with protists in wastewater treatment plants. Our analyses showed that denitrifying endosymbionts belonging to the Ca. Azoamicus genus are present in 20%-50% of wastewater treatment plants worldwide. Time-resolved amplicon data from four Danish WWTPs showed high temporal fluctuations in the abundance and composition of the denitrifying endosymbiont community. Twelve high-quality metagenome-assembled genomes of denitrifying endosymbionts, four of which were circular, were recovered. Genome annotation showed that a newly described, globally widespread species, Ca. Azoamicus parvus, lacked a nitrous oxide reductase, suggesting that its denitrification pathway is incomplete. This observation further expands the diversity of metabolic potentials found in denitrifying endosymbionts and indicates a possible involvement of microbial eukaryote holobionts in wastewater ecosystem dynamics of nitrogen removal and greenhouse gas production.},
}

@article {pmid41358150,
year = {2025},
author = {Coufal, S and Zakostelska, ZJ and Thon, T and Roubalova, R and Kadleckova, D and Salakova, M and Tachezy, R and Hrncir, T and Kverka, M and Ticha, V and Pavelcova, M and Kleinova, P and Preiningerova, JL and Kovarova, I and Kreisinger, J and Tlaskalova-Hogenova, H and Havrdova, EK},
title = {Ocrelizumab transiently alters microbiota and modulates immune response depending on treatment outcome.},
journal = {iScience},
volume = {28},
number = {12},
pages = {113872},
pmid = {41358150},
issn = {2589-0042},
abstract = {Multiple sclerosis (MS) is an autoimmune disease characterized by central nervous system atrophy. Microbiota dysbiosis is implicated in MS pathogenesis and treatment outcomes. In our study, we observed microbiota changes already present in treatment-naïve individuals with clinically isolated syndrome, affecting both bacteria and viruses. Gut bacteria alterations were transient during the first 12 months of anti-CD20 therapy. After 12 months, responders showed increased gut microbiota alpha diversity approaching healthy control levels, while non-responders showed a significant decline. Key changes involved Parabacteroides spp., producers of short-chain fatty acids that support gut barrier function and have anti-inflammatory potential. We detected altered gut barrier biomarkers and antibodies against common commensals in MS patients, which were modulated by anti-CD20 treatment. Notably, lipopolysaccharide-binding protein and mannose-binding lectin decreased only in responders. These findings suggest that intestinal barrier damage contributes to immune responses linked to microbial translocation, MS pathogenesis, and treatment outcomes.},
}

@article {pmid41358148,
year = {2025},
author = {Liang, S and Huang, L and Ma, K and Wang, R and Ji, F and Shi, M and Piao, M and Liang, Z and Guo, R and Chen, R and Chen, C and Xie, L},
title = {Pediatric diarrhea management with probiotics supplementation: Results from a randomized controlled trial.},
journal = {iScience},
volume = {28},
number = {12},
pages = {113981},
pmid = {41358148},
issn = {2589-0042},
abstract = {Diarrhea remains a major cause of illness in children, and probiotics are often explored as adjunctive therapies. In this randomized, double-blind, placebo-controlled trial, 141 children aged 6 months to 6 years were assigned to receive either Limosilactobacillus reuteri FPHC2951, Bifidobacterium breve FPHC4024, or placebo alongside standard care for one month. Gut microbiota composition was analyzed before and after intervention using 16S rRNA gene sequencing. While all groups showed increased microbial α-diversity, greater enrichment of Limosilactobacillus and Bifidobacterium occurred in the probiotic groups. Clostridioides difficile levels declined across all groups. Among children receiving antibiotics, microbiota changes were notable only in the probiotic groups. However, no significant differences were observed in diarrhea duration or clinical symptoms between groups. These results suggest that probiotic supplementation can enhance gut microbial recovery during pediatric diarrhea and antibiotic exposure, although the added clinical benefits beyond standard care remain limited.},
}

@article {pmid41357544,
year = {2025},
author = {Firozpoor, J and Gardini, R and Escobar Huezo, ME and Eccard, JA},
title = {Rodent species composition in urban and forested areas in eastern Germany.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e143224},
pmid = {41357544},
issn = {1314-2828},
abstract = {BACKGROUND: Zoonoses are major concerns for public health and after the recent pandemic, have been under a global spotlight for their often unpredictable spread and rapid evolution. In particular, the relationship between wildlife biodiversity and zoonoses lies at the core of the challenges of disease dynamics in a changing world. To address the challenge of rodent-borne diseases, transmitted by rodents acting as hosts for various zoonoses and thriving in different environments, we focus on rodent species composition in European temperate forests and urban parks, where human-wildlife interactions are likely to occur. Using live-trapping, we describe rodent communities for integration into an eco-health framework.

NEW INFORMATION: The dataset introduced here is part of the European project BiodivERsA-BioRodDis (https://www6.inrae.fr/biodiversa-bioroddis), whose goal is to examine the connection between rodent biodiversity, the dynamics of rodent-borne diseases and temporal variations in a changing climate. We provide records of small mammals (Rodentia) captured from forested habitats, with different levels of urbanisation in northeast Germany, within the district of Potsdam (Brandenburg). The trapping took place between winter 2020 and spring 2022 at four different sites. All four sites were sampled in winter 2020, three were revisited in spring 2021 and two in autumn 2021 and spring 2022. This variation was mainly due to logistical constraints and low trapping success at some sites. Using live traps, we collected a total of 620 occurrence records of rodents, including the species Apodemus flavicollis, Apodemus agrarius, Myodes glareolus and Microtus arvalis. A subset of the captures (n = 264) was subsequently dissected for pathogen screening and gut microbiome characterisation, not reported here.},
}

@article {pmid41357037,
year = {2025},
author = {Syromyatnikov, MY and Burakova, IY and Smirnova, YD and Morozova, PD and Pogorelova, SV and Chirkin, EA and Tolkacheva, AA},
title = {Study of Akkermansia muciniphila Effect on the Gut Microbiome of Mice Under LPS-Induced Systemic Inflammation.},
journal = {International journal of inflammation},
volume = {2025},
number = {},
pages = {8695182},
pmid = {41357037},
issn = {2090-8040},
abstract = {Probiotics are strains of living bacteria and yeast that play an important role in regulating the gut microbiota and enhancing host immunity. In the last decade, the bacterial species Akkermansia muciniphila has attracted great interest due to its possible probiotic properties, which play an important role in human health. However, the mechanisms of action of A. muciniphila are still poorly understood. The effect of the A. muciniphila on the intestinal microbiome of model animals with systemic inflammation induced by lipopolysaccharide (LPS) is unexplored. This study aims to investigate the impact of A. muciniphila on the microbiological composition of the mouse gut under LPS-induced systemic inflammation using high-throughput sequencing. The study used a new generation sequencing method aimed at genome-wide sequencing of microorganisms, which makes it possible to study changes in the composition of the microbiome at the bacterial species level, as well as to identify the genes of the metabolic pathways of intestinal bacteria in the studied mice. Our analysis revealed statistically significant differences across all studied groups, with a notable predominance of members from the families Muribaculaceae, Rikenellaceae, and Oscillospiraceae. Consumption of A. muciniphila increased the alpha diversity of gut bacteria (Shannon index) in the context of induced inflammation. Evaluation of the effect of LPS and A. muciniphila on metabolic pathways showed statistically significant differences for the pathways of synthesis and degradation of amino acids, transforming folic acid, and synthesis of sugars. Genetic analysis showed that the probiotic bacterium A. muciniphila reduced the degree of negative effects of LPS on the mouse gut microbiome under systemic inflammation.},
}

