@article {pmid41034629,
year = {2025},
author = {Brown, JL and Johnston, W and Butcher, MC and Burleigh, M and Ramage, G},
title = {The butterfly effect: collateral damage and impacts of antimicrobial strategies on the oral microbiome.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {84},
pmid = {41034629},
issn = {2731-8745},
support = {BB/V509541/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/V509541/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {The oral cavity is a complex environment hosting diverse microbial biofilms on different surfaces, all immersed in saliva that enables recolonisation and spread. These microbial populations fluctuate with diet, hygiene, antimicrobials, and disease. While biofilm control measures aim to protect health, they may cause unintended effects, including antimicrobial resistance (AMR). Persistent resistant microbes reshape oral and systemic niches through ecological disruption and genetic adaptation, which may negatively impact human health.},
}

@article {pmid41034550,
year = {2025},
author = {Low, JM and Gupta, A and Toh, R and Lim, SL and Chan, SY and Swarup, S and Lee, LY},
title = {Vertical Transmission of Gut Dysbiosis From Mothers With Gestational Diabetes to Infants.},
journal = {Journal of diabetes},
volume = {17},
number = {10},
pages = {e70148},
doi = {10.1111/1753-0407.70148},
pmid = {41034550},
issn = {1753-0407},
support = {NUS DBS R-154-Rb77-133//National University of Singapore (NUS)'s Institute for Health Innovation & Technology (iHealthtech)/ ; NUHSRO/2020/077/MSC/02/SB//NUS Medicine Synthetic Biology Translational Research Program/ ; NCSP2.0/2023/PVO/LJM//NUHS Clinician Scientist program, Singapore/ ; MOH-RTF23jan-0004/MOH-001381-00//National Medical Research Council (NMRC), Singapore, Research Training Fellowship/ ; },
abstract = {BACKGROUND: Vertical transmission of microbes from a mother's gut to their offspring plays a crucial role in the genesis of the early life gut microbiome. Gestational Diabetes Mellitus (GDM) is the commonest metabolic disorder during pregnancy, which has adverse short- and long-term effects on both maternal and infant health. We aimed to capture the GDM-associated biosignatures in infants' gut microbiome from birth to the first 6 weeks of life.

METHODS: 53 GDM mother-infant dyads and 16 healthy mother-infant dyads were recruited. We performed targeted 16S rRNA gene amplicon sequencing on stool samples. Various statistical analyses were performed to understand the changes in the microbiome profile of infants and identify GDM-associated bacterial biomarkers in mothers and their transfer to infants.

RESULTS: GDM altered the gut microbiome of pregnant women as compared to healthy counterparts (PERMANOVA, p.adjusted < 0.05), with predominance of bacterial members associated with insulin resistance, proinflammatory conditions, and other metabolic processes. Infants born to GDM mothers have distinctive early life microbiome (meconium and six weeks stools) compared to infants born to control mothers (PERMANOVA, p.adjusted < 0.05). We also identified the presence of various GDM-associated microbial signatures such as Blautia and Collinsella in both meconium and one-month-old stool samples of infants born to GDM mothers.

CONCLUSION: This study provides a better understanding of the impact of GDM on the seeding of a specific set of microbes during the early life colonization event in the infant gut that increases the risk of inflammatory and metabolic diseases in the future.},
}

@article {pmid41034461,
year = {2025},
author = {Łętocha, A and Michalczyk, A and Bielecka, E and Kantyka, T and Miastkowska, M and Sikora, E},
title = {Skin microbiome friendly topical formulations containing probiotic - loaded alginate microspheres: in vitro studies.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34246},
pmid = {41034461},
issn = {2045-2322},
}

@article {pmid41033907,
year = {2025},
author = {Embleton, ND and van den Akker, CHP and Alshaikh, BN},
title = {Probiotic supplementation - does it prevent or cause neonatal sepsis?.},
journal = {Seminars in fetal & neonatal medicine},
volume = {},
number = {},
pages = {101668},
doi = {10.1016/j.siny.2025.101668},
pmid = {41033907},
issn = {1878-0946},
abstract = {Probiotic supplementation in preterm infants is one of the most extensively studied interventions in neonatal medicine, with over 50 randomised controlled trials. This paper examines the relationship between probiotic supplementation and late onset sepsis (LOS), considering mechanistic pathways, clinical evidence, and safety profile. Multiple systematic reviews and meta-analyses consistently show that probiotics reduce necrotising enterocolitis (NEC) incidence and all-cause mortality in preterm infants, establishing them as one of the most beneficial interventions in neonatology. Current evidence suggests modest effects on LOS, with Cochrane systematic reviews reporting relative risk 0.89 (95 % CI 0.82-0.97) but with low certainty. Mechanisms supporting LOS reduction include competitive pathogen exclusion, enhanced epithelial barrier function, improved immune responses, and reduced time to full enteral feeding with decreased intravenous access requirements. The safety profile of probiotics is reassuring, with serious adverse events being exceptionally rare. Probiotic-induced sepsis probably occurs in less than 0.5 % of treated infants, representing a very low risk that must be weighed against the likely substantial benefits for NEC and mortality reduction. Product contamination and other quality issues exist but appear manageable with appropriate quality control. Given the robust evidence for NEC and mortality reduction, probiotics represent a valuable intervention for preterm infants but may have limited, if any impact on sepsis. While their specific role in LOS prevention and impacts on the resistome requires further investigation, the overall benefit-risk profile strongly favors their use. Future research will further refine understanding of optimal strain selection and implementation strategies for maximizing clinical benefits while maintaining safety.},
}

@article {pmid41033906,
year = {2025},
author = {Ommert, I and Mägi, CA and Lilliesköld, S and Blomqvist, YT and Axelin, A and Linnér, A},
title = {The role of parents to prevent infections in the neonatal intensive care unit.},
journal = {Seminars in fetal & neonatal medicine},
volume = {},
number = {},
pages = {101669},
doi = {10.1016/j.siny.2025.101669},
pmid = {41033906},
issn = {1878-0946},
abstract = {Late onset sepsis is a major cause of morbidity and mortality in the neonatal intensive care unit, and it is frequently acquired from the environment. Infant- and family-centered developmental care, which involves skin-to-skin contact, breastfeeding and continuous parental participation in the care, is an effective infection prevention strategy. Kangaroo mother care, including skin-to-skin contact supports the development of a diverse skin microbiome, distinct from that of the hospital environment. Breastmilk further contributes to infection prevention and immune system development through multiple mechanisms. Parental involvement may improve the safety and quality of care delivery by hospital staff. In summary, parents play an important role in infection prevention in the neonatal intensive care unit. The risks of not including parents in the care of their infants should be further considered both in research and clinical practice.},
}

@article {pmid41033689,
year = {2025},
author = {Li, K and Li, T and Liu, Y and Zou, B and Geng, G and Xu, Y and Liu, J and Wang, Y},
title = {Decoding Rhizosphere Synergies: Pseudomonas and Bacillus Enhance Microbiome-Mediated Suppression of Rhizoctonia solani in Sugar Beet.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-05-25-0159-R},
pmid = {41033689},
issn = {0031-949X},
abstract = {Sugar beet is a crucial sugar crop with substantial economic and nutritional value. The occurrence of damping-off disease severely impacts sugar beet quality and yield. Here, we successfully isolated two endophytes from sugar beet, and it follow as Bacillus albus SB-3 and Pseudomonas chlororaphis SB-35, via morphological observation and molecular identification. Both SB-3 and SB-35 exhibited nitrogen-fixing and potassium mobilization capabilities, with SB-35 demonstrating additional traits including phosphate solubilization, potassium mobilization. SB-3 and SB-35 promoted the growth of sugar beet, resulting in increased biomass, and improved soil available nutrient. Besides, SB-3 and SB-35 had also extracellular protease activities and inhibited the mycelium growth of Rhizoctonia solani. In independent pot experiments, SB-3 and SB-35 exhibited significantly controlling the damping-off of seedlings for sugar beet. Further analysis indicated that SB-3 and SB-35 may alter microbial community structure, reducing the abundance of Rhizoctonia solani, promoting the recruitment of beneficial microorganisms, such as Hypocrea, Peziza, and Talaromyces, to occupy ecological niches, thereby reducing the numbers of pathogen. The two bacterial strains modulated the diversity and community structure of rhizosphere microorganisms, suggesting a microbiome-mediated mechanism underlying their host-beneficial effects. This study advances our understanding of harnessing endophytes to enhance sugar beet productivity and suppressing sugar beet damping-off caused by Rhizoctonia solani.},
}

@article {pmid41033626,
year = {2025},
author = {Kong, F and Guan, DX and Lu, L and Lu, S and Xu, J and Wang, H},
title = {Multi-element amendment reshaped rhizosphere microbiome: A microbially driven Fe/Mn/S synergistic action for Cd immobilization.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122985},
doi = {10.1016/j.envres.2025.122985},
pmid = {41033626},
issn = {1096-0953},
abstract = {Cadmium (Cd) contamination in soils threatens rice safety, necessitating effective remediation strategies. While the silicon-calcium-magnesium amendment (FSY) is known to reduce Cd bioavailability, its precise microbial mechanisms remain underexplored. This study integrated metagenomics and machine learning to investigate FSY's impact on the rice rhizosphere microbiome and to elucidate the biological drivers of Cd immobilization. FSY application and rice growth stage were the core factors that significantly reshaped bacterial and archaeal community structures, shifting archaeal community assembly toward deterministic processes, while the fungal community remained relatively stable. Co-occurrence network analysis revealed that FSY enhanced the complexity and stability of microbial interactions, strengthening the roles of key functional taxa. Crucially, functional profiling showed that FSY significantly upregulated genes related to multi-barrier systems: (1) iron/manganese oxidation (e.g., feoB) associated with iron-manganese plaque (IP) formation; (2) sulfate reduction (e.g., dsrA) linked to cadmium sulfide (CdS) precipitation; and (3) microbial Cd resistance (e.g., the czcA gene). Machine learning identified 14 core species, including key taxa in Campylobacterota and Thermoproteota, as the pivotal drivers of synergistic Fe/Mn/S-Cd interaction. These findings substantiated the microbially driven Fe/Mn/S synergistic model for Cd immobilization through three interconnected mechanisms: enhanced microbially mediated mineral fixation (IP thickening and CdS precipitation), and strengthened community-level Cd resistance. This research provided a deep mechanistic understanding of how chemical amendments induced microbial functions to mitigate heavy metal risks, thereby offering a scientifically-grounded strategy for remediation and safe use of Cd-contaminated field.},
}

@article {pmid41033577,
year = {2025},
author = {Dai, X and Chen, Y and Fang, S},
title = {Impact of Fidaxomicin on the Microbiome in Pediatric Clostridioides Difficile Infection: Proposal of a Microbiota-Sparing Metric.},
journal = {The Journal of pediatrics},
volume = {},
number = {},
pages = {114842},
doi = {10.1016/j.jpeds.2025.114842},
pmid = {41033577},
issn = {1097-6833},
}

@article {pmid41033479,
year = {2025},
author = {Lewis, DA},
title = {Gonorrhea.},
journal = {Clinics in dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clindermatol.2025.09.006},
pmid = {41033479},
issn = {1879-1131},
abstract = {Neisseria gonorrhoeae, a Gram-negative intracellular pathogen, causes gonorrhea. While usually sexually transmissible, it can be acquired by direct inoculation. Untreated gonococcal infections have deleterious impacts, including adverse pregnancy outcomes, ectopic pregnancy, infertility, and even blindness. Extended-spectrum cephalosporins remain the mainstay of therapy, and gonococcal culture is essential to determine susceptibility to these agents. Antimicrobial resistance is a global public health concern, and few new agents are in the pipeline. Gonorrhea control programs rely on health education, access to diagnostic testing (where possible), effective therapy, and partner notification. Introducing inexpensive, sensitive, and specific point-of-care tests will aid antimicrobial stewardship efforts in countries utilizing the syndromic management approach. Targeted vaccination of higher-risk populations with cross-protective outer membrane vesicle-based meningococcal B-vaccines could reduce N. gonorrhoeae transmission in the future. Doxycycline post-exposure prophylaxis may further reduce gonococcal incidence in the short term; however, its long-term impact on the human resistome/microbiome remains unknown.},
}

@article {pmid41033368,
year = {2025},
author = {Wang, Q and Zhang, Y and Yao, X and Wang, C and Chen, S and Liu, B and Sun, L and Zou, X and Cao, B},
title = {Distinct microbiome variation in children and adults following RSV infection and its association with host response.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108075},
doi = {10.1016/j.micpath.2025.108075},
pmid = {41033368},
issn = {1096-1208},
abstract = {Respiratory syncytial virus (RSV) hospitalization rates are higher in children than in adults, which may be related to differences in respiratory microbiota composition. The relationship between differences in the pharyngeal microbiome and the host immune response in adults and children infected with RSV remains unclear. This study aims to investigate changes in the microbiota of RSV-infected adult and pediatric patients receiving inpatient and outpatient care, and to explore their relationship with the host immune response. A total of 223 participants were enrolled in the study, including 30 adult RSV patients, 92 pediatric RSV patients, 51 community-acquired pneumonia (CAP) patients, and 50 healthy controls. Throat swabs were collected for 16S rRNA gene sequencing and transcriptome analysis. We found that the abundance of oral anaerobes (Prevotella and Veillonella) was higher in pediatric inpatients compared to pediatric outpatients. Differences in pharyngeal microbiome composition were observed between pediatric inpatients and outpatients, while not in adult patients. More differentially expressed genes were observed between pediatric inpatients and outpatients than in adults, primarily related to neutrophil chemotaxis and migration pathways. Furthermore, Alphaproteobacteria and Actinobacteria were positively correlated with the expression of CXCL10 and CXCL11 in pediatric inpatients, suggesting a potential link with neutrophil recruitment and inflammatory responses in these patients. Taken together, these findings improve our understanding of the associations between the host transcriptome and microbiome in the context of RSV infection, which may provide insights into factors related to the increased pathogenicity observed in children.},
}

@article {pmid41033313,
year = {2025},
author = {de Oliveira Formiga, R and Li, Q and Zhao, Y and Campos Ribeiro, MA and Guarino-Vignon, P and Fatouh, R and Dubois, L and Creusot, L and Puchois, V and Amouyal, S and Alonso Salgueiro, I and Bredon, M and Chollet, L and Ledent, T and Scandola, C and Auger, JP and Danne, C and Krönke, G and Tkacz, E and Emond, P and Chevreux, G and Pham, HP and Pontoizeau, C and Lamaziere, A and Argüello, RJ and Rolhion, N and Michel, ML and Wai, T and Sokol, H},
title = {Immunometabolic reprogramming of macrophages by gut microbiota-derived cadaverine controls colon inflammation.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.09.009},
pmid = {41033313},
issn = {1934-6069},
abstract = {Cadaverine is a polyamine produced by the gut microbiota with links to health and disease, notably inflammatory bowel disease (IBD). Here, we show that cadaverine shapes monocyte-macrophage immunometabolism in a context- and concentration-dependent fashion to impact macrophage functionality. At baseline, cadaverine is taken up via L-lysine transporters and activates the thioredoxin system, while during inflammation, cadaverine signals through aconitate decarboxylase 1 (Acod1)-itaconate. Both pathways induce activation of transcription factor, nuclear factor erythroid 2-related factor 2 (Nrf2), which supports mitochondrial respiration and promotes immunoregulatory macrophage polarization. Conversely, under higher concentrations, cadaverine acts via histamine 4 receptor, leading to glycolysis-driven inflammation and pro-inflammatory functions in macrophages. Likewise, cadaverine exhibits paradoxical effects in experimental colitis, either protective or detrimental, evoking opposite fates on macrophages depending on levels dictated by Enterobacteriaceae. In IBD patients, elevated cadaverine correlated with higher flare risk. Our findings implicate cadaverine as a microbiota-derived metabolite manipulating macrophage energy metabolism with consequences in intestinal inflammation and implications for IBD pathogenesis.},
}

@article {pmid41032862,
year = {2025},
author = {Ghosh Chowdhury, M and Singh, AA and Bhattacharyya, M and Muthukumar, V and Kapoor, S and Srivastava, A and Kumar, H and Shard, A},
title = {Thiazole-Based Tumor Pyruvate Kinase M2 Inhibitors: A Paradigm-Shifting Therapeutic Strategy Targeting Metabolic and Microbial Synergy in Colorectal Cancer.},
journal = {Journal of medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jmedchem.5c02169},
pmid = {41032862},
issn = {1520-4804},
abstract = {Colorectal cancer (CRC) remains a major global health burden, with current treatments primarily focused on eradicating cancer cells. However, chemotherapy-induced gut dysbiosis exacerbates inflammation and disease progression, necessitating innovative therapeutic strategies. While various metabolic inhibitors and microbiome-modulating approaches have been explored separately, no reported agent to date simultaneously targets both cancer cell survival and gut microbiome restoration. We designed thiazole-based pyruvate kinase M2 (PKM2) inhibitors, hypothesizing that selective modulation may suppress tumor growth while restoring gut microbial balance. 10j selectively inhibited PKM2 in a cell-free assay (0.01 ± 0.0009 μM) and in CRC cells (4.21 ± 0.04 μM), disrupting key pathways driving CRC progression. Remarkably, metagenomic analysis revealed that 10j restored gut microbiota balance. These findings suggest that dual-function anticancer agents, which kill cancer cells while simultaneously restoring gut microbiota, represent an unexplored therapeutic avenue. Thiazole-based PKM2 inhibitors are pioneering this novel strategy in CRC treatment.},
}

@article {pmid41032844,
year = {2025},
author = {Ashique, S and Paul, D and Debnath, B and Chellappan, DK and Das, J and Bhui, U and Ramzan, M and Sharma, N and Kumar, B and Sridhar, SB and Panigrahy, UP and Hussain, MS},
title = {Probiotics, psychobiotics, and postbiotics: a therapeutic modality for the management of schizophrenia.},
journal = {Nutritional neuroscience},
volume = {},
number = {},
pages = {1-27},
doi = {10.1080/1028415X.2025.2560658},
pmid = {41032844},
issn = {1476-8305},
abstract = {Schizophrenia is a debilitating, chronic neuropsychiatric disorder, a multifactorial disorder combining genetic, neurodevelopmental, immunological, and environmental factors. Common antipsychotic treatments may be effective against positive symptoms, but still lack when dealing with negative symptoms, cognitive defects, and side effects of medication. Recent innovations show how the gut-brain axis is an important modulator of neuropsychiatric health, identifying microbial dysbiosis as a cause of schizophrenia. This review examines the therapeutic potential of such treatments of probiotics, psychobiots, and postbiotics as an adjunctive or alternative treatment targeting the way of modulating neuroinflammation, neurotransmitter synthesis, experience, and maintenance of blood-brain barrier integrity. Probiotics, which are live beneficial microbes, have immunomodulatory and neuroactive effects; psychobiotics, a subclass that has specific mental effects, modify stress-response systems and neurotrophic factors. Postbiotics, consisting in turn of microbial metabolism like short-chain fatty acids, present improved safety and stability with anti-inflammatory and antioxidant functions. Available clinical and preclinical evidence suggests the ability of these agents to attenuate the symptoms of schizophrenia and cognitive impairment, as well as to increase the tolerability of treatment. Regarding the conclusive presumptions, however, strain-specific variability and inconsistent methodologies confined by the sparse large-scale trials limit them. New technologies of nanocarrier systems, artificial intelligence, and personalized microbiome profiling might provide the best precision of the therapy. In this review, pitfalls in mechanistic insights, progress reports on translational studies, and future research prospects are deconstructively examined to support microbiota-based interventions as promising paradigms of holistic schizophrenia management.},
}

@article {pmid41032499,
year = {2025},
author = {Castro, C and Badillo, J and Tumen-Velasquez, M and Guss, AM and Collins, TS and Harmon, F and Coleman-Derr, D},
title = {Bacteria isolated from the grape phyllosphere capable of degrading guaiacol, a main volatile phenol associated with smoke taint in wine.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0331854},
doi = {10.1371/journal.pone.0331854},
pmid = {41032499},
issn = {1932-6203},
mesh = {*Vitis/microbiology ; *Guaiacol/metabolism ; *Wine/analysis/microbiology ; *Smoke ; Biodegradation, Environmental ; *Gordonia Bacterium/metabolism/genetics/isolation & purification ; },
abstract = {Recent wildfires near vineyards in the Pacific United States have caused devastating financial losses due to smoke taint in wine. When wine grapes (Vitis vinifera) are exposed to wildfire smoke, their berries absorb volatile phenols derived from the lignin of burning plant material. Volatile phenols are released during the winemaking process giving the finished wine an unpleasant, smokey, and ashy taste known as smoke taint. Bacteria are capable of undergoing a wide variety of metabolic processes and therefore present great potential for bioremediation applications in many industries. In this study, we identify two strains of the same species that colonize the grape phyllosphere and are able to degrade guaiacol, a main volatile phenol responsible for smoke taint in wine. We identify the suite of genes that enable guaiacol degradation in Gordonia alkanivorans via RNAseq of cells growing on guaiacol as a sole carbon source. Additionally, we knockout guaA, a cytochrome P450 gene involved in the conversion of guaiacol to catechol; ΔguaA cells cannot catabolize guaiacol in vitro, providing evidence that GuaA is necessary for this process. Furthermore, we analyze the microbiome of berries and leaves exposed to smoke in the vineyard to investigate the impact of smoke on the grape microbial community. We found smoke has a significant but small effect on the microbial community, leading to an enrichment of several genera belonging to the Bacilli class. Collectively, this research shows that studying microbes and their enzymes has the potential to identify novel tools for alleviating smoke taint.},
}

*Vitis/microbiology
*Guaiacol/metabolism
*Wine/analysis/microbiology
*Smoke
Biodegradation, Environmental
*Gordonia Bacterium/metabolism/genetics/isolation & purification

@article {pmid41032474,
year = {2025},
author = {Aplasca, AC and Johantgen, PB and Madden, C and Soares, K and Junge, RE and Hale, VL and Flint, M},
title = {Environment and weight class linked to skin microbiome structure of juvenile Eastern hellbenders (Cryptobranchus alleganiensis alleganiensis) in human care.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0319317},
doi = {10.1371/journal.pone.0319317},
pmid = {41032474},
issn = {1932-6203},
mesh = {Animals ; *Skin/microbiology ; *Microbiota/genetics ; *Caudata/microbiology/physiology ; Humans ; RNA, Ribosomal, 16S/genetics ; *Body Weight ; Environment ; Skin Microbiome ; },
abstract = {Amphibian skin is integral to promoting normal physiological processes in the body and promotes both innate and adaptive immunity against pathogens. The amphibian skin microbiota is comprised of a complex assemblage of microbes and is shaped by internal host characteristics and external influences. Skin disease is a significant source of morbidity and mortality in amphibians, and increasing research has shown that the amphibian skin microbiota is an important component in host health. The Eastern hellbender (Cryptobranchus alleganiensis alleganiensis) is a giant salamander declining in many parts of its range, and captive-rearing programs are important to hellbender recovery efforts. Survival rates of juvenile hellbenders in captive-rearing programs are highly variable, and mortality rates are overall poorly understood. Deceased juvenile hellbenders often present with low body condition and skin abnormalities. To investigate potential links between the skin microbiota and body condition, we collected skin swab samples from 116 juvenile hellbenders and water samples from two holding tanks in a captive-rearing program. We used 16s rRNA gene sequencing to characterize the skin and water microbiota and observed significant differences in the skin microbiota by weight class and tank. The skin microbiota of hellbenders that were housed in tanks in close proximity were generally more similar than those housed physically distant. A single taxa, Parcubacteria, was differentially abundant by weight class only and observed in higher abundance in low weight hellbenders. These results suggest a specific association between this taxa and Low weight hellbenders. Additional research is needed to investigate how husbandry factors and potential pathogenic organisms, such as Parcubacteria, impact the skin microbiota of hellbenders and ultimately morbidity and mortality in the species.},
}

Animals
*Skin/microbiology
*Microbiota/genetics
*Caudata/microbiology/physiology
Humans
RNA, Ribosomal, 16S/genetics
*Body Weight
Environment
Skin Microbiome

@article {pmid41032469,
year = {2025},
author = {Kaur, N and Yadav, N and Sachan, S and Sharma, P and Khetarpal, P},
title = {Dysbiosis in PCOS: A Systematic Review of Microbiome Alterations Across Body Sites with GRADE Assessment of Evidence Quality.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00072.2025},
pmid = {41032469},
issn = {1531-2267},
abstract = {Polycystic Ovary Syndrome (PCOS) is a prevalent endocrine-metabolic disorder that adversely affects reproductive, metabolic, and cardiovascular health in females, leading to menstrual irregularities and an increased risk of endometrial malignancies. Emerging research evidence suggests that the gut and extra gastrointestinal microbiome dysbiosis may play a significant role in the pathophysiology of PCOS. This systematic review aims to elucidate the microbiome dysbiosis patterns in PCOS patients compared to healthy controls. A systematic search was conducted across PubMed, Scopus, and Web of Science from inception until February 28[th], 2025, encompassing all original cross-sectional, cohort, or case-control studies that examined the gut, oral, blood, and lower genital tract (LGT) microbiomes of PCOS patients (cases) against healthy females (controls). Of the 4,377 studies identified, 64 were assessed for eligibility through full-text screening, and ultimately, 29 studies met inclusion criteria and were included into the systematic review. The results revealed inconsistent patterns in alpha and beta diversity, with reports of increased, decreased, or unchanged microbial diversity across studies. Key alterations were observed at different taxonomic levels, such as phylum, family, genus, and species. The most significant bacterial alterations include changes in the relative abundance of various bacterial taxa such as Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Verrucomicrobia, Gammaproteobacteria, Fusobacteria, Eubacterium, Streptococcus, Paraprevotella, Tucibacter, and Tenericutes. These findings indicate that complex dysbiotic microbial shifts may be involved in the pathogenesis of PCOS. As per the GRADE assessment, the quality of evidence is low for most of the studies. This systematic review supports the role of microbial dysbiosis in PCOS pathogenesis, however, additional research is required to elucidate these interactions to guide the development of therapeutic strategies in the future.},
}

@article {pmid41032415,
year = {2025},
author = {Wang, Y and Mu, W and Guan, J and Ma, P and Li, Y and Zhang, Y and Zhu, W and Zhou, Y and Zou, Y and Zeng, T and Zhou, J and Lin, X and Yan, X and Shi, W and Guo, X and Zhu, XQ and Cai, X and Sun, Y and Guo, A and Wang, S},
title = {Bile acid synthesis dysregulation in liver diseases promotes ectopic expansion of oral streptococci in the intestine.},
journal = {Cell reports},
volume = {44},
number = {10},
pages = {116374},
doi = {10.1016/j.celrep.2025.116374},
pmid = {41032415},
issn = {2211-1247},
abstract = {Liver diseases often coincide with dysregulated gut homeostasis and Streptococcus overgrowth, yet the underlying mechanisms remain unclear. Here, we study patients with liver echinococcosis and other liver conditions. We observe that these patients frequently exhibit a co-occurrence of an ectopic expansion of orally derived Streptococcus species implicated in intestinal inflammation, alongside a bile acid deficiency in the gut. This association is typically characterized by the reduction of 12-ketolithocholic acid (12-KetoLCA), which exerts potent membrane-disrupting activity. We show that liver disorders compromise gut resistance to oral microbes due to a loss of ecological control from bile acids, particularly 12-KetoLCA. This bile-acid-conferred gut barrier is regulated by cytochrome P450 enzymes and can be reconstituted through adeno-associated virus (AAV) gene therapy targeting these genes. Additionally, we reveal that supplementation with 12-KetoLCA prevents oral Streptococcus-driven gut inflammation through antibacterial activity. Our findings underscore the essential role of bile acids in maintaining the oral-gut barrier.},
}

@article {pmid41032256,
year = {2025},
author = {Fuentes Rojas, LJ and Bussiman, F and Cardoso, TF and Colmenarez, GA and Conteville, LC and Antonio, BCP and Ventura, HT and Paschoal, JJ and Lourenco, D and Regitano, LCA},
title = {Microbiota diversity and association with performance phenotypes in beef bulls.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf340},
pmid = {41032256},
issn = {1525-3163},
abstract = {BACKGROUND: Feed efficiency, nutrient utilization, and methane emission are highly dependent on the gastrointestinal microbiota, implying an influence of these microorganisms on economically important traits (e.g., carcass traits and meat quality). The interaction between microbial composition, diet, and host performance suggests that microbiota-targeted strategies may increase production in livestock animals. However, little is known about this interaction in beef cattle. We aimed to characterize the gastrointestinal microbiota and identify taxa associated with performance phenotypes in Nellore bulls.

RESULTS: We identified 1,268 bacterial and 75 archaeal amplicon sequence variants (ASVs). For both bacteria and archaea, alpha diversity showed significant within-year variation. No statistical differences were found for the Shannon index for bacteria in 2019 versus 2021 or archaea in 2019-2020 and 2021-2022. Except for 2022 (bacteria), no clusters were observed for bacteria or archaea beta diversity across years. Ten different bacteria ASVs were found to affect ribeye area (RA), whereas only five did so for metabolic weight (MW). For archaea, eight ASVs had a significant effect on RA, whereas 15 were found to affect MW. Coefficients of the regression of phenotype on ASV ranged from (± SE, in SD units) -0.40 ± 0.08 (ASV 892, Bacteroidales RF16 spp.) to 0.36 ± 0.11 (ASV 605, Marvinbryantia spp.) for MW, and from -0.72 ± 0.20 (ASV 188, Faecalibacterium spp.) to 0.65 ± 65 (ASV 457, Christensenellaceae R-7 spp.) for RA.

CONCLUSION: Our study revealed significant associations between ASV and traits of economic importance in beef cattle, including carcass, feed efficiency, and morphology, indicating that the microbiome influences animal performance. Further research is needed to elucidate the biological mechanisms behind these associations.},
}

@article {pmid41032035,
year = {2025},
author = {Kale, T and Yoo, L and Kroeger, E and Iqbal, A and Kane, S and Shihab, S and Conley, S and Kamp, K},
title = {Menopause and Inflammatory Bowel Disease: A Systematic Review.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf204},
pmid = {41032035},
issn = {1536-4844},
support = {F31 NR020426/NR/NINR NIH HHS/United States ; K23 NR020044/NR/NINR NIH HHS/United States ; },
abstract = {BACKGROUND: Research is limited on the impacts of menopause, defined as the permanent cessation of ovarian function and decline of reproductive hormones, on gastrointestinal symptom severity and disease progression in women with inflammatory bowel disease (IBD). This review synthesizes current evidence on the impact of menopause, menopause transition, and hormonal therapy (HT) on disease activity, IBD and menopause symptom severity, and disease progression among individuals with IBD.

METHODS: A systematic literature review was reported following PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines and preregistered at PROSPERO (CRD42024564901). Five databases were searched without date restrictions. Data extraction and risk-of-bias assessment were performed independently by multiple reviewers. Results were qualitatively synthesized.

RESULTS: Of 1667 records, 15 studies met inclusion criteria (5 cohort, 3 case-control, 7 cross-sectional) with IBD sample sizes from 37 to 1367. Evidence on HT and IBD risk was mixed: some studies linked HT to increased ulcerative colitis risk while others found no significant association after adjusting for confounders. Women with IBD experience earlier menopause than healthy control subjects. While most women reported no change in IBD symptoms postmenopause, a minority reported symptom worsening. HT may reduce flare severity. Women with IBD reported more severe vulvovaginal symptoms and had distinct vaginal microbiome profiles compared with healthy control subjects.