@article {pmid41356942,
year = {2025},
author = {Alasbily, H and Mohamed, HH and Asheibi, A and Bazina, MS and Alkaseh, A and Ghaith, HM and Ali Fahmi, F},
title = {Probiotics in Periodontal Diseases: Mechanisms, Evidence Mapping, Limitations, and Future Directions.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e96042},
pmid = {41356942},
issn = {2168-8184},
abstract = {Periodontal disease represents a spectrum of inflammatory disorders that impact the teeth's supporting tissues. It is initiated by the buildup of microbial plaque and sustained by dysbiosis, an imbalance in the oral microbiome that causes tissue damage and disturbs host-microbe homeostasis. These diseases can range from reversible inflammation of the gingiva (gingivitis) to irreversible destruction of the periodontal apparatus (periodontitis). While scaling and root planing, with or without antimicrobials, can effectively reduce bacterial burden, mechanical debridement by itself may not restore microbial symbiosis and may allow disease-associated microbial populations to persist. Incomplete pathogen clearance from deep pockets, residual calculus, or inaccessible root surfaces frequently results in bacterial regrowth and disease progression. Probiotics have emerged as a possible alternative or supplement in periodontal therapy. Their possible benefits include microbial balance restoration in the oral cavity, as well as anti-inflammatory, immunomodulatory, and bone-preserving actions. Nonetheless, the strain-specific effects, dosage regimen, safety profile especially in certain patients and the absence of large-scale, long‑term randomized controlled trials to definitively establish their efficacy remain as concerns. This review discusses the mechanisms through which probiotics may influence periodontal diseases, systematically maps preclinical and clinical evidence, and highlights current limitations and future directions for their application in periodontal therapy.},
}

@article {pmid41356879,
year = {2025},
author = {Farhad, ME and Belal, I and Baana, M and Childs, C and Al-Rufayie, M},
title = {Biomarkers of Probiotic Therapy in Ulcerative Colitis: A Systematic Review of Mechanisms Underlying Remission.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e96126},
pmid = {41356879},
issn = {2168-8184},
abstract = {Ulcerative colitis (UC) is a chronic immune-mediated inflammatory bowel disease of unknown aetiology that affects the colon. Patients with UC typically exhibit dysbiosis - an altered gut microbiota profile compared with healthy individuals, who have a more diverse microbial community - suggesting that dysbiosis may be either a cause or a consequence of UC. Current therapeutics include aminosalicylates and steroids with anti-inflammatory and immunosuppressive properties; however, these treatments do not address dysbiosis and instead relieve symptoms. Antibiotics are sometimes used to exert selective pressure on the microbiota and eliminate Gram-negative bacteria, but they are associated with significant side effects, including diarrhoea, Clostridioides difficile infection, thrush, and peripheral neuropathy. Probiotics, live microorganisms that confer a health benefit on the host, represent a growing area of interest in the treatment of inflammatory bowel disease (IBD), with the potential to modulate the gut microbiota. Randomised controlled trials (RCTs) measuring biomarkers in patients with UC treated with probiotics were identified through searches of four databases. After screening against predefined inclusion and exclusion criteria, eligible studies were assessed for risk of bias. Thirteen RCTs were included, using interventions such as VSL#3 (Actial Nutrition Inc., Covington, Louisiana) and bifidobacteria-fermented milk (BFM), and measured biomarkers including cytokines over follow-up periods of up to one year. Pro-inflammatory signalling markers, such as nuclear factor-κB (NF-κB), were measured in two of 13 studies and showed significant reductions following probiotic therapy. Conversely, anti-inflammatory biomarkers such as interleukin-10 (IL-10) were significantly increased in all four studies that assessed them. These findings provide insights into the inflammatory pathways targeted by probiotics, including down-regulation of Toll-like receptor 2 (TLR2), leading to reduced pro-inflammatory cytokine production. Such results may inform the development of novel therapeutics targeting these pathways and support the use of biomarkers as objective indicators of disease activity or treatment response, in contrast to potentially biased clinical scores.},
}

@article {pmid41356810,
year = {2025},
author = {Akpınar, A and Markiewicz, LH and Harsa, HŞ and Paveljšek, D and Domínguez-Soberanes, J and Agirbasli, Z and Naziri, E and El Jalil, MH and Bouchaud, G and Salminen, S and Savary-Auzeloux, I and Humblot, C and Chassard, C and Pracer, S and Vergères, G and Karakaş-Budak, B},
title = {Efficacy of fermented foods for the prevention and treatment of bacterial vaginosis and vulvovaginal candidiasis.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1658988},
pmid = {41356810},
issn = {2296-861X},
abstract = {Vaginal function in healthy women is closely associated with a lactobacilli-dominated microbiome. Among the most common conditions arising from dysbiosis are bacterial vaginosis (BV) and vulvovaginal candidiasis (VVC). While the efficacy of oral probiotics for the treatment of BV and VVC is well documented, the role of consuming fermented foods remains underexplored. This systematic review aims to present a systematic evaluation of the potential role of fermented foods in the prevention and treatment of BV and VVC and establish the extant research gap between the realm of the clinical sciences and the field of food science and technology. For this purpose, under the guidance of COST Action CA20128-Promoting Innovation of Fermented Foods (PIMENTO), a systematic literature review was conducted in two phases. PubMed, Scopus, and Cochrane databases were used for Phase I to analyze articles on human trials and observational studies where the intervention/exposure involved oral consumption of fermented food. In Phase II, a two-step search strategy was employed: (i) identifying microorganisms with demonstrated clinical efficacy in managing BV and VVC, and (ii) reviewing food science literature where these strains are utilized for fermentation. It was observed that 87% of the food starter applications exploited only two of the 54 efficacious strains identified through clinical studies, namely Lactobacillus rhamnosus GG and Lactobacillus acidophilus LA-5. Findings underscore the potential of fermented foods as carriers for beneficial microorganisms and their relevance in supporting vaginal health. This review contributes to a deeper understanding of the interplay between nutritional consumption of viable probiotic strains and their importance in immunomodulation, highlighting the need for more integrated research efforts across disciplines. Future research aimed at filling this gap will enable informed clinical decisions and dietary recommendations.},
}

@article {pmid41356732,
year = {2025},
author = {Cai, L and Li, Y and Liu, Y and Ma, G and Zhang, Q and Li, X and Li, N},
title = {Endotracheal intubation-related oral mucosal membrane pressure injuries: a narrative review of biomechanical insights, biomaterial optimization, and intelligent monitoring.},
journal = {Frontiers in medical technology},
volume = {7},
number = {},
pages = {1667748},
pmid = {41356732},
issn = {2673-3129},
abstract = {OBJECTIVES: This article is a narrative review that synthesizes current evidence on orotracheal intubation-related oral mucosal membrane pressure injuries in intensive care unit (ICU) patients, focusing on mechanisms, risk factors, and prevention strategies. The review is intended to inform clinicians and researchers by integrating insights from intensive care, biomechanics, biomaterials, and oral microbiology.