CONCLUSIONS: Few studies have explored the relationship between menopause and IBD. There is a need for continued research on the relationship between IBD disease activity and menopause symptoms to create tailored interventions to improve women's health with IBD across the lifespan.},
}

@article {pmid41031883,
year = {2025},
author = {Tian, X and Zhang, L and Qian, X and Peng, Y and Chen, F and Bengtson, S and Wang, Z and Wu, M},
title = {Gut complement system: a new frontier in microbiota-host communication and intestinal homeostasis.},
journal = {The Journal of clinical investigation},
volume = {135},
number = {19},
pages = {},
doi = {10.1172/JCI188349},
pmid = {41031883},
issn = {1558-8238},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Homeostasis/immunology ; Animals ; Inflammatory Bowel Diseases/immunology/microbiology/pathology ; Complement Activation ; *Complement C3/immunology ; *Complement System Proteins/immunology ; Colorectal Neoplasms/immunology/microbiology/pathology ; *Intestines/immunology/microbiology ; Immunity, Innate ; },
abstract = {The gut microbiota plays a crucial role in maintaining intestinal homeostasis and influencing various aspects of host physiology, including immune function. Recent advances have highlighted the emerging importance of the complement system, particularly the C3 protein, as a key player in microbiota-host interactions. Traditionally known for its role in innate immunity, the complement system is now recognized for its interactions with microbial communities within the gut, where it promotes immune tolerance and protects against enteric infections. This Review explores the gut complement system as a possibly novel frontier in microbiota-host communication and examines its role in shaping microbial diversity, modulating inflammatory responses, and contributing to intestinal health. We discuss the dynamic interplay between microbiota-derived signals and complement activation, with a focus on the C3 protein and its effect on both the gut microbiome and host immune responses. Furthermore, we highlight the therapeutic potential of targeting complement pathways to restore microbial balance and treat diseases such as inflammatory bowel disease and colorectal cancer. By elucidating the functions of the gut complement system, we offer insights into its potential as a target for microbiota-based interventions aimed at restoring intestinal homeostasis and preventing disease.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Homeostasis/immunology
Animals
Inflammatory Bowel Diseases/immunology/microbiology/pathology
Complement Activation
*Complement C3/immunology
*Complement System Proteins/immunology
Colorectal Neoplasms/immunology/microbiology/pathology
*Intestines/immunology/microbiology
Immunity, Innate

@article {pmid41031864,
year = {2025},
author = {Khan, I and Wang, Y and Zhang, T and Malanchuk, K and Xu, S and Crevecoeur, S and Wang, J and Zastepa, A and Liu, X},
title = {Microbial biodiversity of agricultural surface waters in Ontario, Canada.},
journal = {Canadian journal of microbiology},
volume = {71},
number = {},
pages = {1-9},
doi = {10.1139/cjm-2025-0015},
pmid = {41031864},
issn = {1480-3275},
mesh = {Ontario ; *Biodiversity ; *Bacteria/classification/genetics/isolation & purification ; Agriculture ; Animals ; *Microbiota ; Cattle ; Manure/microbiology ; *Rivers/microbiology/chemistry ; *Water Microbiology ; Lakes/microbiology ; Nitrogen/analysis ; },
abstract = {Understanding the microbial diversity is the first step to monitor the microbial quality of agricultural surface waters. Here we report a study comparing the microbial composition and diversities in agricultural surface waters in Ontario, Canada, including the streams adjacent to dairy cattle production in eastern Ontario and the field runoffs from the manure-impacted experimental farm of south-western Ontario. We also studied the quality of the surface water in the western basin of Lake Erie during a harmful algal bloom (cHAB). In eastern Ontario, we found significantly lower (P < 0.01) abundance of Proteobacteria and Burkholderiales in the streams adjacent to dairy production than the non-agriculture site. Bacteroidetes was more abundant (P < 0.0001) in medium/high order streams and agriculture/urban mixed site. Seasonal peaks of Flavobacterium were observed in low order streams but the trend was not in medium/high order streams. In south-western Ontario, the dominant bacterial taxa in field runoffs was Pseudomonas, regardless of manure types. We also discovered that the elevated total dissolved nitrogen, total dissolved phosphorus and chlorophyll a associated with the cHAB zone in Lake Erie was further away rather from the agricultural sites. In conclusion, our studies identified unique microbiome patterns associated with agricultural surface waters in Ontario.},
}

Ontario
*Biodiversity
*Bacteria/classification/genetics/isolation & purification
Agriculture
Animals
*Microbiota
Cattle
Manure/microbiology
*Rivers/microbiology/chemistry
*Water Microbiology
Lakes/microbiology
Nitrogen/analysis

@article {pmid41031848,
year = {2025},
author = {Aghzaf, S and Poli, J-P and Brunel, M and Costa, J and Lorenzi, V and Guinoiseau, E and Berti, L},
title = {Characterization of the bacterial and fungal diversity in habitats of Corsica Island.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0075625},
doi = {10.1128/aem.00756-25},
pmid = {41031848},
issn = {1098-5336},
abstract = {Indoor environments may impact human health significantly since microbial diversity made of various bacteria, fungi, and other microorganisms constitutes the habitat's microbiome. These microorganisms originate from diverse sources, such as the environment, humans, and pets. Understanding such microbial diversity is crucial for assessing related health impacts. The aim of this study was to investigate bacterial and fungal microorganisms from different surfaces in a set of houses on Corsica Island (southeastern France). We conducted sampling and high-throughput sequencing of PCR-amplified microbial DNA from 40 habitats (eight different surfaces tested for each) located on diverse regions of the island. Following nucleic acid recovery, we performed PCR targeting V3-V4 regions of 16S rRNA for bacteria and ITS1 region for fungi. Bioinformatics processing allowed the identification of distinct microbial species and the analysis of their distribution. Our findings highlighted that the most represented bacterial genera in the Corsican homes tested were Ralstonia (16.9%), Staphylococcus (4.8%), Corynebacterium (2.7%), Enhydrobacter (6.8%), and Methylorubrum (6.0%). Regarding fungal diversity, the most common genera identified were Dipodascaceae (21.6%), Rhodotorula (10.9%), Aspergillus (8.9%), Clavispora (7.3%), and Candida (6.8%). Our results also showed differences in microbial composition among the habitats studied, while a higher bacterial and fungal diversity was observed in rural habitats and in those with pets.IMPORTANCEThis study provides valuable insights into the microbial diversity present in indoor environments of Corsican homes, specifically highlighting bacterial and fungal communities on various household surfaces. By identifying the predominant microbial genera and revealing differences linked to habitat characteristics, such as rural settings and pet ownership, this research enhances our understanding of how indoor microbial communities vary.},
}

@article {pmid41031813,
year = {2025},
author = {Mavrodi, DV and Blankenfeldt, W and Mavrodi, OV and Weller, DM and Thomashow, LS},
title = {Microbial phenazines: biosynthesis, structural diversity, evolution, regulation, and biological significance.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0014723},
doi = {10.1128/mmbr.00147-23},
pmid = {41031813},
issn = {1098-5557},
abstract = {SUMMARYPhenazines are small, redox-active secondary metabolites produced by various bacterial species. These compounds participate in electron-transfer reactions, aiding microbes in surviving stressful or oxygen-limited environments. In this review, we examine the extensive structural diversity of phenazines and trace the evolutionary history of their biosynthetic pathways, which often move between distantly related species through horizontal gene transfer. We also explore how environmental factors such as nutrient levels and cell-to-cell signaling regulate phenazine production. Beyond their roles in microbial physiology, phenazines influence interactions among organisms, acting as antimicrobial agents, signaling molecules, and factors that shape microbiome dynamics in soils, plant roots, and other habitats. A better understanding of phenazine biology reveals how microbes adapt and thrive in diverse environments and emphasizes the potential applications of these compounds in agriculture and human health.},
}

@article {pmid41031624,
year = {2025},
author = {Guimaraes, AF and Meirelles, GS and Alagao Querido, LC and Fernandes, KM and Ribeiro, W and Oliveira, RTM and Silva, ER and Canaan, M and Lira, MFP and Ostle, N and Berg, E},
title = {The haunting of the Soul's hill: Uncoupled responses of plant functional traits and soil microbes to serpentine soils lead to Bonsai effect in the Neotropics.},
journal = {Tree physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/treephys/tpaf121},
pmid = {41031624},
issn = {1758-4469},
abstract = {PURPOSE: We investigated the plant-soil linkages of C. Langsdorffii, a widely distributed species in the Neotropics, and how the serpentine syndrome leads to dwarfism by comparing soil microbes, soil properties and tree functional traits in serpentine and non-serpentine soils. For that we evaluated the presence of heavy metals in the soils and how it affects plant functional traits; differences of C:N ratio between serpentine and non-serpentine sites as well as soil microbiome by using PLFA technique approach to assess microbial functional groups.

METHODS: We explored the relations between soil microbes (by using phospholipid fatty acid, i.e., components of cell membranes in microbes used as an indicator of microbial biomass), soil properties, vegetation attributes, leaf nutrients and leaf functional traits.

RESULTS: We found correlation between soil gram-positive bacteria and iron in the plant leaves.; the C:N ratios are higher in serpentine sites, but the two areas are similar to the non-serpentine area; there was no difference between the soil microbes in our study areas and finally; there's a tendency to dwarfism and xeromorphism in the functional traits of C. Langsdorffii in serpentine soils.

CONCLUSIONS: We found that even though we have differences when comparing C. langsdorffii plants in serpentine and non-serpentine sites regarding the functional traits analysed in our study, the only soil microbe that seems to be interacting with the heavy metals is the gram-positive bacteria, possibly due to chelating mechanisms.},
}

@article {pmid41031610,
year = {2025},
author = {Quan, L and Shi, M and Yang, Z and Rong, H and Zhou, J and Sang, D and Xu, J and Yue, J and Chen, S and Liu, J and Yuan, P},
title = {Dynamics of the intratumoural microbiome across malignant transformation and treatment in breast cancer.},
journal = {Clinical and translational medicine},
volume = {15},
number = {10},
pages = {e70492},
doi = {10.1002/ctm2.70492},
pmid = {41031610},
issn = {2001-1326},
support = {D012401//National Natural Science Foundation of China/ ; },
mesh = {Female ; Humans ; *Breast Neoplasms/microbiology/therapy/pathology ; *Microbiota/genetics ; *Cell Transformation, Neoplastic ; Middle Aged ; RNA, Ribosomal, 16S ; Adult ; Aged ; },
abstract = {Breast cancer (BC) is the most common malignancy in women, yet the dynamics of the intratumoural microbiome during tumour initiation, progression, and treatment remain poorly understood. Prior studies are predominantly cross-sectional and limited by indirect microbial inference from RNA-seq data. This study presents a comprehensive analysis of intratumoural microbiota across breast tissue samples by high-depth 16S rRNA sequencing (11 W tags), featuring two longitudinally paired cohorts for dynamic microbial profiling during tumour progression and treatment. Samples included 165 benign nodules (82 non-transforming, 83 that later progressed to cancer with matched malignant tissues); 180 primary BC tissues and 165 benign controls; and 101 neoadjuvant therapy (NAT) specimens (15 pCR, 86 non-pCR, with paired pre/post-treatment samples). We identified a cluster of taxa (Aeromicrobium, Halomonas, Dietzia, Nesterenkonia, Delftia, Nitriliruptor) depleted in nodules undergoing malignant transformation, declining with disease progression and partially restored after NAT, with transient enrichment early in transformation. Opposing trends were observed for Paenibacillus and Methyloversatilis. These changes corresponded to shifts in amino acid, lipid, and glycan metabolism. FISH and TEM analyses identified Paenibacillus pasadenensis and Halomonas hamiltonii within tumour cells, with opposing effects on tumour proliferation and activation. In addition, we developed two predictive models with high clinical relevance: one stratifying malignancy risk in nodules, and another predicting NAT response, both of which achieved strong performance in external validation. This longitudinal characterisations of intratumoural microbiota during breast tumourigenesis and treatment offer novel insights for precision oncology and microbiome-based interventions in breast cancer.},
}

Female
Humans
*Breast Neoplasms/microbiology/therapy/pathology
*Microbiota/genetics
*Cell Transformation, Neoplastic
Middle Aged
RNA, Ribosomal, 16S
Adult
Aged

@article {pmid41031579,
year = {2025},
author = {Nykyforuk, CA and Ford, LA and Torwalt, EC and Steffler, MV and Neraasen, AF and Lind, JC and Stewart, CB and Boyd, A and Shahriari, A and Madsen, DC and Tierney, KB},
title = {Alternative proteins support somatic and muscular development while remodeling the microbiome in zebrafish.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo01990g},
pmid = {41031579},
issn = {2042-650X},
abstract = {Protein intake is fundamental to growth, well-being and long-term health. Unfortunately, many diets rely upon animal-based proteins, which are environmentally costly. To feed a growing population, alternative protein sources will be necessary. To determine the health implications of switching entirely away from animal-based diets, we fed alternative proteins to a model vertebrate during development. Zebrafish were fed diets including protein from fishmeal, pea, milk and whey, and their growth and health were monitored. Most diets supported growth, with the exception of those high in whey and milk protein, which resulted in fish that were ∼10% shorter in body length and had muscle fibers ∼30% smaller than control. Of interest, genes associated with insulin sensitivity and fat storage were upregulated in some diets (lepr, 2 to 3.5 fold, and fasn, 2.5 to 4 fold, respectively). The microbiome changed dramatically between animal and alternative proteins, shifting from Fusobacteriota to Proteobacteria dominance, with Cetobacterium positively affecting health, and Aeromonas doing the opposite. Our findings indicate that more environmentally friendly diets can lead to healthy outcomes, but that the protein source is critically important.},
}

@article {pmid41031366,
year = {2025},
author = {Van Caesbroeck, A and Lipovac, M and van den Borst, E and Palma, P and Téblick, L and Vorsters, A},
title = {Unveiling Chlamydia trachomatis immunity in urogenital secretions: A systematic review.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113453},
pmid = {41031366},
issn = {2589-0042},
abstract = {Chlamydia trachomatis (CT) is a highly prevalent bacterial sexually transmitted infection (STI), associated with severe disease complications. CT targets a unique immunological environment: the genital tract epithelium. Although sampling the genital tract is challenging, previous studies have shown that genital CT-specific antibodies exhibit enhanced neutralizing capacity compared with serum antibodies. Furthermore, tissue-resident memory T (TRM) cells provide superior protection compared with circulating T cells. However, further research is required to identify correlates of protection and explore correlations between local and systemic responses. This review provides an overview of the sampling methods suitable for identifying mucosal immune biomarkers associated with CT infection, as well as the immunoassays used. We identified the microbiome, presence of coinfections, hormonal influences, genetics, and CT infection state, load, and genotype as confounding factors to be considered in trial design. Finally, we discuss challenges related to the detection of mucosal immune biomarkers and offer recommendations for future research.},
}

@article {pmid41031151,
year = {2025},
author = {Chen, J and Zhang, M and Gong, Y and Gu, Z and Zhou, H and Gu, Y and Shen, F and Zhou, G and Ding, J},
title = {The Role of the Vaginal Microbiome in Immune Modulation in Cervical Cancer: Composition, Molecular Mechanisms, and Therapeutic Potential.},
journal = {Clinical Medicine Insights. Oncology},
volume = {19},
number = {},
pages = {11795549251380470},
pmid = {41031151},
issn = {1179-5549},
abstract = {Accumulating evidence demonstrates that the tumor microenvironment (TME) drives immune suppression through complicated regulations including host-microbe interactions, which poses vaginal microbiome as one of vital regulators of immune microenvironment. This narrative review examined the composition and dynamic changes of vaginal microbiota during carcinogenesis, focusing on mechanistic insights linking microbial dysbiosis to tumor immunity. Notably, commensal bacteria exhibit diverse immunoregulatory functions that can either potentiate or inhibit anti-tumor responses. Clinical evidence further reveals that CST IV microbiota associates with significantly elevated cancer risk, while probiotic interventions show promise in restoring immune surveillance. Critical gaps in standardization of microbiota-based therapies are addressed, emphasizing the need for strain-specific characterization and optimized delivery systems. Collectively, deciphering vaginal microbiome-immune crosstalk opens new avenues for precision interception against cervical cancer.},
}

@article {pmid41031112,
year = {2025},
author = {Li, N and Yi, F and Wang, Y and Geng, F and Liu, Y and Liu, Q and Guo, Y and Long, D},
title = {Effects of Shenfu injection on intestinal microbiota and inflammation in sepsis mice.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1599903},
pmid = {41031112},
issn = {2235-2988},
mesh = {Animals ; *Sepsis/drug therapy/microbiology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/administration & dosage/pharmacology ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; Mice ; *Inflammation/drug therapy ; RNA, Ribosomal, 16S/genetics ; Cytokines/blood ; Intestinal Mucosa/drug effects/microbiology ; Cecum ; },
abstract = {INTRODUCTION: Sepsis remains a critical challenge in intensive care medicine, necessitating novel therapeutic approaches.

METHODS: In this study, healthy 8-week-old male C57BL/6J mice were treated with cecal ligation and puncture (CLP) to induce a sepsis model. After successful model establishment, mice in the sham and CLP groups were injected with 200 μL of normal saline, while mice in the SFI group were injected with 200 μL of SFI. Changes in intestinal mucosal barrier function, inflammation, and intestinal microbiota were assessed in septic mice after SFI treatment.

RESULTS: SFI treatment significantly ameliorated intestinal inflammation and reduced serum levels of pro-inflammatory cytokines (IL-1β, IL-6) and renal injury markers (SCr, BUN). 16S rRNA sequencing revealed SFI-mediated gut microbial remodeling, characterized by a marked reduction in pathogenic Escherichia-Shigella abundance and concurrent enrichment of beneficial probiotics, including Akkermansia and Lactobacillus. Mechanistically, SFI exhibited dual regulatory effects on both systemic inflammation and gut microbiota homeostasis.

DISCUSSION: These findings not only validate SFI's efficacy in sepsis treatment but also propose a novel mechanism involving gut microbiome modulation. This study provides critical experimental evidence for repurposing traditional Chinese medicine in sepsis therapy and establishes a foundation for future research on microbiota-targeted interventions in critical care.},
}

Animals
*Sepsis/drug therapy/microbiology/pathology
*Gastrointestinal Microbiome/drug effects
*Drugs, Chinese Herbal/administration & dosage/pharmacology
Male
Disease Models, Animal
Mice, Inbred C57BL
Mice
*Inflammation/drug therapy
RNA, Ribosomal, 16S/genetics
Cytokines/blood
Intestinal Mucosa/drug effects/microbiology
Cecum

@article {pmid41030606,
year = {2025},
author = {Golly, KM and Doku, ET and Amponsah, AS and Kyei, P and Gyadua, C},
title = {Microbial Diversity, Nutritional Composition, and Health Implications of Fermented Locust Bean Seed (Dawadawa) From Ghana.},
journal = {International journal of food science},
volume = {2025},
number = {},
pages = {8444101},
pmid = {41030606},
issn = {2314-5765},
abstract = {Fermented foods play a vital role in global nutrition, and dawadawa, a traditional African locust bean (Parkia biglobosa) fermentation product, is a key dietary component in Northern Ghana. This study investigates the microbial diversity, nutritional composition, and health implications of dawadawa produced across six major communities. The determination of nutritional composition and bacterial communities in dawadawa was conducted using standard spectrometric methods and 16S RNA sequencing, respectively. Proximate analysis revealed significant variations in fat (17.45%-27.70%), protein (36.12%-50.00%), and fiber (6.39%-7.32%) across different locations, with Sunyani samples exhibiting the highest protein content. Mineral analysis showed notable differences in iron (79.60-135.00 mg/kg), zinc (37.75-91.77 mg/kg), and calcium (0.73%-1.61%), suggesting potential nutritional benefits. Microbial profiling using 16S rRNA sequencing identified Bacillus, Staphylococcus, Streptococcus, and Lactobacillus as predominant genera, with Bacillus subtilis being the most abundant species. Domestic dawadawa exhibited higher microbial diversity compared to commercial samples, with greater amplicon sequence variant (ASV) richness. Functional bacterial groups correlated with enhanced protein and mineral bioavailability, supporting dawadawa's role as a probiotic and functional food. Findings highlight the impact of fermentation practices on microbial diversity and nutrient composition, underscoring the importance of preserving traditional methods while optimizing production for food security and sustainability.},
}

@article {pmid41030555,
year = {2025},
author = {Worku, AT and Sciarretta, A and Guarnieri, A and Falcone, M and Brancazio, N and Minwuyelet, A and Cutuli, MA and Atenafu, G and Nicolosi, D and Colacci, M and Yewhalaw, D and Di Marco, R and Petronio Petronio, G},
title = {Microbial gatekeepers: midgut bacteria in Aedes mosquitoes as modulators of arboviral transmission and targets for sustainable vector control.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656709},
pmid = {41030555},
issn = {1664-302X},
abstract = {Arboviral diseases such as Dengue virus, Zika virus, Chikungunya virus, and West Nile virus pose significant global public health and economic challenges, particularly in tropical and subtropical regions. The absence of effective vaccines and sustainable vector control strategies continues to drive high morbidity and mortality rates. Symbiotic bacteria residing in the mosquito midgut can produce antimicrobial compound, stimulate the host immune response, disrupt nutrient pathways critical for pathogen development, and interfere with the pathogen's lifecycle and dissemination. Additionally, these microbes may reduce vector reproduction and shorten the lifespan of both immature and adult stages. Genetically modified symbiotic bacteria can release effector molecules that target pathogens without harming mosquitoes. Advances in genomic and metagenomic tools have deepened our understanding of the mosquito gut microbiome. This review highlights current knowledge of gut bacteria and arbovirus interactions and explores strategies to reduce arboviral transmission. Comprehensive literature searches were conducted using global databases, including PubMed, Web of Science, and Scopus, with a focus on English-language publications.},
}

@article {pmid41030548,
year = {2025},
author = {Zhang, Y and Li, C and Tang, L and Li, F and Fu, X and Hao, Y and Li, J and Feng, X and Hu, W},
title = {Age-stratified gut microbial changes in diarrheal calves: insights from 16S rRNA sequencing across early development.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1633162},
pmid = {41030548},
issn = {1664-302X},
abstract = {INTRODUCTION: Neonatal calf diarrhea (NCD) remains a leading cause of mortality in calves under 1 month, yet how gut microbial responses vary across developmental stages remains unexplored. This study investigates age-stratified microbiome dynamics during NCD to enable precision interventions.

MATERIALS AND METHODS: This study investigated 60 female Holstein calves (1, 21, and 30 days old) from a commercial dairy farm, equally divided between healthy and diarrheal groups based on standardized fecal scoring. Fecal samples were collected aseptically, flash-frozen, and processed for 16S rRNA gene sequencing (V3-V4 region) using Illumina NovaSeq. Bioinformatics analyses included DADA2 pipeline for ASV calling, SILVA 138 database for taxonomic annotation, ANCOM-BC2 for differential abundance analysis (FDR < 0.05), PICRUSt2 for functional prediction, and SparCC networks (|r| > 0.6, p < 0.001) with Gephi visualization. Multivariate statistics, including PERMANOVA and canonical correspondence analysis were performed in QIIME2 and R (phyloseq/vegan packages), with all analyses rarefied to 39,161 sequences/sample.

RESULTS: The gut microbiome exhibited age-dependent succession, transitioning from Pseudomonadota dominance (47.2 ± 0.7%) at day 1 to Bacillota/Bacteroidota co-dominance (85.5 ± 8.2%) by day 30. Age explained significantly more compositional variance than diarrhea status (3.68% vs. 1.96%, p < 0.001). Three distinct age-specific diarrheal patterns emerged: (1) Early-stage (1-day-old) showed Bacillota/Pseudomonadota imbalances (84% of differential ASVs) with reduced network complexity (total node count, total edge count, average degree and modularity); (2) Mid-lactation (21-day-old) featured Kurthia as both significantly enriched (log2FC = 5.32) and a network hub (degree = 14); (3) Mature microbiota (30-day-old) displayed complex multi-phylum dysbiosis involving 10 metabolic pathways. Clostridia_UCG-014 persisted across diarrheal networks, while healthy calves showed age-progressive increases in microbial connectivity (edges: 125 to 1,104). Only 2 ASVs demonstrated consistent differential abundance across age groups, confirming the temporal specificity of diarrheal dysbiosis.

CONCLUSION: NCD-associated dysbiosis progresses through distinct developmental phases, from resilient phylum-level shifts in neonates to complex network disruptions in mature microbiota. The identification of stage-specific biomarkers (e.g., day 21 Kurthia) opens new avenues for age-tailored probiotic therapies and early intervention strategies.},
}

@article {pmid41030386,
year = {2025},
author = {Connolly, D and Minj, J and Arbizu, S and Kirkendall, A and Nalbandian, E and Ganjyal, GM and Murphy, KM and Solverson, P and Carbonero, F},
title = {In vitro fecal fermentation demonstrates the prebiotic-like properties of quinoa modulated by different preparation methods.},
journal = {Current research in food science},
volume = {11},
number = {},
pages = {101198},
pmid = {41030386},
issn = {2665-9271},
abstract = {Quinoa grain represents an excellent source of nutrition, including protein, lipids, and fiber. Quinoa processing and cooking alters its chemical composition and bioavailability of nutrients, and while extracts have been studied, little is known about the impact of quinoa food products on the human gut microbiota. One selected quinoa line was tested in raw, boiled, extruded, and baked (cookie) forms for its ability to modulate fecal microbiota from 10 healthy donors. After in vitro digestion, samples underwent fecal fermentation with measurements taken at 0, 6, 12, 24, and 48 h (h). Boiled and extruded quinoa exhibited significantly higher total polyphenol content when compared to raw quinoa (p < 0.05), while baked quinoa had lower polyphenol content, though the difference was not significant. Fecal fermentation of pre-digested raw and processed quinoa significantly increased (p < 0.05) beneficial lactic acid-producing bacterial (LAB) genera, including Bifidobacterium and Lactobacillus. All quinoa samples (raw, boiled, extruded, and baked) significantly increased Bifidobacterium abundance from 6 to 48 h compared to the start of fermentation (0 h), while Lactobacillus increased significantly in boiled, baked, and extruded samples at 12-48 h. Pediococcus and Weissella were more abundant in raw quinoa, suggesting that less-processed plant material might be harder to ferment. These findings highlight quinoa's prebiotic properties, which are largely preserved across various cooking methods. Future studies on quinoa and other grain products should integrate food chemistry and gut microbiota outcomes to identify physicochemical properties that influence microbiota responses.},
}

@article {pmid41030253,
year = {2025},
author = {Bautista, J and Villegas-Chávez, JA and Bunces-Larco, D and Martín-Aguilera, R and López-Cortés, A},
title = {The microbiome as a therapeutic co-driver in melanoma immuno-oncology.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1673880},
pmid = {41030253},
issn = {2296-858X},
abstract = {Melanoma, one of the most aggressive skin cancers, remains a major clinical challenge due to its high metastatic potential, therapy resistance, and rising global incidence. Although immune checkpoint inhibitors have transformed management, variable responses and acquired resistance limit durable benefit. Emerging evidence positions the microbiome as a pivotal determinant of melanoma biology and therapeutic outcomes. Dysbiosis in the skin, gut, and oral compartments fosters tumor-promoting inflammation, immune evasion, and oncogenic signaling, whereas enrichment of specific commensals, such as Akkermansia muciniphila and Faecalibacterium prausnitzii, enhances antigen presentation and effector T cell activity, improving ICI efficacy. Mechanistically, microbial metabolites, including short-chain fatty acids, tryptophan derivatives, and bile acids, modulate epigenetic programs, G-protein-coupled receptor signaling, and oncogenic cascades such as PI3K-AKT and RAS-RAF-MEK-ERK. Beyond the gut, cutaneous microbiota such as Staphylococcus epidermidis exert direct antitumor effects, while pathogenic oral taxa propagate systemic inflammation that shapes the melanoma tumor microenvironment. These insights are driving the development of microbiome-targeted interventions, including fecal microbiota transplantation, defined consortia, probiotics, and dietary modulation, with early clinical studies showing the potential to overcome resistance to immunotherapy. Integration of circadian biology further suggests that host-microbiome-immune interactions are temporally regulated, opening new dimensions for therapeutic optimization. By synthesizing mechanistic, clinical, and translational advances, this review highlights the microbiome as both a biomarker and a therapeutic axis in melanoma, underscoring its promise to transform precision immuno-oncology.},
}

@article {pmid41030120,
year = {2025},
author = {Kraus, O and Schwarz, Y and Motro, Y and Marom, T and Lamdan, R and Kapuller, V and Ovnat, ST and Moran-Gilad, J},
title = {Adenotonsillar Microbiome Shifts in Children With Obstructive Sleep Apnea Syndrome.},
journal = {The Laryngoscope},
volume = {},
number = {},
pages = {},
doi = {10.1002/lary.70119},
pmid = {41030120},
issn = {1531-4995},
support = {17.15.41//Ben Gurion University of the Negev/ ; },
abstract = {OBJECTIVE: To characterize the microbiomes of adenoids and tonsils in pediatric Obstructive Sleep Apnea Syndrome (OSAS) patients compared to healthy controls. We hypothesized that the microbiome composition of the tonsils and adenoids in OSAS patients differs significantly from that of healthy controls.

METHODS: Thirty OSAS patients and 30 healthy controls were included. Samples from adenoids and tonsils were analyzed using 16S rRNA amplicon sequencing to characterize bacterial communities. Differential abundance and alpha and beta diversity were used to compare the microbiome compositions between groups.

RESULTS: Significant differences in the microbial composition of adenoids and tonsils were observed within both OSAS and control groups. The tonsillar microbiome in OSAS patients exhibited lower alpha diversity and distinct microbial composition compared to controls, with an overrepresentation of pathogenic genera such as Haemophilus and Neisseria. Adenoid microbiomes, however, showed no significant differences in alpha diversity between OSAS and controls but displayed a trend toward variation in beta diversity.

CONCLUSION: This study highlights distinct microbiome profiles in adenoids and tonsils, with significant microbial shifts in the tonsillar microbiome of OSAS patients. These findings underscore the importance of syndrome-specific studies and suggest the potential contribution of microbial communities to pathogenesis. Future research should focus on further characterizing the microbiomes of healthy individuals and OSAS patients, aiming to establish a clearer distinction between normal and pathological microbial populations, which could inform the development of novel, non-invasive therapies.},
}

@article {pmid41030102,
year = {2025},
author = {Ribeiro, AJ and Silva, F and Teixeira, P and Saraiva, CM},
title = {Dry-Aged Beef: A Global Review of Meat Quality Traits, Microbiome Dynamics, Safety, and Sustainable Strategies.},
journal = {Journal of food science},
volume = {90},
number = {10},
pages = {e70589},
doi = {10.1111/1750-3841.70589},
pmid = {41030102},
issn = {1750-3841},
support = {//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {Animals ; Cattle ; *Microbiota ; *Red Meat/microbiology/analysis ; *Food Handling/methods ; Humans ; Food Quality ; Food Microbiology ; Taste ; *Meat/microbiology/analysis ; },
abstract = {Dry-aged beef is valued for its tenderness, complex aroma, and concentrated flavor. However, variability in aging protocols and limited understanding of underlying biological and technological processes can compromise consistent quality and safety. This review examines factors influencing meat characteristics, including genetics, breed, sex, age, diet, intramuscular fat deposition, antioxidant reserves, and endogenous enzyme pools. Postmortem biochemical pathways, such as proteolysis, lipid oxidation, and nucleotide degradation, are discussed in relation to flavor and texture development. The dynamics of surface microbiota are analyzed, highlighting the succession from psychrotrophic spoilage bacteria to molds and yeasts, which collectively form an enzymatic crust that contributes umami and nutty notes while providing antimicrobial barriers. Regulatory frameworks in major markets are reviewed, alongside valorization strategies that convert crust trimmings into umami-rich powders, bioactive peptides, starter cultures, or industrial enzymes. Despite advances, critical knowledge gaps remain, including the functional roles of minor crust taxa, the efficacy of defined starter cultures or bacteriophage blends, and standardized methods for texture and flavor measurement. By focusing on these biochemical and microbiological mechanisms and their applications, this review provides a roadmap for transforming dry aging into a reproducible, safe, and high-quality process in modern meat science.},
}

Animals
Cattle
*Microbiota
*Red Meat/microbiology/analysis
*Food Handling/methods
Humans
Food Quality
Food Microbiology
Taste
*Meat/microbiology/analysis

@article {pmid41029975,
year = {2025},
author = {Al Meslamani, AZ and Jarab, AS and Elrefae, A},
title = {Advances in type 2-high asthma therapy: what remains missing?.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2025.2569844},
pmid = {41029975},
issn = {1747-6356},
abstract = {INTRODUCTION: Type 2-high asthma (T2HA) accounts for most severe asthma morbidity and is driven by eosinophilic, IgE- and alarmin-mediated inflammation. Although five biologics are licensed, many patients remain symptomatic, corticosteroid-dependent or financially excluded.