METHODS: A comprehensive literature search was conducted in PubMed, Web of Science, Embase, and CNKI using the terms "orotracheal intubation", "oral mucosal injury", "device-related pressure injury", "biomechanics", "biomaterials" and "oral microbiome". Studies published between 2000 and 2025, including both clinical and experimental research, were considered without language restrictions.

RESULTS: Evidence indicates that vertical pressure, shear force, and friction from endotracheal tubes are key contributors to oral mucosal injury. Reported risk factors include advanced age, prolonged intubation, malnutrition, and inflammation. Preventive strategies have been explored in four domains: biomechanical modeling using finite element analysis, biomaterial optimization such as hydrogel and nanocoatings, regulation of the oral microecosystem through probiotics, and intelligent monitoring systems incorporating artificial intelligence and Internet of Things technologies.

CONCLUSIONS: Orotracheal intubation-related oral mucosal pressure injuries are multifactorial and preventable. This narrative review integrates biomechanical insights, optimized biomaterials, microbiome regulation, and intelligent monitoring into a multidimensional prevention framework. Such strategies may enhance early identification, reduce complications, and improve clinical outcomes in ICU patients.},
}

@article {pmid41356699,
year = {2025},
author = {Kim, SM and Praveen, Z and Kim, YH and Ko, JH and Choi, YS and Park, JY and Lee, JH and Choi, SW and Kim, MK},
title = {Functional profiling of the oral microbiome reveals microbial and oncogenic signatures in never-smoking female patients with oral squamous cell carcinoma.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2594842},
pmid = {41356699},
issn = {2000-2297},
abstract = {BACKGROUND: The pathogenesis of oral squamous cell carcinoma (OSCC) in never-smoking females remains poorly understood, as these patients lack traditional risk factors. This subgroup accounts for an increasing proportion of OSCC cases and may exhibit distinct tumor biology. Here, we investigated the association between the alterations in the salivary microbiome and OSCC in never-smoking female patients.

MATERIALS AND METHODS: Saliva samples from 72 never-smoking female patients with OSCC and 494 never-smoking healthy female controls were analyzed using 16S rRNA gene sequencing. Microbial community structure and function were compared using statistical analyses, machine learning algorithms, and pathway prediction with PICRUSt2.

RESULTS: Patients with OSCC exhibited significantly different microbial diversity and composition compared to controls. The genera Rhodococcus, Slackia, Lactobacillus, and Enterobacterales_g were enriched in the OSCC group, whereas Corynebacterium was more abundant in the Control group. These taxa were associated with oncogenic pathways, including PI3K-Akt signaling and nicotinate/nicotinamide metabolism. Functional inference also indicated enrichment of cancer-related orthologs such as LKB1, NFKB1, ITGAV, and TRAF4.

CONCLUSIONS: Salivary microbiome alterations, both taxonomic and functional, are associated with OSCC in never-smoking females. These findings suggest a potential microbial contribution to carcinogenesis in this unique patient population and offer novel insights into disease mechanisms.},
}

@article {pmid41356698,
year = {2025},
author = {Xu, Y and Leng, X and Liu, Q and Ji, Q and Li, J and Huang, X and Li, L and Lin, Y and Karlsson, I and Zhan, Y},
title = {The oral microbiome as mediators in the association between smoking and all-cause mortality.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2594296},
pmid = {41356698},
issn = {2000-2297},
abstract = {BACKGROUND: Smoking increases mortality risk and alters the oral microbiome, but its mediating role in the smoking-survival relationship remains unclear. This study examined whether oral microbiome diversity mediates the association between smoking and all-cause mortality.

METHODS: We included 8,223 participants from the National Health and Nutrition Examination Survey with linked mortality data through 2019. Oral microbiome diversity was assessed using alpha and beta diversity metrics. Associations between smoking, diversity, and mortality were assessed using Weibull Accelerated Failure Time models. Multivariable linear regression evaluated the relationship between smoking and oral microbiome diversity. Mediation analysis estimated the Natural Direct Effect (NDE) and Natural Indirect Effect (NIE). Sensitivity analyses assessed effect heterogeneity.

RESULTS: Among participants, 429 were deceased. Current smoking was associated with a 42.3% shorter survival time (TR = 0.577). Greater ln-transformed observed Operational Taxonomic Units (OTU) richness was associated with 33.2% longer survival time (TR = 1.332). Smoking was associated with survival time through NIE = 1.013 (95% CI: 1.003, 1.033) and NDE = 0.577 (95% CI: 0.474, 0.697). Sensitivity analyses supported the findings.

DISCUSSION: Oral microbiome diversity partially mediated the association between smoking and mortality. Although smoking shortened survival, its effect on increasing OTU richness modestly suppressed this risk. These results highlight a complex microbial pathway and support further investigation into species-level mechanisms and potential microbiome-targeted interventions.},
}

@article {pmid41356486,
year = {2025},
author = {Dedecius, D and Kolář, J and Martinů, J and Štefka, J and Nováková, E and Hypša, V},
title = {Generalist vs. specialist strategy shapes microbiomes in blood feeding parasite Polyplax serrata.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1720127},
pmid = {41356486},
issn = {1664-302X},
abstract = {Insects live in association with bacterial communities, collectively referred to as the microbiome. Microbiome composition varies widely across insect taxa and is shaped by multiple factors, including host phylogeny, environmental conditions, geographic distribution, and nutritional ecology. One hypothesis is that microbiome composition may also reflect whether the host adopts a generalist or specialist ecological strategy. We tested this hypothesis using the sucking louse Polyplax serrata, which offers several advantages as a model system. First, as permanent ectoparasites, lice inhabit a relatively stable and simplified environment, thereby minimizing potential confounding variables. Second, within P. serrata, two closely related lineages have been identified: one restricted to a single rodent host (Apodemus flavicollis), and the other exploiting two hosts (A. flavicollis and A. sylvaticus). We analyzed and compared microbiome structure in these two lineages using 16S rRNA gene amplicon sequencing. While alpha diversity did not differ between the lineages, beta diversity differed significantly, particularly in pairwise dissimilarities among individual samples. These results suggest that in P. serrata, host specialization strategy influences microbiome diversity, with the "generalist" lineage harboring more heterogeneous communities. This finding extends previous observations on ecological divergence between the two lineages, showing that closely related cryptic species with highly similar genomes, living sympatrically in the same environment, can rapidly evolve distinct life strategies that, in turn, shape both their genetic structure and their microbiomes.},
}

@article {pmid41356485,
year = {2025},
author = {Bai, B and Ma, J and Xu, W and Chen, X and Chen, X and Lv, C and Su, W and Li, Y and Sun, H and Zhang, B and Xiang, D and Li, Z and Wu, Y and Sun, J and Yin, M},
title = {Gut microbiota and colorectal cancer: mechanistic insights, diagnostic advances, and microbiome-based therapeutic strategies.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699893},
pmid = {41356485},
issn = {1664-302X},
abstract = {Colorectal cancer (CRC) is closely linked to gut microbiota dysbiosis. We synthesize evidence that carcinogenic microbes promote CRC through chronic inflammation, bacterial genotoxins, and metabolic imbalance, highlighting key pathways involving Fusobacterium nucleatum, pks [+] Escherichia coli, and enterotoxigenic Bacteroides fragilis (ETBF). Building on these mechanisms, we propose a minimal diagnostic signature that integrates multi-omics with targeted qPCR, and a pathway-therapy-microbiome matching framework to guide individualized treatment. Probiotics, fecal microbiota transplantation (FMT), and bacteriophage therapy show promise as adjunctive strategies; however, standardization, safety monitoring, and regulatory readiness remain central hurdles. We advocate a three-step path to clinical implementation-stratified diagnosis, therapy matching, and longitudinal monitoring-supported by spatial multi-omics and AI-driven analytics. This approach aims to operationalize microbiome biology into deployable tools for risk stratification, treatment selection, and surveillance, advancing toward microbiome-informed precision oncology in CRC.},
}

@article {pmid41356481,
year = {2025},
author = {Rao, AV and Ghare, SS and Gautam, V and Hoffman, KL and Petrosino, J and So-Armah, K and Samet, JH and Patts, GJ and Cheng, DM and Blokhina, E and Krupitsky, EM and Lioznov, D and Zvartau, E and McClain, CJ and Tindle, H and Freiberg, MS and Barve, SS},
title = {Sex differences in beneficial and pathogenic bacteria in People With HIV (PWH) with a history of heavy alcohol drinking.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1632949},
pmid = {41356481},
issn = {1664-302X},
abstract = {BACKGROUND: HIV-1 infection and hazardous levels of alcohol consumption have been independently linked to gut dysbiosis affecting beneficial butyrate-producing bacteria. However, sex-based differences in the composition and function of gut microbiome of People With HIV (PWH) with a history of heavy alcohol drinking remain undetermined, which is the focus of this study.

METHODS: Cross-sectional study examining structural and functional features of the gut microbiome in PWH between men and women with a history of hazardous alcohol drinking recruited at St. Petersburg, Russia. 16S rDNA sequencing information was used for metataxonomic, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) and Linear Discriminant Analysis Effect Size (LEfSe) analyses. Group-wise comparisons were done using Mann-Whitney U-test. Further, linear and logistic regression models were used to evaluate the association between sex and measures of gut microbial dysbiosis and Firmicutes/Bacteroidota (F/B) ratio, respectively. Data were adjusted for confounding covariates particularly, HIV-viral load, Anti-retroviral Therapy (ART) and alcohol usage.

RESULTS: Metataxonomic analysis demonstrated that women depicted significantly higher microbial diversity (Operational Taxonomic Units, OTUs and Shannon Index), higher percent relative abundance (%RA) of Firmicutes, lower %RA of Bacteroidota and higher F/B ratio. Importantly, logistic regression revealed that women had twice the odds of having F/B ratio > 1. Notably, women demonstrated significantly higher %RA of butyrate-producing bacterial families, i.e., Lachnospiraceae, Oscillospiraceae, Rikenellaceae and Marinifilaceae and genera. Correspondingly, significantly greater expression of bacterial genes involved in butyrate synthesis in women was demonstrated by PICRUSt2 analysis. Additionally, women depicted lower %RA of pathobiont, Prevotellaceae particularly, Prevotella_9 genus.

CONCLUSION: Overall, we observed significant sex-based differences in the relative abundances of beneficial bacterial communities such as butyrate producers and potential pathogenic Prevotella community in the gut microbiome of PWH with a history of heavy alcohol consumption. The observed sex-based differences are clinically relevant and could inform therapeutic strategies with evidence-based probiotics.},
}

@article {pmid41356477,
year = {2025},
author = {Chakraborty, A and Roy, A and He, S and Castellano-Hinojosa, A and Asiegbu, FO and Coutinho, TA},
title = {Editorial: Forest microbiome: dynamics and interactions in the anthropocene era.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1729625},
pmid = {41356477},
issn = {1664-302X},
}

@article {pmid41356475,
year = {2025},
author = {Wang, L and Liu, W and Wang, L and Zhang, K and Li, D and Ji, J and Luo, J and Zhu, X and Cui, J and Gao, X},
title = {Cross-generational ripples: sublethal fipronil exposure alters Binodoxys communis microbiome without lethal consequences.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1637234},
pmid = {41356475},
issn = {1664-302X},
abstract = {INTRODUCTION: Fipronil, a broad-spectrum phenylpyrazole insecticide, demonstrates high efficacy against Aphis gossypii (cotton aphid). However, its potential effects on Binodoxys communis, a key natural enemy of A. gossypii, remain largely unexplored. This study comprehensively assessed the safety of fipronil for B. communis, with particular emphasis on sublethal effects and associated microbiome alterations.

METHODS: We evaluated the sublethal effects of fipronil on the development of B. communis across parental (F0) and offspring (F1) generations. Furthermore, the alterations in the microbial diversity and community structure of B. communis were analyzed using 16S rRNA sequencing. Functional prediction of the microbiota was performed via PICRUSt2.

RESULTS: Indirect fipronil exposure significantly prolonged larval development in the parental generation (F0, p = 0.017), while showing no statistically significant impact on the offspring generation (F1). 16S rRNA sequencing revealed apparent alterations in the microbial community. In adults, the dominant genus shifted from Akkermansia to Muribaculum after 1 h exposure, while the dominant phylum showed significantly reduced abundance after 3 d. In larvae, the major phylum (Proteobacteria) remained unchanged, but the major genus shifted from Brevitalea to Vicinamibacter. Functional prediction indicated that the predicted genes were predominantly enriched in metabolic pathways (75% of the functional repertoire).