AREAS COVERED: PubMed, Embase, Web of Science, Scopus, Cochrane Library, EconLit, ClinicalTrials.gov and WHO-ICTRP were searched (1 January 2005 - 30 June 2025). Evidence from randomized trials, economic evaluations and translational studies on biologics, small-molecule drugs, cell-based and microbiome-directed interventions was synthesized across four domains: late-stage attrition, ultra-long-acting biologic limitations, slow small-molecule progress, and cost - access barriers. Durability, pediatric data and OCS-sparing potential were also examined.

EXPERT OPINION: Phenotype-guided biologics have replaced corticosteroid escalation after two decades of research; nevertheless, plateaus in effectiveness, uncertain long-term safety profiles, and exorbitant costs persist. Future progress will depend on value-based pricing that facilitates global adoption, adaptive biomarker-anchored clinical trials, rational combination or bispecific therapeutics, and rigorous post-marketing surveillance of cell-based and microbiome-directed therapies. Delivering sustainable, equitable management of T2HA necessitates the coordination of scientific, regulatory, and economic mechanisms rather than focusing on increasingly narrow cytokine targets.},
}

@article {pmid41029962,
year = {2025},
author = {Ben Valid, O and Shouval, R},
title = {Predictors of response to CD19 chimeric antigen receptor T-cell therapy in large B-cell lymphoma: a consolidated review.},
journal = {Current opinion in oncology},
volume = {},
number = {},
pages = {},
pmid = {41029962},
issn = {1531-703X},
abstract = {PURPOSE OF REVIEW: CD19-directed chimeric antigen receptor T-cell (CAR-T) therapy has transformed outcomes for relapsed/refractory large B-cell lymphoma (LBCL), yet nearly half of treated patients relapse, and toxicities remain frequent. A deeper understanding of response predictors is urgently needed to guide patient selection, treatment optimization, and development of rational combination strategies.

RECENT FINDINGS: Emerging data reveal that response to CAR-T therapy is shaped by patient-specific, tumor-intrinsic, and treatment-related factors. Clinical variables such as age, performance status, inflammation, and microbiome composition influence efficacy. Tumor burden, disease distribution, histologic subtype, and genomic alterations correlate with resistance. Treatment factors, including bridging strategies, lymphodepletion regimen, and CAR-T product design, affect expansion, persistence, and clinical outcomes. Novel insights from immune profiling, radiomics, and single-cell transcriptomics offer further granularity and predictive potential.

SUMMARY: Predictors of CAR-T response span diverse biological and clinical domains and are increasingly actionable. Integrating multimodal biomarkers into routine workflows can personalize care and improve outcomes. Prospective validation, real-time monitoring, and adaptive trial designs are essential next steps toward precision CAR-T therapy.},
}

@article {pmid41029787,
year = {2025},
author = {Lemieux, É and Monger, XC and Saucier, L and Charette, SJ and Guay, F and Pouliot, É and Fournaise, S and Vincent, AT},
title = {Effect of an antibiotic and a probiotic on phage communities in the swine gut microbiota.},
journal = {BMC research notes},
volume = {18},
number = {1},
pages = {402},
pmid = {41029787},
issn = {1756-0500},
support = {RGPIN-2022-03321//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Swine/microbiology ; *Bacteriophages/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Feces/microbiology/virology ; Cross-Over Studies ; },
abstract = {OBJECTIVE: The impact of dietary treatments on the phage community of porcine intestinal microbiota is not well understood. An antibiotic (tylvalosin), a probiotic (Pediococcus acidilactici), and a combination of these were given to six cannulated pigs in a double crossover design study. Samples of ileal digesta and feces were collected and whole genome shotgun sequencing was performed. The variations in phage and bacterial communities were compared for each treatment and sample type.

RESULTS: The bacteriophages present in the gut microbiome exhibited greater variations in both α- and β-diversity between sample types (digesta, feces) than between treatments. β-diversity and differential abundance showed that the effect of the combined antibiotic and probiotic treatment was the same as with the antibiotic alone. However, the effects of the probiotic and antibiotic treatments were statistically significantly different in the fecal samples. β-diversity was different in those two treatments, and differential abundance analysis identified multiple phages as markers for each treatment. No significant variations in relative abundance were found in phage lifestyle (i.e., virulent, temperate) between treatments.},
}

Animals
*Probiotics/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
Swine/microbiology
*Bacteriophages/drug effects/genetics
*Anti-Bacterial Agents/pharmacology
Feces/microbiology/virology
Cross-Over Studies

@article {pmid41029586,
year = {2025},
author = {Li, L and Wang, X and Huang, X and Li, C and Wu, Z and Zhu, T and Tian, M and Zhan, Q and Zhuang, Y and Sun, R},
title = {Hypertensive disorders of pregnancy were more strongly associated with the functional and network profiles than with the community composition of the gut bacteriome: a pilot study.},
journal = {BMC pregnancy and childbirth},
volume = {25},
number = {1},
pages = {965},
pmid = {41029586},
issn = {1471-2393},
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome/physiology ; Pilot Projects ; Case-Control Studies ; Adult ; *Hypertension, Pregnancy-Induced/microbiology ; Feces/microbiology ; RNA, Ribosomal, 16S ; },
abstract = {BACKGROUND: Recent studies implicate that hypertensive disorders of pregnancy (HDP) is associated with gut microbiome. However, the different associations of different microbial features with HDP are little known. This study investigates the different associations of gut bacterial taxonomic composition, functional and network profiles with HDP.

METHODS: A case-control study was conducted in Hefei Maternal and Child Health Hospital from February to August 2024. Twenty-four women with HDP and twenty-one normotensive pregnant controls were included. Fecal samples were collected and the bacterial community in fecal samples were measured using high-throughput sequencing targeting the V4 region of the bacterial 16 S rRNA. The taxonomic composition, functional and network profiles of gut bacterial community in both Control and Case groups were determined, and the associations between HDP and gut bacterial profiles were analyzed.

RESULTS: There were no significant differences in gut bacterial community composition between the Control and Case groups. However, the Case group had significantly higher relative abundance of functional taxa associated with intestinal inflammation, primary pathogens involved in gastroenteritis and diarrhea. Furthermore, while the Case group exhibited higher network complexity in gut bacterial interactions, it showed lower ecological variability compared to the Control group. Intriguingly, correlation analyses indicated significantly positive associations between HDP and both microbial functional profiles and species interaction intensity, while no significant correlation was observed with taxonomic composition.

CONCLUSION: Although the gut microbial composition remained unchanged in hypertensive pregnancies, functional dysbiosis characterized by proinflammatory features and altered ecological network properties were significantly associated with pregnant women's blood pressure. The dissociation between taxonomic profiles and functional profiles, as well as taxon interactions, highlights the importance of microbial function and interactions in the gut microbiome-targeted diagnosis and therapy of HDPs.},
}

Humans
Female
Pregnancy
*Gastrointestinal Microbiome/physiology
Pilot Projects
Case-Control Studies
Adult
*Hypertension, Pregnancy-Induced/microbiology
Feces/microbiology
RNA, Ribosomal, 16S

@article {pmid41029580,
year = {2025},
author = {Guan, F and Zhang, X and Gou, W and Wang, Q and Du, S and Su, C and Jia, X and Zheng, J and Wang, H and Ding, G},
title = {Long-term body mass index trajectories and dyslipidemia and related gut microbial features: results from the China health and nutrition survey 1991-2018.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {3203},
pmid = {41029580},
issn = {1471-2458},
mesh = {Humans ; *Dyslipidemias/epidemiology/microbiology ; *Gastrointestinal Microbiome/physiology ; China/epidemiology ; *Body Mass Index ; Female ; Male ; Middle Aged ; Adult ; Nutrition Surveys ; Obesity/epidemiology ; Overweight/epidemiology ; Risk Factors ; },
abstract = {OBJECTIVE: To discover the associations between long-term body mass index (BMI) trajectories and dyslipidemia, and the internal mechanism within different BMI trajectory populations.

METHODS: We chose 11,499 adults from China Health and Nutrition Survey (CHNS) for trajectory modeling. Selected those with two blood lipid measurements (n = 2,003), and determine the risk trajectory group associated with dyslipidemia. We selected two subsets of the 2015 CHNS, CHNS-1 (n = 3,061) and CHNS-2 (n = 1,409) for gut microbiome analysis. A Lasso regression in both the CHNS-1 and the CHNS-2 confirmed the dominant genera of each dyslipidemia risk trajectory. We also used a subset of CHNS-2 (n = 779) with metabolomics data to identify the differential metabolites. We ascertained the connection between microbiome and metabolites via correlation analysis.

RESULTS: We identified three BMI trajectories: The developing into overweight (DO) group and the overweight to obesity (OTO) group had increased dyslipidemia risks compared to the normal stable (NS) group, OR: 1.69(95%CI: 1.30,2.20);1.93(95%,CI:1.34,2.77). There are significant differences in gut microbiota between OTO/DO group and NS group, PERMANOVA R[2] = 0.50 and 0.23, p < 0.001. we found six taxa in the OTO group and five taxa in the DO group had lower abundance than in the NS group. after adjusting for covariates, yielded an AUC of 0.759 and 0.646 in the validation set. In the OTO and DO groups we also found 36 metabolites and 5 metabolites, respectively, with differential concentrations than in the NS group.

CONCLUSIONS: A high-level BMI change trajectory will increase the risk of developing dyslipidemia in the future. The growth trajectory of BMI affects lipid metabolism mediated by gut microbiota.These findings may reveal the mechanism of BMI changes leading to dyslipidemia, and indicate the corresponding microbiome targets for prevention.},
}

Humans
*Dyslipidemias/epidemiology/microbiology
*Gastrointestinal Microbiome/physiology
China/epidemiology
*Body Mass Index
Female
Male
Middle Aged
Adult
Nutrition Surveys
Obesity/epidemiology
Overweight/epidemiology
Risk Factors

@article {pmid41029521,
year = {2025},
author = {Bao, XG and Chong, PF and He, C and Wang, XY and Zhang, F and Tan, BB and Lou, KX},
title = {Bacillus tequilensis S40 inoculation alleviates salt stress by modifying bacterial community structure and regulating elemental cycling rhizosphere of Reaumuria soongorica.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1251},
pmid = {41029521},
issn = {1471-2229},
support = {32160407//the National Natural Foundation of China/ ; 23YFFA0065//the Gansu Provincial Key Research and Development Program/ ; 25ZDWA007//the Major Special Project of Gansu Provincial Science and Technology Plan - International Cooperation Field/ ; },
mesh = {*Rhizosphere ; Soil Microbiology ; *Bacillus/physiology ; *Salt Stress ; *Microbiota ; *Tamaricaceae/microbiology/growth & development/physiology ; Salt Tolerance ; },
abstract = {Plant growth‒promoting rhizobacteria (PGPRs) are pivotal in forest cultivation and saline‒alkaline soil improvement by altering the structure of rhizosphere bacterial communities and improving soil nutrient utilization efficiency. However, there are few reports on the exploration of PGPR bacterial resources and the mechanism by which PGPR enhance the salt tolerance of Reaumuria soongorica (R. soongorica) in desert shrubs. This study focused on Bacillus tequilensis (B. tequilensis) S40, which is a PGPR isolated from the rhizosphere of R. soongorica by our research group. We investigated the effects of the S40 strain on the rhizosphere microbial community and functional genes of R. soongorica through pot experiments. The results demonstrated that inoculation with the S40 strain could alleviate the negative effects of NaCl stress on the plant height, total root length, and rhizome leaf biomass. Proteobacteria, Bacteroidetes, and Planctomycetota were the dominant phyla. Notably, inoculation with S40 strain significantly increased the absolute abundances of functional genes involved in carbon (C), nitrogen (N), and phosphorus (P) cycling (p < 0.05). Furthermore, the genes related to C, N, and P cycling were significantly correlated with soil properties (available phosphorus, urease activity, sucrase activity), and the biomass of R. soongorica leaves, stems, and roots (p < 0.05). In conclusion, the PGPR strain S40 mediates the reorganization of bacterial community, drives the element cycle, and enhances soil nutrient availability, thus promoting plant growth and enhancing salt tolerance of plants and providing a method and scientific basis for cultivating shrub seedlings and alleviating the degree of soil salinization.},
}

*Rhizosphere
Soil Microbiology
*Bacillus/physiology
*Salt Stress
*Microbiota
*Tamaricaceae/microbiology/growth & development/physiology
Salt Tolerance

@article {pmid41029470,
year = {2025},
author = {Cutajar, S and Braglia, C and Alberoni, D and Mifsud, M and Baffoni, L and Spiteri, J and Di Gioia, D and Mifsud, D},
title = {Gut microbiome of Vespa orientalis: functional insights and potential honey bee pathogen dynamics.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {95},
pmid = {41029470},
issn = {2524-4671},
support = {TESS 2022//Tertiary Education Scholarships Scheme by the Ministry for Education, Sport, Youth, Research and Innovation in Malta (TESS 2022)./ ; CN00000022//European Union Next-GenerationEU, PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1032 17/06/2022/ ; CN00000022//European Union Next-GenerationEU, PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1032 17/06/2022/ ; },
abstract = {Vespa orientalis, the oriental hornet, is an emerging predator of honey bees whose ecological impact and microbial ecology remain poorly understood. Here, we present the first detailed characterisation of its gut microbiota by integrating 16S rRNA gene sequencing, predicted microbial function, pathogen screening, and a three-year beekeeper survey across urban and rural sites in Malta. Hornets were sampled from four locations and classified by observed foraging behaviour, either predation on honey bees or scavenging on cat food.Survey data confirmed consistent V. orientalis sightings and seasonal colony losses, particularly during peak foraging months. Microbiome analysis revealed a conserved core community dominated by Spiroplasma, Arsenophonus, and Rosenbergiella, with overall diversity stable across sites and diets. However, specific taxa varied with foraging behaviour. For example, Arsenophonus was enriched in bee-predating hornets, while Enterobacter and Serratia were more common in scavenging individuals, suggesting environmental and dietary influences on microbiota composition. Predicted functional profiles remained broadly conserved, reflecting robust nutrient metabolism and potential detoxification capabilities, with some variations related to the diet behaviour.Pathogen screening detected Nosema ceranae and Crithidia bombi in a substantial proportion of hornets, including those not observed feeding on bees. Although our findings do not demonstrate pathogen transmission, they support the hypothesis that V. orientalis may act as a transient carrier, potentially contributing to pathogen persistence via environmental exposure.Together, these results reveal the dietary flexibility and microbial flexibility within the gut microbiome of V. orientalis, and highlight its potential involvement in pollinator pathogen dynamics.},
}

@article {pmid41029348,
year = {2025},
author = {Brante, A and Bustos, P and Ortega-Muñoz, C and Acuña Gómez, EP and Brante, V and Farlora, R},
title = {Environmental variability drives functional plasticity in the gill-associated microbiome of Lithodes santolla: a meta-transcriptomic perspective.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {197},
pmid = {41029348},
issn = {2049-2618},
support = {R20F0009//Agencia Nacional de Investigación y Desarrollo/ ; },
mesh = {*Gills/microbiology ; *Microbiota/genetics ; Animals ; Transcriptome ; *Bacteria/classification/genetics/isolation & purification ; Gene Expression Profiling ; Antarctic Regions ; *Brachyura/microbiology ; Host Microbial Interactions ; },
abstract = {BACKGROUND: Environmental variability shapes microbial community composition and function, yet its influence on microbial gene expression and host-microbiome interactions in sub-Antarctic regions remains poorly understood. Gills serve as the primary interface between aquatic organisms and their environment, harboring diverse and dynamic microbial communities that play a fundamental role in host physiology. Using a metatranscriptomic approach, this research aims to explore the influence of abiotic fluctuations in Patagonian fjords on the functional profile of the gill-associated microbiome in the southern king crab (Lithodes santolla) holobiont. By assessing shifts in microbial composition and gene expression, this research aims to uncover functional pathways linked to microbial metabolic adjustments and the host's resilience. The findings provide insights into microbiome-driven functional responses in marine species and may inform conservation strategies under environmental change.