DISCUSSION: These results suggest that fipronil exposure induces previously unrecognized sublethal effects on a key natural enemy insect, primarily by disrupting its symbiotic microbiota, which may play a major role in host metabolism. Our findings highlight the ecological risks of fipronil and emphasize the need for pesticide risk assessments that consider sublethal effects on beneficial insects and their microbiota.},
}

@article {pmid41356464,
year = {2025},
author = {Zhou, W and Huang, S and Huang, X},
title = {Editorial: Mutualistic and antagonistic interactions in the human oral microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1731807},
pmid = {41356464},
issn = {1664-302X},
}

@article {pmid41356350,
year = {2025},
author = {Adeosun, WB and Poswayo, SK and Parihar, SP and Loots, DT},
title = {The Functionality of the Cysteinyl Leukotriene Receptor 1 (CysLTR1) in the Lung by Metabolomics Analysis of Bronchoalveolar Lavage Fluid.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8052995/v1},
pmid = {41356350},
issn = {2693-5015},
abstract = {Introduction The cysteinyl leukotriene receptor 1 (CysLTR1) is known as a potent lipid mediator with a well-established role in inflammatory regulation and lung disease. While its involvement in immune cell recruitment has been previously reported, its broader impact on pulmonary metabolism remains poorly understood. Objectives The study aims to investigate the metabolic consequences of a CysLTR1 deletion in mice to elucidate its role in pulmonary metabolic homeostasis. Methods Bronchoalveolar lavage fluid (BALF) was collected from CysLTR1 knockout (KO) and wild-type (WT) mice and analysed using standardized untargeted gas chromatography-time-of-flight mass spectrometry (GC-TOFMS) metabolomics. Results Metabolomics analyses of the BALF collected from the CysLTR1 KO mice presented significantly reduced levels of glucose, glucosamine, and glyceric acid, indicating the role of the CysLTR in lung glucose uptake and consequently lung glycolysis and gluconeogenesis. This is further supported by reductions in myo-inositol and D-chiro-inositol, also supporting previous findings that this occurs due to insulin resistance. Consequential disruption of various glucose-dependent pathways, including the pentose phosphate pathway (reduced gluconic acid, sedoheptulose and xylose) and purine metabolism (reduced 1-methylinosine) indicates a consequential altered nucleotide turnover, and the significantly reduced concentrations of butanoic acid, decan-2-ol, and 1-hexadecanol, indicate changes to fatty acid metabolism in the lung, as a compensatory response to the initial glucose deficiency induced by the CysLTR1 KO. Lastly, the changes to mandelic acid, glutaric acid, tricarballylic acid, and decan-2-ol, furthermore, indicate the role of CysLTR1 in the composition/metabolism of the microbiome. Conclusion This study expands our knowledge on the role of CysLTR1 beyond its role in immune regulation, that may later serve towards a better understanding of CysLTR1 associated lung diseases and in the development of improved therapeutic strategies.},
}

@article {pmid41356328,
year = {2025},
author = {Mehravaran, S and Pop, M},
title = {Sequencing the ocular surface microbiome: a review of methodological practices and considerations.},
journal = {Frontiers in ophthalmology},
volume = {5},
number = {},
pages = {1660816},
pmid = {41356328},
issn = {2674-0826},
abstract = {PURPOSE: The human ocular surface microbiome (OSM) plays a vital role in ocular health, infection prevention, and immune modulation. However, use of sequencing technology for researching the OSM is challenged by low sample biomass, high sample variability, and methodological inconsistencies. This review systematically evaluates existing literature on OSM research, identifying methodological challenges and proposing standardization strategies to enhance data quality, comparability, and clinical relevance.

METHODS: A comprehensive analysis of peer-reviewed studies was conducted to assess methodologies used in sequencing-based OSM research, with focus on considerations in scope: sample size, selection, choice of eye, time frame, recruitment and enrollment criteria; sample collection and handling: sampling environment, topical anesthesia, sample collection tools and ocular region; sample preservation: temperature and use of buffers; and sample analysis: DNA extraction, quantification, and sequencing approach. Advantages and limitations of different approaches were identified, and best practices for standardization were explored.

RESULTS: This review identified substantial variations in sample collection and processing methodologies, many of which are known to impact OSM composition. However, the influence of certain approaches remains unclear. Additionally, large reporting gaps were observed, as many studies failed to describe critical methodological elements, including specific sample handling procedures and sequencing parameters.

CONCLUSIONS: While sequencing technologies offer valuable insights, our findings highlight the need for further investigation of different methodological approaches to determine best practices and establish standardized methodological protocols, as well as the need for standardized reporting protocols in OSM research. These standards are essential for enhancing data reliability and translating findings into clinical applications.},
}

@article {pmid41356285,
year = {2025},
author = {Karmazyn, M},
title = {Targeting Gut Microbiome Dysbiosis as a Potentially Effective Therapeutic Approach for the Treatment of Heart Failure.},
journal = {Reviews in cardiovascular medicine},
volume = {26},
number = {11},
pages = {47146},
pmid = {41356285},
issn = {2153-8174},
}

@article {pmid41356231,
year = {2025},
author = {Abou-Khalil, R},
title = {Nutritional Interventions for Enhancing Sleep Quality: The Role of Diet and Key Nutrients in Regulating Sleep Patterns and Disorders.},
journal = {Food science & nutrition},
volume = {13},
number = {12},
pages = {e71309},
pmid = {41356231},
issn = {2048-7177},
abstract = {Sleep disorders and poor sleep quality are increasingly recognized as global health concerns, with substantial consequences for mental and physical health. While pharmacological treatments are available, growing evidence suggests that nutritional interventions offer effective, sustainable alternatives for enhancing sleep quality. This review aims to synthesize current evidence on the impact of key nutrients, dietary patterns, bioactive compounds, and gut microbiome modulation on sleep regulation, and to explore emerging personalized nutrition approaches for managing sleep disorders. A comprehensive review of clinical trials, observational studies, and mechanistic research published over the past two decades was conducted. Key focus areas included sleep-supportive nutrients, dietary patterns (e.g., Mediterranean, ketogenic, plant-based diets), chrononutrition, gut-brain axis modulation, functional foods, and personalized nutrition strategies. Evidence supports the role of specific nutrients (e.g., magnesium, tryptophan, omega-3 fatty acids) and dietary patterns rich in anti-inflammatory and antioxidant compounds in improving sleep outcomes. Functional foods such as tart cherry juice and kiwifruit demonstrate potential benefits. The gut microbiome emerges as a significant regulator of sleep physiology, suggesting probiotics and prebiotics as novel interventions. Personalized nutrition approaches, incorporating genetic, metabolic, and lifestyle factors, offer promising individualized solutions. Nutritional interventions represent a promising, non-pharmacological strategy for improving sleep quality and managing sleep disorders. Future research should focus on personalized approaches and large-scale clinical trials to validate and refine these strategies for clinical practice.},
}

@article {pmid41355950,
year = {2026},
author = {Muhammad, S and Li, M and Jia, Q and Ijaz, M and Liang, S and Zeng, W and Chen, D and Zhang, Y and Du, X and Song, W and Guo, B},
title = {Advances in the engineering of living probiotics for cancer immunotherapy.},
journal = {Theranostics},
volume = {16},
number = {3},
pages = {1164-1226},
pmid = {41355950},
issn = {1838-7640},
mesh = {*Probiotics/administration & dosage/therapeutic use ; Humans ; *Neoplasms/therapy/immunology ; *Immunotherapy/methods ; Tumor Microenvironment/immunology ; Animals ; Bacteria/genetics ; Drug Delivery Systems/methods ; },
abstract = {The role of bacteria in tumor development has been increasingly recognized through advances in sequencing technologies, revealing their influence on the tumor microenvironment and immune system. Live bacterial therapy, known for its unique ability to target tumors, colonize cancerous tissues, and activate immune responses, is emerging as a novel approach to cancer treatment. To enhance the therapeutic efficacy and safety of this strategy, various engineering techniques have been developed to modify bacteria, enabling the creation of advanced bacteria-based drug delivery systems. Living probiotics can selectively colonize the tumor microenvironment, where they interact with immune cells to enhance antitumor responses. This review provides an overview of the complex relationship between bacteria and tumors and discusses engineering methods for bacterial modification, including physicochemical approaches and synthetic biology. It further highlights the applications of these strategies in enhancing cancer therapies. Finally, it examines the future opportunities for engineered bacteria in cancer therapy, focusing on the potential of combination therapies, personalized medicine, and the role of the microbiome in enhancing therapeutic outcomes. With ongoing advancements, engineered bacteria hold great promise for improving the efficacy and safety of cancer treatments, offering a new frontier in oncology.},
}

*Probiotics/administration & dosage/therapeutic use
Humans
*Neoplasms/therapy/immunology
*Immunotherapy/methods
Tumor Microenvironment/immunology
Animals
Bacteria/genetics
Drug Delivery Systems/methods

@article {pmid41355913,
year = {2025},
author = {Roganovic, J and Radosevic, M and Dordevic, A},
title = {Role of the gut microbiome in the development and prognosis of pediatric leukemia.},
journal = {World journal of clinical oncology},
volume = {16},
number = {11},
pages = {111419},
pmid = {41355913},
issn = {2218-4333},
abstract = {The gut microbiome plays a pivotal role in immune homeostasis and systemic inflammatory regulation, both of which are critically involved in the pathogenesis and progression of pediatric leukemias. Recent evidence reveals that children with leukemia often exhibit distinct gut microbiome profiles at diagnosis, marked by reduced microbial diversity and the enrichment of pro-inflammatory taxa such as Enterococcus and Streptococcus. This microbial dysbiosis may promote leukemogenesis by disrupting immune regulation and driving chronic inflammation. Chemotherapy significantly alters the gut microbiome, inducing dysbiosis characterized by a loss of beneficial commensals and the dominance of pathobionts. Specific microbial signatures, such as the enrichment of Bacteroides, correlate with reduced inflammation and improved prognosis, underscoring the gut microbiome's prognostic value. Emerging therapies, including dietary adjustments, probiotics, and fecal gut microbiome transplantation, aim to restore microbial balance and reduce treatment-related complications. Moreover, gut microbiome profiling shows potential for identifying biomarkers linked to leukemia predisposition, paving the way for early diagnosis and tailored preventive strategies. This mini-review explores recent advancements in understanding the influence of the gut microbiome on pediatric leukemias, emphasizing its role as both a therapeutic target and a prognostic biomarker. Integrating gut microbiome research into clinical practice may help optimize treatment outcomes and improve quality of life for children with leukemia.},
}

@article {pmid41355723,
year = {2025},
author = {Murphy, K and Gromisch, M and Connolly, J and Wang, T and McWalters, J and Atrio, J and Mahant, AM and Gera, S and Colanta, A and Cajigas, A and Kelly, L and Estrella, H and Gustafson, D and Minkoff, H and Anastos, K and Keller, MJ and Herold, BC},
title = {Impact of vaginal estradiol on the genitourinary syndrome of menopause, vaginal microbiome and mucosal immune mediators in women living with HIV.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciaf669},
pmid = {41355723},
issn = {1537-6591},
abstract = {BACKGROUND: Women with HIV (WWH) experience early onset menopause and symptoms may impact antiretroviral therapy (ART) adherence. Vaginal estradiol is safe and effective for treatment of the genitourinary syndrome of menopause (GSM) but has not been studied in WWH. The study objective was to test whether vaginal estradiol would improve GSM symptoms in menopausal WWH.

METHODS: Menopausal WWH were randomized 1:1 to 12-weeks of open-label vaginal estradiol (n=25) versus no treatment (n=26). Participants had at least one GSM vulvovaginal symptom in the month prior (dryness, itching, irritation, soreness, or dyspareunia) and clinical atrophy. The primary outcome was difference in mean symptom severity (scale 0-3) defined by the composite vaginal symptom index (VSI) between baseline and week 12. Changes in severity of participants' most bothersome symptom (MBS), vaginal maturation index (VMI), vaginal microbiome, and mucosal immune mediators were assessed. Results were compared by paired t-test or Wilcoxon signed rank tests; a mixed effect model examined differences in VSI improvement between groups.

RESULTS: Mean age was 59 years, 78% self-reported as Black, and all were on ART. Both groups had significant reductions in VSI, however the magnitude was significantly greater in the estradiol group (p<0.0001). Estradiol and younger age were associated with VSI improvement. VMI and MBS improved significantly only in the estradiol group. There were no significant changes in the microbiome or mucosal mediators.

CONCLUSIONS: The favorable response to estradiol suggests that treatment perhaps initiated earlier may be beneficial for GSM in WWH and should be studied in larger clinical trials.},
}

@article {pmid41355585,
year = {2026},
author = {Liu, Y and Wang, F and Zhou, Z and Xiao, Y and Zhang, Z and Lu, X and Yan, H and Yang, X and Lu, B},
title = {The Safety and Quality of Staple Root and Tuber Crops: A Review on Hazards, Detection Methods, and Mitigation Strategies.},
journal = {Comprehensive reviews in food science and food safety},
volume = {25},
number = {1},
pages = {e70353},
doi = {10.1111/1541-4337.70353},
pmid = {41355585},
issn = {1541-4337},
support = {//China Agriculture Research System of MOF and MARA/ ; //National Key Research and Development Program of China/ ; },
mesh = {*Plant Roots/chemistry ; *Crops, Agricultural/chemistry ; *Plant Tubers/chemistry ; *Food Safety ; Food Contamination/analysis/prevention & control ; Quality Control ; },
abstract = {Staple root and tuber crops (SRTCs), including potatoes, cassava, sweet potatoes, yams, and taros, play vital roles in global nutrition. However, they present significant safety hazards, which poses threats to human health, have garnered widespread public concern, and consequently constrain the further development and utilization of SRTCs. This review systematically examines recent advances in quality and safety control for SRTCs, with a particular focus on the progress and challenges in detection methods and mitigation strategies for the associated hazards. It further proposes the establishment of an integrated farm-to-fork quality control system for SRTCs. This review identifies shared hazard profiles (endogenous toxins, heavy metals, pesticides, mycotoxins, acrylamide, microplastics) across SRTCs and highlights key strategies for mitigation. Significant advancements in rapid detection technologies (sensors, immunoassays, spectral imaging) offer enhanced sensitivity and field applicability compared to traditional methods. Crucially, establishing an integrated farm-to-fork quality control system, incorporating genetic improvement, optimized cultivation/postharvest practices, and innovative processing, is essential for comprehensive hazard reduction. Future research priorities include multiomics approaches, rhizosphere microbiome engineering, and Industry 4.0 integration to further enhance SRTCs safety and utilization. Our work aims to enhance the safety and quality of SRTCs, thereby promoting their broader development and utilization.},
}