RESULTS: Microbial gene expression profiles from individuals collected at two environmentally distinct locations, Ballena Sound and Choiseul Bay, revealed slight differences in microbial composition, with Proteobacteria dominating at both sites. Functional annotation identified key metabolic pathways involved in energy production, stress response, and microbial interactions, highlighting distinct adaptive mechanisms to environmental fluctuations. Differential expression analysis revealed shifts in carbon fixation, ion transport, and oxidative stress responses, suggesting that these physiological responses could be modeled by environmental conditions. Additionally, host-associated transcripts showed differential enrichment in immune regulation and metabolic homeostasis pathways, suggesting microbiome-mediated effects on host physiology.

CONCLUSIONS: These findings offer first insights into the dynamic relationship between environmental factors and microbial functionality in L. santolla, highlighting the significance of gill-associated microbiome plasticity in adapting to changing habitats. These results improve our understanding of microbiome-driven functional responses to sub-Antarctic environments, offering valuable perspectives for assessing holobiont resilience in these fluctuating ecosystems. Video Abstract.},
}

*Gills/microbiology
*Microbiota/genetics
Animals
Transcriptome
*Bacteria/classification/genetics/isolation & purification
Gene Expression Profiling
Antarctic Regions
*Brachyura/microbiology
Host Microbial Interactions

@article {pmid41029195,
year = {2025},
author = {Debnath, S and Sorongpong, S and Das, N and Choure, K and Agnihotri, VK and Pandey, P},
title = {Sustainable lentil intensification in rice-fallow systems through bioaugmentation with atypical rhizobia and endophytes modulates rhizosphere and nodule microbiome dynamics.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1237},
pmid = {41029195},
issn = {1471-2229},
mesh = {*Oryza/microbiology/growth & development ; *Lens Plant/growth & development/microbiology ; *Rhizosphere ; *Endophytes/physiology ; *Root Nodules, Plant/microbiology ; Soil Microbiology ; *Microbiota ; *Rhizobium/physiology ; Serratia/physiology ; },
abstract = {BACKGROUND: Rice-fallow agroecosystems face challenges such as poor soil fertility and low crop productivity. This study evaluates a multi-species bacterial consortium-comprising atypical rhizobia (Pararhizobium giardinii, Ochrobactrum sp.) and non-rhizobial endophytes (Serratia plymuthica, Serratia sp.)-for improving lentil cultivation in these soils. Multilocation field trials assessed its effects on plant growth, soil nutrients, microbial diversity, and nifH gene expression in nodules. The goal is to offer a sustainable, biologically based alternative to chemical fertilizers like diammonium phosphate (DAP), enhancing soil health and enabling lentil intensification on fallow land.

RESULTS: In greenhouse pot experiments, the bacterial consortium increased lentil growth by 166% in sterile and 116% in non-sterile soils compared to the uninoculated control. Scanning electron microscopy (SEM) confirmed enhanced root hair development in treated plants. Further, the consortium treatment modulated the root exudate profiles, which demonstrated higher concentrations of fatty acids, triterpenes, and methyl esters. This markedly affected the composition of the rhizosphere microbial population. The consortium facilitated a proliferation of beneficial taxa, including Mesorhizobium, Rhizobium, and Bradyrhizobium, enhancing synergistic microbial interactions associated with enhanced plant development. The bacterial treatment increased nifH gene expression inside root nodules and augmented leghemoglobin content by 275%. Field experiments at five rice-fallow sites exhibited enhancements in soil pH, organic carbon (16%), nitrogen (6.5%), phosphorus (8%), and enzymatic activity. Meta-transcriptomic analysis demonstrated a 200% augmentation in nifH expression inside the root nodules, in the plots treated with the consortium. 16 S rRNA amplicon sequencing revealed that the microbiota in the rhizosphere and nodules was predominantly composed of Pseudomonadota, with elevated numbers of rhizobia in both environments. Microbiome alterations correlated with a significant yield increase, with lentil grain output reaching 1168 kg/ha, surpassing both the uninoculated control and DAP treatment.

CONCLUSIONS: The study showed that a multi-species bacterial consortium of atypical rhizobia and non-rhizobial endophytes (NREs) improved plant growth and soil health in rice-fallow soils. It enhanced nifH gene expression in root nodules and altered root exudation, fostering a beneficial, plant growth-promoting microbial community. Importantly, these effects were achieved without chemical fertilizers, highlighting the consortium's potential for sustainable lentil intensification on fallow land.},
}

*Oryza/microbiology/growth & development
*Lens Plant/growth & development/microbiology
*Rhizosphere
*Endophytes/physiology
*Root Nodules, Plant/microbiology
Soil Microbiology
*Microbiota
*Rhizobium/physiology
Serratia/physiology

@article {pmid41029180,
year = {2025},
author = {Comba, IY and Hoops, S and Till, L and Vangay, PJ and Johnson, S and Xiao, Y and Louwies, T and Culhane Pera, K and Pergament, S and Knights, D and Kashyap, PC},
title = {Shared environments can facilitate microbial transmission and alter metabolic outcomes.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2562345},
doi = {10.1080/19490976.2025.2562345},
pmid = {41029180},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; Thailand ; Humans ; Mice ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Feces/microbiology ; United States ; Male ; Female ; Diet ; Mice, Inbred C57BL ; },
abstract = {While dietary changes are often implicated in the adaptation of traditional microbiomes to highly industrialized society, it only partially explains the observed microbial shifts post-immigration. Here, we used germ-free mice colonized with human donor stool from the United States and Thailand to investigate how person-to-person transmission of gut commensals - via shared air and physical contact - affects U.S. and Thai microbiomes and subsequent health outcomes. We found that both air sharing and physical contact enabled bidirectional transmission: U.S. mucus-degrading taxa (e.g., Akkermansia) was transferred into Thai microbiomes, while Thai-derived, potentially health-promoting bacteria colonized U.S. microbiomes. The host's baseline gut microbiome composition emerged as a key factor influencing the extent of the microbial remodeling. When exposed to 13 dietary ingredients and food additives prevalent in industrialized diets, the U.S. microbiome responded differently from its Thai counterpart, with food additives reducing Akkermansia. Corroborating these changes, the U.S. microbiome showed a predisposition toward weight gain under industrialized dietary conditions. However, sharing air supply or co-housing mitigated this effect - likely through the transfer of health-promoting bacteria (e.g., Lactobacillus). Our findings show the complexity of microbiome adaptation to industrialization, revealing how environmental microbial exchange and diet interplay can shape gut communities and their metabolic consequences.},
}

*Gastrointestinal Microbiome/physiology
Animals
Thailand
Humans
Mice
*Bacteria/classification/genetics/isolation & purification/metabolism
Feces/microbiology
United States
Male
Female
Diet
Mice, Inbred C57BL

@article {pmid41029140,
year = {2025},
author = {Xia, L and Liu, Y and Jiang, B and Zheng, Y and Wang, L and Wang, B and Zhu, PY},
title = {A Mendelian randomization study between air pollutants and benign prostatic hyperplasia.},
journal = {Medicine},
volume = {104},
number = {39},
pages = {e44548},
doi = {10.1097/MD.0000000000044548},
pmid = {41029140},
issn = {1536-5964},
mesh = {Humans ; Male ; *Prostatic Hyperplasia/genetics/epidemiology/etiology ; Mendelian Randomization Analysis ; *Air Pollutants/adverse effects ; Gastrointestinal Microbiome/genetics ; *Air Pollution/adverse effects ; Nitrogen Dioxide/adverse effects ; },
abstract = {An increasing number of studies have investigated the relationship between air pollution and human health, yielding significant findings. However, few studies have explored the relationship between air pollution and prostate health. Mendelian randomization was employed to evaluate the causal relationships between 5 major air pollutants and benign prostatic hyperplasia. Univariate Mendelian randomization (UVMR) was used to test the primary causal relationships, whereas multivariate Mendelian randomization (MVMR) was applied to construct risk-adjusted models, enhancing the robustness of the causal inference. Finally, we further assessed the potential mediating role of the gut microbiome in the relationships identified. We found a significant positive causal association between NO2 and benign prostatic hyperplasia (OR = 2.39, 95% CI = 1.17-4.91, P = .01). The results of the MVMR analysis are consistent with UVMR (OR = 2.01, 95% CI = 1.05-3.85, P = .03). Additionally, we identified significant positive associations between several gut microbial species and benign prostatic hyperplasia. However, further mediated Mendelian randomization analyses did not reveal a mediating effect in the causal relationship between NO2 and benign prostatic hyperplasia. Mendelian randomization analysis showed that there is a genetic causal relationship between air pollution and benign prostatic hyperplasia, and high exposure to NO2 will increase the risk of benign prostatic hyperplasia.},
}

Humans
Male
*Prostatic Hyperplasia/genetics/epidemiology/etiology
Mendelian Randomization Analysis
*Air Pollutants/adverse effects
Gastrointestinal Microbiome/genetics
*Air Pollution/adverse effects
Nitrogen Dioxide/adverse effects

@article {pmid41029023,
year = {2025},
author = {Yeerkenbieke, D and Guan, Y and Cui, J and Zhang, Q and Wang, G and Zhou, Y and Li, Z and Wang, C and Wang, D},
title = {Ginsenoside Rg2 Ameliorates Alzheimer's Disease by Alleviating Neuroinflammation in APP/PS1 Mice.},
journal = {Current neuropharmacology},
volume = {},
number = {},
pages = {},
doi = {10.2174/011570159X395496250911104139},
pmid = {41029023},
issn = {1875-6190},
abstract = {INTRODUCTION: Ginsenoside Rg2 (GRg2), a naturally occurring triterpenoid derived from ginseng rhizomes, exhibits neuroprotective properties. Neuroinflammation is recognized as one of the key pathogenic mechanisms underlying Alzheimer's disease (AD). This research aims to investigate the beneficial effects of GRg2 on AD and explore its potential mechanisms.

METHODS: In APP/PS1 mice, cognitive and behavioral assessments were first performed. Subsequently, brain tissue analyses were performed using immunohistochemical analysis and Western blot. A combined analysis of the gut microbiome and metabolomics was conducted to explore potential mechanisms. Finally, key findings were further validated through immunofluorescence and enzymelinked immunosorbent assay.

RESULTS: GRg2 enhanced learning, memory, and cognitive functions. And inhibits the deposition of β- amyloid and phosphorylated tau. GRg2 effectively inhibits the production of Bacteroides and Helicobacter. In addition, it reduced the levels of pyruvaldehyde and trimethylamine N-oxide, metabolites closely related to neuroinflammation. GRg2 effectively inhibited the activation of astrocytes and microglia in the brains of APP/PS1 mice, and also reduced the expression of neuroinflammatory mediators IL-6, IL-1β, and TNF-α.

DISCUSSIONS: The findings of this study substantiate the neuroprotective efficacy of GRg2, providing a novel therapeutic strategy and theoretical foundation for natural product-based interventions against AD.

CONCLUSION: GRg2 improves cognitive function and mitigates AD pathology, which is at least partially attributed to its regulation of gut microbiota and metabolites, as well as its anti-neuroinflammatory effects.},
}

@article {pmid41029020,
year = {2025},
author = {Zhou, B and Li, Z and Fan, S and Wang, H and Wang, J},
title = {Comprehensive Immune Subtyping and Multi-Omics Profiling of the Tumor Microenvironment in Colorectal Cancer: Implications for Prognosis and Personalized Immunotherapy.},
journal = {Current cancer drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115680096395386250910130110},
pmid = {41029020},
issn = {1873-5576},
abstract = {INTRODUCTION: The Tumor microenvironment (TME) plays a crucial role in colorectal cancer (CRC) prognosis and treatment response. However, comprehensive understandings of TME-related immune subtypes and their mechanisms for precision medicine remain insufficient. This study aims to identify immune subtypes in CRC, develop a prognostic model, and explore the role of microbial diversity in tumor progression.

METHODS: Multi-omics data and non-negative matrix factorization (NMF) were used to classify CRC into immune subtypes. Differentially expressed TME-related genes were identified, and a prognostic risk model was developed using Cox and LASSO regression. Single-cell RNA sequencing (scRNA-seq) assessed cellular interactions and gene set variations. Microbiome profiling was integrated to evaluate the impact of microbial diversity on CRC progression and immune modulation. Key findings were validated using immunohistochemistry, external datasets, and qPCR in patient-derived organoids.

RESULTS: Four TME-related immune subtypes were identified: immune-exhausted C1 (poor prognosis, high immune infiltration), immune-activated C2/C3 (better prognosis), and immune-desert C4 (worst prognosis). A risk model based on genes (SOX9, CLEC10A, RAB15, RAB6B, PCOLCE2, FUT1) stratified patients into high- and low-risk groups. High-risk groups exhibited increased Enterobacteriaceae and Clostridium, while low-risk groups showed higher Porphyromonadaceae and Peptostreptococcaceae, correlating with better immunotherapy responses. scRNA-seq revealed distinct cell-cell communication patterns across subtypes.

DISCUSSION: The study highlights the complexity of CRC's TME and its role in prognosis and treatment. Findings support personalized treatment strategies, considering immune and microbial factors.

CONCLUSION: This research integrates TME subtyping, risk modeling, single-cell analysis, and microbiome profiling to advance CRC prognosis and precision therapy, emphasizing personalized strategies for better outcomes.},
}

@article {pmid41028744,
year = {2025},
author = {Chen, C and Su, Q and Zi, M and Hua, X and Zhang, Z},
title = {Harnessing gut microbiota for colorectal cancer therapy: from clinical insights to therapeutic innovations.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {190},
pmid = {41028744},
issn = {2055-5008},
mesh = {Humans ; *Colorectal Neoplasms/therapy/microbiology ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Prebiotics/administration & dosage ; Fusobacterium nucleatum ; },
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer morbidity and mortality worldwide, yet improvements in survival have been modest despite advances in conventional therapies. The gut microbiota has emerged as a critical player in CRC pathogenesis and a promising therapeutic target to enhance clinical outcomes. Mounting evidence implicates specific microorganisms, notably Escherichia coli, Fusobacterium nucleatum, and Bacteroides fragilis, in tumor initiation and progression through DNA damage, inflammatory modulation, and immunosuppressive mechanisms. Clinical trials investigating microbiome modulators-including faecal microbiota transplantation, probiotics, prebiotics, and engineered biotherapeutics-highlight their potential to augment chemotherapy, radiotherapy, immunotherapy, and surgical recovery, with encouraging preliminary efficacy in treatment-resistant CRC subtypes. Nonetheless, translating microbiome interventions into standardized clinical practice requires rigorous mechanistic validation, robust biomarker development, and careful management of safety concerns. Future research must focus on integrating high-resolution multi-omics, spatial microbiome mapping, artificial intelligence analytics, and innovative microbiome-targeted nanotechnologies to precisely reshape gut microbial communities, thereby ushering in a new era of precision oncology in colorectal cancer management.},
}

Humans
*Colorectal Neoplasms/therapy/microbiology
*Gastrointestinal Microbiome
Fecal Microbiota Transplantation
Probiotics/therapeutic use
Prebiotics/administration & dosage
Fusobacterium nucleatum

@article {pmid41028733,
year = {2025},
author = {Singh, R and McDonald, D and Hernandez, AR and Song, SJ and Bartko, A and Knight, R and Salathé, M},
title = {Temporal nutrition analysis associates dietary regularity and quality with gut microbiome diversity: insights from the Food & You digital cohort.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8635},
pmid = {41028733},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; *Diet ; Female ; Male ; Cohort Studies ; Adult ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Machine Learning ; Feeding Behavior ; },
abstract = {The gut microbiota is profoundly influenced by dietary choices, with emerging evidence linking it to various health outcomes. Here, we investigate diet-microbiota associations using detailed temporal nutrition intake data captured through real-time food logging via a smartphone app and gut microbiota profiles from 16S rDNA sequencing in ~ 1,000 participants from a digital cohort on personalized nutrition ("Food & You" - clinicaltrials.gov NCT03848299). The primary outcome of the parental trial was to investigate post-meal glucose response variations between individuals in function of their individual factors such as diet, microbiome composition and lifestyle. Our analysis reaffirms that high-quality diets rich in vegetables, fruits, nuts, micronutrients, and favorable dietary indices like HEI (calculated both as standard HEI and daily HEI to capture day-to-day diet quality regularity) correlate with increased microbial diversity and improved stool quality, while fast food-rich diets show opposite effects. Regular consumption of beneficial food groups emerges as a key factor, with regularity in both food intake and diet quality sometimes showing stronger associations than average intake quantities. Machine learning analyses reveal strong bidirectional predictability between gut microbiota composition and dietary factors (ROC AUC up to ~ 0.85-0.9). These findings highlight the critical role of both diet quality and regularity in shaping gut microbiota, the importance of temporal nutrition tracking in offering insights for targeted nutritional strategies, and suggest that the gut microbiota can be used to estimate dietary indices.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
*Diet
Female
Male
Cohort Studies
Adult
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Machine Learning
Feeding Behavior