*Plant Roots/chemistry
*Crops, Agricultural/chemistry
*Plant Tubers/chemistry
*Food Safety
Food Contamination/analysis/prevention & control
Quality Control

@article {pmid41355544,
year = {2025},
author = {Chaudhary, V and Singh, AP and Sharma, H and Taumar, D},
title = {Next-Generation Probiotics in Allergy Therapy: Scientific Evidence and Clinical Applications.},
journal = {Anti-inflammatory & anti-allergy agents in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715230407403251105101126},
pmid = {41355544},
issn = {1875-614X},
abstract = {The global increase in allergic diseases, such as atopic dermatitis, allergic rhinitis, asthma, and food allergies, has become a major public health issue. These diseases typically involve immune dysregulation, including a Th1/Th2 imbalance, increased IgE levels, regulatory T cell (Treg) dysfunction, and epithelial barrier dysfunction. New research has recognised an important role for the gut and mucosal microbiome in regulating immune responses and has prompted interest in the therapeutic utility of probiotics. Probiotics are live microbes that, when given in adequate amounts, confer health benefits, generally such as immunomodulation or restoration of gut barrier function. Traditional probiotics (i.e., Lactobacillus and Bifidobacterium species) reduce allergic inflammation through promotion of Treg differentiation, increases in antiinflammatory cytokines (e.g., IL-10), suppression of Th2 cytokines (e.g., IL-4), and modification of IFNγ. Traditional probiotics also support mucosal barrier function and restore microbial composition by producing short-chain fatty acids (SCFAs), like butyrate, which act directly on Gprotein- coupled receptors and histone deacetylases to suppress inflammation. Next-generation probiotics (NGPs), such as Akkermansia muciniphila, Faecalibacterium prausnitzii, Bacteroides fragilis, and some clusters of Clostridia, can provide more targeted effects. These NGPs can secrete anti-inflammatory metabolite compounds, such as polysaccharide A (PSA), which modulate dendritic cells and increase Treg activity, and can promote mucin production to improve gut barrier function. Overall, there are key issues with strain specificity, dose, safety in immunocompromised individuals, and possible regulatory classification issues. Future opportunities may include precision microbiome profiling, synthetic biology, and artificial intelligence-driven strain discovery to develop personalised approaches to allergy immunotherapy.},
}

@article {pmid41355462,
year = {2025},
author = {Morais-Almeida, M and Baptista-Pestana, R},
title = {Environmental factors influencing the microbiome in adult asthma: emerging mechanistic insights.},
journal = {Current opinion in allergy and clinical immunology},
volume = {},
number = {},
pages = {},
pmid = {41355462},
issn = {1473-6322},
abstract = {PURPOSE OF REVIEW: Asthma is a mosaic of phenotypes shaped by complex host-environment interactions. Among these, the microbiome has moved to a central determinant of disease expression, and airway and gut microbiome should be seen as active players in asthma pathophysiology. This review critically examines how environmental exposures, including pollution, drugs, diet, and climate, remodel microbial ecosystems, and reprogram immune responses in adults with asthma, with emphasis on clinical translation.

RECENT FINDINGS: Advances from multiomics, large-scale cohorts, and Mendelian randomization studies reinforce the concept of the gut-lung axis as a decisive modulator of asthma outcomes. Airway dysbiosis, often marked by Proteobacteria dominance, consistently correlates with poor asthma control, exacerbations, and steroid resistance. Environmental determinants of microbiome reshape erode immune tolerance. Microbial metabolites such as short-chain fatty acids act as molecular messengers capable of restoring epithelial and immune balance. These findings challenge the traditional inflammatory-centric view of asthma and demand broader mechanistic frameworks.

SUMMARY: The microbiome should be considered a central piece of the puzzle in asthma research. Precision medicine in adult asthma will remain aspirational unless microbiome-informed biomarkers and interventions are embraced. Robust interventional studies are urgently needed to translate this promise into practice.},
}

@article {pmid41355426,
year = {2026},
author = {Muhammad, A and Kong, X and Li, L and Khan, MHU and Jia, P and Miao, C and Zhang, Z},
title = {Melatonin Enhances Peanut Productivity by Enriching Root-Associated Nitrogen-Fixing Bacteria.},
journal = {Journal of pineal research},
volume = {78},
number = {1},
pages = {e70105},
doi = {10.1111/jpi.70105},
pmid = {41355426},
issn = {1600-079X},
support = {//This work was partially supported by the Key R&D and Promotion Projects of Henan Province (242102111094, 242102111148, 252102111077), the International Science and Technology Cooperation Project of Henan Province (242102521050), the Henan Province High-Talent Foreign Experts Introduction Plan (HNGD2024030), and the Henan Center of Outstanding Overseas Scientists (GZS2024018)./ ; },
mesh = {*Melatonin/pharmacology ; *Arachis/microbiology/drug effects/growth & development ; *Plant Roots/microbiology/drug effects ; *Nitrogen-Fixing Bacteria/drug effects ; Microbiota/drug effects ; Soil Microbiology ; Nitrogen Fixation/drug effects ; },
abstract = {Melatonin, a pleiotropic phytohormone, is widely recognized as a promising bio-stimulant, yet its integrative effects on root development, yield gain, and microbiome assembly in legumes remain underexplored. In this study, we investigated the effects of melatonin seed treatment across three peanut genotypes, focusing on plant productivity and the composition and structure of bacterial communities in root, rhizosphere, and bulk soil compartments. Melatonin treatment substantially improved root biomass, nodulation, nitrogen balance index, and yield-related traits, with the highest response observed in the genotype Xinbaihua 16. Amplicon sequencing revealed that melatonin induced distinct genotype and compartment specific shifts in bacterial community composition, with the root bacteria showing the increased remodeling, including a 45.9% increase in unique amplicon sequence variants (ASVs). Melatonin selectively enriched key Proteobacteria taxa such as Rhizobium, Sphingomonas, and Enterobacter hormaechei, known for their plant-growth promoting and biocontrol capabilities. Notably, melatonin-enriched taxa also included widely recognized nitrogen-fixing symbionts such as Pararhizobium and Ensifer, underscoring a direct link between melatonin-induced microbiome shifts and enhanced nitrogen acquisition capacity. Co-occurrence network analysis indicated that melatonin-treated roots harbored more complex bacterial networks, and Modules 3 and 4, dominated by melatonin-induced Proteobacteria, were strongly correlated with most plant traits. Collectively these findings highlight melatonin dual role as a bio-stimulant and microbiome modulator, promoting a functionally enriched and responsive bacteria that support enhanced plant performance. This study provides novel insights into the melatonin-mediated coordination of plant performance and bacterial assembly, offering a foundation for microbiome-informed crop improvement strategies.},
}

*Melatonin/pharmacology
*Arachis/microbiology/drug effects/growth & development
*Plant Roots/microbiology/drug effects
*Nitrogen-Fixing Bacteria/drug effects
Microbiota/drug effects
Soil Microbiology
Nitrogen Fixation/drug effects

@article {pmid41354993,
year = {2025},
author = {Zhang, W and Zhang, M and Xie, J and Huang, H and Schmitz-Esser, S and Li, W and Liu, H and Li, D},
title = {Dynamics of the gut microbiome and resistome in response to prophylactic antibiotic treatment in post-surgical giant pandas.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-25645-6},
pmid = {41354993},
issn = {2045-2322},
support = {2023NSFSC0011//Natural Science Foundation of Sichuan Province/ ; 2023NSFSC0011//Natural Science Foundation of Sichuan Province/ ; QD2023A46//Mianyang Teachers' College/ ; QD2023A46//Mianyang Teachers' College/ ; 2022 CPB-B09//the grants from the independent project of Chengdu Research Base of Giant Panda Breeding/ ; },
abstract = {For giant pandas, the ecological impact of prophylactic postoperative antibiotics on their gut microbial communities and resistome is not well characterized. Here, we assessed the impact of intravenous cefotaxime administration by analyzing longitudinal fecal samples from five giant pandas via 16 S rRNA sequencing (n = 304 samples) and shotgun metagenomics (n = 22 samples). 16 S-based analysis revealed that antibiotic exposure significantly altered bacterial community structure, resulting in a pronounced increase in the abundance of Pseudomonadota (from 50% ± 24% to 60% ± 38%; P < 0.001) and a reduction in Shannon diversity (from 2.8 ± 0.4 to 2.4 ± 1.3; P < 0.05). In contrast, metagenomic analysis indicated that cefotaxime exposure did not significantly increase the overall diversity of antimicrobial resistance genes (ARGs) or virulence factor genes (VFGs). However, we observed a marked expansion in the diversity of the CTX-M β-lactamase family (blaCTX-M), which persisted into the recovery phase. We also recovered 10 metagenome-assembled genomes (MAGs) harboring both ARGs and VFGs, identifying them as potential antibiotic-resistant pathogens (ARPs). Their abundance, however, remained unchanged throughout treatment. These findings provide new insights into the effects of short-term antibiotic exposure in giant pandas, highlighting its transient effect on microbial community structure and a limited effect on resistome diversity.},
}

@article {pmid41354859,
year = {2025},
author = {Robas-Mora, M and Fernández-Pastrana, VM and González-Reguero, D and Probanza, A and Jiménez-Gómez, PA},
title = {Effect of PGPB-enriched organic fertilizer ORGAON[®]PK on the rhizospheric microbiota and biomass of Lupinus albus (L.): a sustainable alternative to chemical fertilizer.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00827-x},
pmid = {41354859},
issn = {2524-6372},
support = {TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; },
abstract = {The intensive use of agrochemicals is essential to maintain crop yields, but it has led to overexploitation of land and environmental deterioration. To promote more sustainable agriculture, this study evaluates the novel effects of biofertilizers enriched with plant growth promoting bacteria, such as Bacillus pretiosus and Pseudomonas agronomica, on Lupinus albus var. Orden Dorado, to improve the rhizospheric soil health and plant biomass as well as reducing dependence on chemical fertilizers. The organic matrix ORGAON[®]PK and its sterilized version, both derived from horticultural waste, were tested compared with a traditional chemical fertilizer and a water control. After three months of treatment, metagenomic analyses (16 S rRNA gene amplicons) indicated that the strains remained in the rhizosphere, increasing metabolic diversity without altering the microbial structure (Shannon index). In addition, a significant reduction in the minimum inhibitory concentration against clinical antibiotics (p < 0.05) was observed, highlighting the potential of biofertilizers to decrease microbial resistance in the soil. Principal component analysis showed clear differences between treated and control groups, and ANCOM-BC revealed changes in non-culturable bacteria. Biometric analyses revealed increases of 70-88% in shoot weight, ~ 80% in total biomass, and up to 36% in shoot elongation compared with the control. Biofertilizers improved nutritional quality and plant biomass, suggesting their potential as a sustainable and efficient alternative to the use of chemical fertilizers.},
}

@article {pmid41354833,
year = {2025},
author = {M'Bra, PEH and Suárez-Uribe, I and Avino, M and Ng Kwan Lim, E and Mayhue, M and Balthazar, P and Aumont, A and Prévost, K and Massé, E and Fernandes, KJL},
title = {Medium-chain triglycerides and ketogenic diet prevent alterations of the gut microbiome in transgenic Alzheimer's disease mice.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09171-9},
pmid = {41354833},
issn = {2399-3642},
abstract = {The systemic mechanisms underlying the benefits of ketogenic interventions on cognition in Alzheimer's disease (AD) are understudied. Interventions involving a carbohydrate-free high-fat ketogenic diet (KD) or dietary supplementation with medium-chain triglycerides (MCT) both improve cognition in AD mouse models, yet with opposing effects on circulating ketones levels, peripheral insulin sensitivity and inflammation. Since the gut microbiome regulates systemic metabolism and inflammation and is altered by aging and disease, we investigated how it is affected in mice subjected to MCT and KD. At early stages of pathology, AD mice exhibited substantially reduced richness and distinct composition of gut microbiome species. Administration of MCT or KD for 1-month increased microbiome diversity, restoring the levels of more than 50% of the bacteria altered in AD mice and inducing novel alterations. Both diets increased levels of short-chain fatty acid-producing bacteria, such as Lachnospiraceae, which directly correlated with improved hippocampal dendritic spine density. Interestingly, longer term administration of KD increased the obesity-associated Firmicutes/Bacteroidota ratio and bodyweight in AD but not WT mice, suggesting that AD-associated metabolic defects should be considered when designing such intervention. We conclude that MCT and KD may influence AD central and peripheral defects in part via modulation of the gut microbiome.},
}