@article {pmid41028669,
year = {2025},
author = {Jasielczuk, I and Ocłoń, E and Żurowski, J and Szmatoła, T and Mizera-Szpilka, K and Gurgul, A},
title = {Effect of intraperitoneal cannabidiol (CBD) injection on intestine microbiome profile in a mouse model.},
journal = {Current genetics},
volume = {71},
number = {1},
pages = {21},
pmid = {41028669},
issn = {1432-0983},
support = {2020/39/B/NZ9/00821//National Science Centre (NCN; Poland)/ ; },
}

@article {pmid41028632,
year = {2026},
author = {Lucarini, E and Toti, A},
title = {In Vitro Study of Microbiota Influence on Enteric Glial Cell Physiology.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2971},
number = {},
pages = {145-151},
pmid = {41028632},
issn = {1940-6029},
mesh = {*Neuroglia/physiology/metabolism/microbiology/cytology ; Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Enteric Nervous System/cytology/physiology/microbiology ; Feces/microbiology ; Culture Media, Conditioned/pharmacology ; },
abstract = {Gut microbiome is an essential partner in the maintenance of gastrointestinal (GI) homeostasis, through its interaction with both epithelium, immune cells, and enteric nervous system (ENS). Under pathological conditions, disturbances of resident bacteria composition and/or metabolism frequently combine with ENS dysfunction. Enteric glial cells (EGCs), accompanying neurons across all the layers of the GI tract, can orchestrate neuronal activity and immune response to microenvironment perturbation, but their interaction with the components of microbiota has been poorly investigated. Indeed, although a reciprocal influence between gut microflora and EGC has been suggested, further research is needed to elucidate the mechanisms governing this crosstalk and its implications in health and disease. To this end, in vitro studies appear necessary as they allow for dissection and selective analysis of microbiota-to-EGCs signaling without the intestinal contour. This chapter has the objective to describe a method to process fecal material from either animals or humans for in vitro studying microbiota-mediated modulation of EGCs activity. It also illustrates the advantage of using whole fecal supernatant (FS) over selected supernatant and/or living bacteria to in vitro mimic microbiota signaling and introduce the possibility to treat EGCs with the conditioned medium of FS pre-treated epithelial cells.},
}

*Neuroglia/physiology/metabolism/microbiology/cytology
Humans
*Gastrointestinal Microbiome/physiology
Animals
*Enteric Nervous System/cytology/physiology/microbiology
Feces/microbiology
Culture Media, Conditioned/pharmacology

@article {pmid41028629,
year = {2026},
author = {Pimenova, E and Fattahi, F and Majd, H},
title = {Methods to Isolate Enteric Glia from hPSC-Derived Enteric Ganglioids.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2971},
number = {},
pages = {109-119},
pmid = {41028629},
issn = {1940-6029},
mesh = {*Neuroglia/cytology/metabolism ; Humans ; *Enteric Nervous System/cytology/metabolism ; *Pluripotent Stem Cells/cytology/metabolism ; Cell Differentiation ; *Cell Culture Techniques/methods ; Cells, Cultured ; Biomarkers ; },
abstract = {Enteric glia play pivotal roles in maintaining the enteric nervous system (ENS) homeostasis, supporting neuronal functions, and initiating and developing enteric neuropathies. However, understanding their diversity and functional roles has been formidably challenging due to difficulties in isolating these cells from human tissue. Here, we describe a detailed method for generating enteric glia from human pluripotent stem cells (hPSCs). This approach involves differentiating hPSCs into enteric glial cells through a vagal and enteric neural crest intermediates, replicating in vivo developmental processes. The hPSC-derived enteric glia express canonical markers (SOX10, GFAP, PLP1, S100B) and display the cellular diversity of primary human enteric glia, confirmed by single-nucleus RNA sequencing (snRNA-seq). These cultures are scalable, enabling high-throughput screening and molecular analysis, and they facilitate the study of glial interactions with other cell types, including immune cells, epithelial cells, and the gut microbiome. hPSC-derived enteric glia represent a significant advancement in enteric neurobiology, providing a versatile platform for disease modeling and therapeutic discovery, thereby improving our understanding of enteric glial cell functions in both health and disease.},
}

*Neuroglia/cytology/metabolism
Humans
*Enteric Nervous System/cytology/metabolism
*Pluripotent Stem Cells/cytology/metabolism
Cell Differentiation
*Cell Culture Techniques/methods
Cells, Cultured
Biomarkers

@article {pmid41028619,
year = {2026},
author = {Esposito, G},
title = {Introducing Enteric Glial Cells.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2971},
number = {},
pages = {1-5},
pmid = {41028619},
issn = {1940-6029},
mesh = {*Neuroglia/cytology/metabolism ; Humans ; *Enteric Nervous System/cytology ; Animals ; Gastrointestinal Microbiome ; },
abstract = {This book emphasizes the pivotal role of enteric glial cells in maintaining gut health and their influence on the gut-brain axis. Although their existence was first noted at the end of the nineteenth century, recent scientific attention has shed light on their crucial functions, especially in inflammatory bowel diseases and potential links to neurodegenerative conditions like Parkinson's disease. Understanding how these cells operate and interact within the complex network of the enteric nervous system is vital, not only for unraveling gut-related disorders but also for exploring their impact on brain health.Designed as a comprehensive guide, this book provides practical protocols to identify, visualize, and isolate enteric glial cells using techniques such as enzymatic digestion, immunofluorescence, and advanced imaging methods like confocal microscopy. It highlights the importance of studying glial cell behavior and their morphological diversity across different states of activation and maturation. Moreover, it explores innovative approaches using transgenic models and human biopsies to investigate their activity, interactions with the microbiome, and responses to inflammation.Understanding these mechanisms may open new avenues for therapies targeting both gastrointestinal and neurodegenerative diseases. This book also discusses possibilities for cell-based interventions, including the potential for enteric glial transplantation into the central nervous system. Overall, this work aims to bridge gastrointestinal and neurological research, underscoring the significance of enteric glia in health, disease, and the intricate communication between the gut and the brain. Advancing knowledge in this area could lead to novel, more precise treatments that address the root causes of complex conditions affecting both the gut and the nervous system.},
}

*Neuroglia/cytology/metabolism
Humans
*Enteric Nervous System/cytology
Animals
Gastrointestinal Microbiome

@article {pmid41028416,
year = {2025},
author = {Sidharthan, VK and Patel, R and Thiyaharajan, M and Krishnappa, C and Pattanaik, S and Kumar, A},
title = {Metabarcoding reveals unique rhizospheric microbiomes of Rhizophora in Indian Mangroves.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41028416},
issn = {1874-9356},
support = {IFB/T-1/WME/23-1//Indian Council of Forestry Research and Education/ ; },
abstract = {Rhizophora species are ecologically significant true mangroves with a broad tropical distribution. We examined the rhizospheric microbiomes of dominant Rhizophora species from two contrasting Indian mangrove ecosystems-Coringa and Pichavaram-using high-throughput metabarcoding. Soil properties differed significantly between sites: Pichavaram exhibited higher electrical conductivity (24.53 dS/m), organic carbon (1.70%), sodium (8811.86 ppm), sodium adsorption ratio (220.15), and exchangeable sodium percentage (64.27%), while Coringa soils showed higher pH (8.01). Sequencing generated 1.31, 1.24, and 1.22 million high-quality reads for archaea, bacteria, and fungi, respectively. Taxonomic profiling revealed Nitrososphaeria (62.3-91.9%), Gammaproteobacteria (16.8-25.1%), and Sordariomycetes (18.6-27.8%) as dominant classes. Core taxa across both sites included Candidatus Nitrosopumilus, Woeseia, and Aspergillus. Alpha diversity indices (Chao1, Shannon, Simpson) indicated significantly higher bacterial richness and evenness in R. apiculata at Coringa (P < 0.001), while archaeal and fungal diversity showed no marked differences. Beta diversity analysis (PCoA, PERMANOVA) revealed distinct community compositions between Coringa and Pichavaram, with stronger segregation in archaeal and bacterial assemblages than in fungi. Differential abundance analysis identified nine archaeal, fifty-nine bacterial, and three fungal genera enriched between sites, with methanogens (Methanosarcina, Methanocella) predominant in Coringa and halophiles (Halococcus, Haloferax) in Pichavaram. Redundancy analysis showed sodium adsorption ratio as the key determinant of microbial assemblages, while electrical conductivity significantly shaped archaeal and fungal communities. These findings provide the first baseline dataset of the Coringa rhizospheric microbiome and new insights into the microbial ecology of Indian mangroves, with implications for ecosystem functioning, methane emissions, and conservation strategies.},
}

@article {pmid41028378,
year = {2026},
author = {Sahil, R and Jain, M},
title = {A Multi-omics Approach for Microbiome Data Analysis in Legumes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2977},
number = {},
pages = {181-196},
pmid = {41028378},
issn = {1940-6029},
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Fabaceae/microbiology/genetics ; *Computational Biology/methods ; Data Analysis ; Metagenome ; Multiomics ; },
abstract = {Microbiome plays a crucial role in influencing the health and function of living beings as well as in regulating the biogeochemical cycles. The plant microbiome, in particular, has garnered significant research interest aimed at exploring the microbes that play a crucial role in regulating plant growth and nutrient acquisition. Recent advancements in omics sciences have played a crucial role in uncovering the complexities of these relationships. While techniques such as amplicon and shotgun metagenomics provide taxonomic profiling up to the species level and even the strain level, metatranscriptomics further elucidates the functional roles of these microbes. These techniques are being rapidly and widely adopted to understand the influence of microbes on the host. However, the challenge lies in their integration. Most studies to date rely on only one of these techniques, which limits the scope of holistic understanding of host-microbe interactions. Additionally, there is currently no well-established workflow that effectively combines these techniques to provide comprehensive biological insights. In this work, we describe an integrated approach for microbiome data analysis to provide biologically meaningful insights.},
}

*Microbiota/genetics
*Metagenomics/methods
*Fabaceae/microbiology/genetics
*Computational Biology/methods
Data Analysis
Metagenome
Multiomics

@article {pmid41028229,
year = {2025},
author = {Estrela, S and Long, JZ and Huang, KC},
title = {How nutrient starvation impacts the gut microbiome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41028229},
issn = {2058-5276},
support = {RM1 GM135102/GM/NIGMS NIH HHS/United States ; },
abstract = {Even when the gut is rich in nutrients, microorganisms can experience nutrient deprivation owing to factors such as fluctuations in host feeding patterns, microbial competition and selective nutrient uptake by the host. Nutrient starvation affects microbial survival, microbiome dynamics and intestinal stability, yet remains underexplored. This Perspective explains how nutrient deprivation shapes microbial physiology, ecology and evolution to drive complex interactions both among microbial species and between microorganisms and their host. We discuss host lifestyles that can result in microbial starvation, including diet shifts, fasting and hibernation. We also highlight critical gaps in our understanding of how starvation affects microbial community assembly, stress responses and cross-feeding from lysed cells, with implications for chronic infections and therapeutic strategies. We outline technological developments needed to unravel microbial survival strategies under nutrient deprivation. Understanding how starvation in all its forms shapes the gut ecosystem will be important to ultimately advance microbiome engineering and health interventions.},
}

@article {pmid41028169,
year = {2025},
author = {Xu, K and Kumar, P and Chang Stauffer, SR and Electricwala, HM and Prabhakar, BS and Corona-Avila, I and Pandya, N and Layden, BT and Priyadarshini, M},
title = {Pancreatic β-cell FFA2 deficiency suppresses multiple low dose streptozotocin induced diabetes in male mice.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1389},
pmid = {41028169},
issn = {2399-3642},
support = {P30DK020595 DRTC P&F grant (B.T.L; M.P)//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1I01BX003382(B.T.L)//U.S. Department of Veterans Affairs (Department of Veterans Affairs)/ ; },
mesh = {Animals ; Male ; *Insulin-Secreting Cells/metabolism/pathology ; Mice ; *Diabetes Mellitus, Experimental/metabolism/genetics/chemically induced/pathology ; Mice, Knockout ; Streptozocin ; *Receptors, G-Protein-Coupled/genetics/deficiency ; Apoptosis ; *Diabetes Mellitus, Type 1/metabolism/genetics ; Mice, Inbred C57BL ; Signal Transduction ; },
abstract = {Reduced enrichment of short-chain fatty acid (SCFA)-producing pathways in the gut microbiome (GM) and SCFA levels are associated with increased risk of type 1 diabetes (T1D). Free fatty acid receptor 2 (FFA2), an SCFA receptor on pancreatic β-cells, mediates GM and β-cell crosstalk. Here, we examine its T1D-specific role in male mice, using a novel tamoxifen-inducible adult-onset β-cell FFA2 knockout (FFA2 βKO) mouse model and its controls (cre and flox), treated with multiple low-dose streptozotocin (MLDS). FFA2 βKO mice show significantly lower diabetes incidence compared to control mice (57% vs 100%). Early in the MLDS insult (7[th] day), FFA2 βKO mice show significantly lower β-cell apoptosis and higher β-cell mass, persisting up to 43 days. Mechanistically, we observed higher SOCS1/3 expression and reduced T1-IFN signaling in FFA2 βKO islets. Our data suggest that β-cell FFA2 modulates early islet apoptosis, likely via the T1-IFN-SOCS1/3 pathway and may be a pharmacological target for slowing T1D progression.},
}

Animals
Male
*Insulin-Secreting Cells/metabolism/pathology
Mice
*Diabetes Mellitus, Experimental/metabolism/genetics/chemically induced/pathology
Mice, Knockout
Streptozocin
*Receptors, G-Protein-Coupled/genetics/deficiency
Apoptosis
*Diabetes Mellitus, Type 1/metabolism/genetics
Mice, Inbred C57BL
Signal Transduction

@article {pmid41027891,
year = {2025},
author = {He, Q and Wang, W and Xu, D and Xiong, Y and Tao, C and You, C and Ma, L and Ma, J},
title = {Correction: Potential causal association between gut microbiome and posttraumatic stress disorder.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {347},
doi = {10.1038/s41398-025-03628-5},
pmid = {41027891},
issn = {2158-3188},
}

@article {pmid41027803,
year = {2025},
author = {Blank, RB and Bu, K and Zhang, X and Chen, W and Cunningham, I and Sokolove, J and Lahey, L and Heguy, A and Medina, R and Ubeda, C and Nayak, RR and Hu, J and Cantor, A and Lee, J and Williams, FMK and Clemente, JC and Scher, JU},
title = {Short-chain fatty acids and their gut microbial pathways distinguish rheumatoid arthritis in discordant monozygotic twins.},
journal = {Annals of the rheumatic diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ard.2025.08.029},
pmid = {41027803},
issn = {1468-2060},
abstract = {OBJECTIVES: Although genetic risk factors, such as HLA-DRB1 alleles, contribute to the pathogenesis of rheumatoid arthritis (RA), the concordance rate in monozygotic (MZ) twins is low, suggesting that other factors are involved in disease development. Further, the relative contribution of nongenetic elements in identical twins has not been characterised. Here, we aimed to characterise host and microbial biomarkers of RA by studying MZ twins discordant for disease using a multiomics approach.

METHODS: Eight pairs of MZ twins discordant for RA (N = 16) were enrolled in the United States (US). The gut microbiome was assessed using shotgun metagenomic sequencing. Autoantibodies, cytokines, and plasma proteins were measured in both plasma and faeces. Levels of short-chain fatty acids (SCFAs) from serum and faeces were quantified using gas chromatography mass spectrometry (GC-MS). Metagenomic data from a UK twin registry (TwinsUK) (N = 14) were used to validate findings in the US population.

RESULTS: Although microbiome diversity and composition did not differ between twins, we observed a significant decrease in the SCFA-producing bacteria Blautia faecis and significantly lower concentrations of faecal butyrate and propionate in affected RA twins in the US. TwinsUK showed a similar reduction in the SCFA-producers Gemmiger formicilis and Faecalicatena fissicatena, as well as bacterial SCFA metabolism pathways.

CONCLUSIONS: Multiomics biomarkers differentiate MZ twins discordant for RA. Faecal butyrate and propionate, as well as SCFA-producing bacteria, were decreased in affected twins. We found a similar decrease in SCFA-producing taxa in affected twins in a geographically distinct cohort in the UK. Our results suggest that, if further validated in larger cohorts, multiomics approaches may improve our understanding of RA pathogenesis and, potentially, contribute to more accurate diagnostics and coadjuvant therapies.},
}

@article {pmid41027346,
year = {2025},
author = {Keohane, E and Prenni, J and Johnson, SA and Van Buiten, C},
title = {Comparing apples to apples: Evaluating foodomics in precision nutrition research featuring the influence of polyphenols on the gut microbiome.},
journal = {Nutrition research (New York, N.Y.)},
volume = {142},
number = {},
pages = {76-90},
doi = {10.1016/j.nutres.2025.09.003},
pmid = {41027346},
issn = {1879-0739},
abstract = {This review aimed to evaluate the use of advanced omics methodologies in dietary intervention clinical trials investigating the influence of polyphenols on the gut microbiome. All published clinical studies in the Cochrane Library database from 2014 to 2024 containing the keywords "polyphenols" and "gut microbiome" were compiled and categorized based on experimental design, analytical methodologies, and findings. We found that despite known variability in food composition across agricultural and processing parameters, omics analysis of the food used in clinical nutrition interventions has not been widely embraced. None of the studies evaluated employed untargeted omics approaches for food composition analysis, while 5 of the 38 studies used untargeted omics for clinical samples analysis. Targeted analytical methods focused on known compounds or proxies were more commonly used for food composition analysis (18 of 38 studies) and clinical samples (24 of 38 studies), though analysis of clinical samples focused on a greater number of target compounds. Data from these studies support relationships between the gut microbiome, clinical outcomes, and specific metabolites. However, several studies highlight inconsistencies between their findings and previous literature, which may be attributed to unrealized differences in polyphenol composition. We propose that inclusion of comprehensive omics-based food composition analyses in dietary intervention clinical trials may increase study value by accounting for variability in food composition and enabling novel discovery. Such data would support the emerging fields of personalized and precision nutrition, aimed at understanding the influence of individual human characteristics on physiological responses to foods, nutrients, phytochemicals, and dietary patterns.},
}

@article {pmid41027194,
year = {2025},
author = {Kong, X and Wang, S and Li, J and Zhang, K and Yin, Y and Li, Y and Zhang, R and Zhang, Z},
title = {Kasugamycin and Validamycin differentially inhibit housefly larval growth through gut microbiota regulation.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119098},
doi = {10.1016/j.ecoenv.2025.119098},
pmid = {41027194},
issn = {1090-2414},
abstract = {Certain bactericides exhibit dual efficacy in suppressing phytopathogens and managing insect pests. The houseflies may ingest organic matter containing bactericide residues, thereby facilitate the bioaccumulation of toxic compounds within ecosystems through trophic transfer mechanisms. Although it is known that gut microbiota regulates insect growth, immunity, and xenobiotic resistance, their responses to bactericide exposure are not well understood. This study examined the toxicological effects of two microbial-derived bactericides, Kasugamycin and Validamycin, on houseflies, along with their regulatory impacts on both the intestinal microbiota of housefly larvae and environmental microorganisms. Our research revealed that Validamycin exposure exhibited no significant effects on larval growth parameters, immune competence, or gut microbial composition. In contrast, Kasugamycin administration markedly inhibited larval development, compromised immunological defenses, and provoked histopathology modifications including fat body depletion and cuticle thinning. Microbiome analysis revealed Kasugamycin-induced dysbiosis characterized by a decrease in Klebsiella and Enterobacter, alongside an increase in Pseudomonas and Bordetella. Based on the aforementioned results, the influence of specific microbial communities' abundance shifts in the living environment on Kasugamycin toxicity was systematically assessed. The results demonstrate that Enterobacter hormaechei and Klebsiella pneumoniae enhanced larval resistance to Kasugamycin toxicity, whereas phage-mediated depletion of Pseudomonas aeruginosa is beneficial for the survival of housefly larvae during Kasugamycin exposure. These findings establish that the differential regulation of gut microbiota underlies the distinct effects of Kasugamycin and Validamycin on dipteran pests, providing mechanistic insights into antibiotic-insect-microbiome interactions and a theoretical framework for developing next-generation antimicrobial pest management strategies.},
}

@article {pmid41027190,
year = {2025},
author = {Feng, Y and Liu, S and Mou, C and Huang, Z and Zhao, Z and Zhao, H and Zhou, J and Li, Q and Deng, Y},
title = {Florfenicol-induced gut microbiome dysbiosis triggers chronic disease pathways and intestinal damage in the benthic fish (Leiocassis longirostris).},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119139},
doi = {10.1016/j.ecoenv.2025.119139},
pmid = {41027190},
issn = {1090-2414},
abstract = {The sub-therapeutic use of antibiotic use in aquaculture disrupts host-microbiota balance and poses ecological risks, though its chronic effects on benthic species remain poorly understood. Here we demonstrate that exposing Chinese longsnout catfish (L. longirostris) to florfenicol at a standard aquaculture dose of 10 mg/kg per day for five days induced severe intestinal dysbiosis and functional impairment. We observed a significant 43.65 % reduction in microbial gene abundance and a 96.16 % decrease in host mRNA expression, accompanied by a marked 69.11 % increase in host DNA contamination, indicating the collapse of the mucosal barrier and loss of microbial ecological function. The core microbiota shifted from beneficial Cetobacterium, which produces antioxidant and neuroprotective metabolites, to opportunistic genera such as Clostridium and Acinetobacter. Metabolically, florfenicol exposure resulted in a significant 29.3 % suppression of functional pathways and a pronounced 5.8-fold upregulation of electron transport genes including petB and fprB, which is associated with the activation of chronic diseases pathways such as Parkinson's, Huntington's and Diabetic cardiomyopathy. These pathways all share common mechanisms with mitochondrial dysfunction and ROS metabolism and further trigger chronic pathological changes including intestinal mucosal injury, mitochondrial oxidative stress and cell apoptosis. Additionally, the loss of Cetobacterium impaired the synthesis of key metabolites such as ascorbic acid and lovastatin acid, exacerbating intestinal structural damage and apoptosis. The transfer risk of antibiotic resistance genes was also significantly elevated. These findings reveal persistent microbiome dysfunction and heightened chronic disease risks following conventional antibiotic exposure, underscoring the urgency of reevaluating antibiotic usage in sustainable aquaculture.},
}

@article {pmid41026946,
year = {2025},
author = {Maminak, K and Janouskova, K and Holy, R and Prasilova, A and Filipovsky, T and Kovar, D and Astl, J},
title = {Characteristics of healthy sinonasal microbiome - single-centre study in the Czech Republic.},
journal = {Journal of applied biomedicine},
volume = {23},
number = {3},
pages = {117-125},
pmid = {41026946},
issn = {1214-0287},
support = {NU22-09-00493//Czech Health Research Council/ ; },
mesh = {Humans ; *Microbiota/genetics ; Adult ; Female ; Male ; Middle Aged ; *Paranasal Sinuses/microbiology ; RNA, Ribosomal, 16S/genetics ; Czech Republic ; Young Adult ; Prospective Studies ; *Nasal Cavity/microbiology ; Bacteria/genetics/classification ; },
abstract = {INTRODUCTION: The human nasal cavity and paranasal sinuses host a complex and dynamic microbiome which has a crucial role in mucosal immunity. A comprehensive profile of the healthy sinonasal microbiome remains limited. The purpose of our study was to characterize the healthy sinonasal microbiome in adults using 16S rRNA long-read sequencing to enable species-level resolution, and to assess its associations with demographical and clinical factors such as smoking, allergy history, and olfactory function.

STUDY DESIGN: We performed a prospective, single-centre study analysing middle meatus samples from 27 healthy individuals undergoing septoplasty in the age range from 21 to 57 years, excluding those with antibiotic and corticosteroid use and those with signs of acute or chronic rhinosinusitis.

RESULTS: A high interindividual variability in the composition of healthy sinonasal microbiome was observed. At the phylum level, it was dominated by Firmicutes (48.96%), Actinobacteria (34.83%), and Proteobacteria (13.85%), while Firmicutes and Actinobacteria were consistently present in all samples. At the genus level, Staphylococcus spp. (32.32%), Cutibacterium (28.04%), and Corynebacterium (4.66%) were most abundant. We observed trend level correlations between phyla and some clinical factors (e.g., smoking and olfactory dysfunction) and selected phyla. However, none remained significant after false discovery rate (FDR) correction across taxa.

CONCLUSION: The study proposes Staphylococcus spp., Corynebacterium spp., and Cutibacterium spp. to be a core taxa in the healthy sinonasal microbiome. Amid the interindividual diversity in our cohort, there was evidence of a stable core microbiome potentially influenced by environmental and host factors. Our findings suggest a baseline reference for distinguishing a dysbiosis in upper respiratory disease.},
}

Humans
*Microbiota/genetics
Adult
Female
Male
Middle Aged
*Paranasal Sinuses/microbiology
RNA, Ribosomal, 16S/genetics
Czech Republic
Young Adult
Prospective Studies
*Nasal Cavity/microbiology
Bacteria/genetics/classification

@article {pmid41026639,
year = {2025},
author = {Cavalcante, YCS and Santos, CS and Dantas, LL and Santos, RP and Matos, YG and Pereira, AG and Beraldo, KRF and Juliano, MA and Brandão, FZ and Feijó, FMC and Franco de Oliveira, M and Mota, RA and Comizzoli, P and Silva, AR},
title = {Relationship between the composition of vaginal bacterial populations and the reproductive stage in captive collared peccaries.},
journal = {Reproduction & fertility},
volume = {},
number = {},
pages = {},
doi = {10.1530/RAF-25-0072},
pmid = {41026639},
issn = {2633-8386},
abstract = {ABSTRACT: The objective of the study was to (1) characterize the aerobic and microaerophilic vaginal microbiota of collared peccaries (Pecari tajacu) across reproductive stages and (2) correlate microbiota findings with progesterone levels and vaginal cytology at each reproductive stage. Samples were collected for progesterone assessment (serum concentration), vaginal cytology, and microbial analysis (after isolation followed by MALDI-TOF identification) from four young pubescent, four non-pregnant, and three pregnant females. Microbial composition varied according to the reproductive stage: young pubescent females predominantly harbored Alcaligenes faecalis (Proteobacteria; 33.3%), non-pregnant females primarily hosted Bacillus badius and Staphylococcus microti (Firmicutes; 85.7%), and pregnant females had more Bacillus cereus and Mammaliicoccus sciuri (Firmicutes; 54.5%). No significant correlation (P > 0.05) was found between microbial proportions and progesterone levels or vaginal cytology. Although no differences were detected in the proportions of different vaginal bacterial populations, there was a great qualitative diversity of species of microorganisms among females at different reproductive stages. While the small sample size may have limited our ability to detect more subtle quantitative differences, these findings provide foundational insights into the reproductive microbiota of collared peccaries, with potential implications for their conservation and management.

LAY SUMMARY: Despite the importance of reproductive microbiomes in animal conservation, there is still a lack of knowledge in many wild species. The present study characterized for the first time the composition of the aerobic and microaerophilic microbiota (bacteria that can survive in the presence of oxygen or in low-oxygen conditions, respectively) of the vaginal tract from collared peccaries (pig-like mammals from Central and South America commonly known as musk hogs) at different reproductive stages. Although no differences were detected in the proportions of different vaginal bacterial populations, there was a great qualitative diversity of species of microorganisms among females at different reproductive stages. These findings provide foundational insights into the reproductive microbiota of collared peccaries, with potential implications for their conservation and management.},
}

@article {pmid41026445,
year = {2025},
author = {Morse, MB and Garcia, B},
title = {Food and Mood: Current Evidence on Mental Health and the Microbiota-Gut-Brain Axis.},
journal = {Current psychiatry reports},
volume = {},
number = {},
pages = {},
pmid = {41026445},
issn = {1535-1645},
abstract = {PURPOSE OF REVIEW: Depression and anxiety are among the most common global mental health conditions. Emerging research highlights the impact of diet and the gut microbiome on the nervous system and mood. We review and discuss the existing research on the effects of various diets-including high-fiber, fermented, ketogenic, and calorie-restricted diets-alongside the roles of prebiotics and probiotics, on anxiety and depression.

RECENT FINDINGS: While mostly observational, mounting data from randomized controlled trials support the idea that dietary modification can improve mental health outcomes by altering gut microbial composition and activity. The efficacy of supplements and probiotics in mood outcomes is conflicting. Additional research is needed to fully understand the mechanisms that link diet, the gut microbiome, and mental health. Overall, findings suggest that dietary modifications are feasible and beneficial in mild cases of anxiety and depression. This review explores the bidirectional relationship between diet, gut microbiome, and mood disorders. Various diets are discussed, and their respective impact on mental health is reviewed. Challenges in food and mood research remain due to variability in research practices. Additional studies are needed to further explore the role of nutrition in optimizing mental health.},
}

@article {pmid41026429,
year = {2025},
author = {Morasi, RM and Biscarini, F and Gini, C and Ceciliani, F and Lecchi, C and Salina, A and Thaler Neto, A and Langoni, H and Gebara, C and Crippa, BL and Silva, NCC},
title = {Assessment of bacterial diversity in bovine bulk tank milk samples from Brazil.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {41026429},
issn = {1678-4405},
support = {2019/17308-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 144471/2021-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {This research aimed to analyze and compare bacterial diversity in bulk tank milk (BTM) samples from five Brazilian regions using 16 S rRNA gene sequencing, while correlating this diversity with Somatic Cell Count (SCC) values. A total of 57 samples from Santa Catarina, São Paulo, Minas Gerais, Goiás, Maranhão, Pará, and Tocantins were sequenced through Next Generation Sequencing (NGS). The analysis revealed one kingdom, four phyla, six classes, 14 orders, 28 families, and 43 genera, with Moraxellaceae (22.3%), Streptococcaceae (14.1%), Acetobacteraceae (13.8%), Pseudomonadaceae (11.0%), and Enterococcaceae (9.0%) as the main families, and Acinetobacter (22.3%), Pseudomonas (11.7%), and Acetobacter (8.1%) as the main genera. Alpha diversity differed significantly in Maranhão and Pará compared to Goiás (set as baseline for comparing alpha diversity across regions), as indicated by Fisher, Chao1, and ACE indices (p < 0.05). In terms of beta diversity, significant differences (p < 0.001) were found among the states, highlighting the heterogeneity of these communities inside the country. While high and low SCC groups showed no significant differences in alpha diversity (p > 0.05), beta diversity did exhibit significant variation (p < 0.001). Tracking the bacterial diversity and SCC found in BTM samples using advanced molecular technologies allowed us to understand microbial diversity for future strategy development, consequently improving the quality and safety of the milk produced on Brazilian farms.},
}

@article {pmid41026409,
year = {2025},
author = {Saini, B and Lakra, AK and Behera, S and Tilwani, YM and Kumbha, SB and Prabhakaran, V and Sundaram, K and Balasingh, S and Isaac, SS and Arul, V},
title = {A Novel Bacteriocin from Insectivorous Bat (Hipposideros speoris) Intestine Mimicking Mammalian FAM216B: Probiotic, Antioxidant, and Antimicrobial Properties of Enterococcus hirae BNT6.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41026409},
issn = {1867-1314},
abstract = {The alarming rise of antibiotic resistance necessitates the search for novel and safe alternatives to conventional therapies. Probiotics and their metabolites, particularly bacteriocins, are increasingly recognized for maintaining gut health, combating pathogens, and alleviating oxidative stress. Bats, with their diverse and underexplored gut microbiota, represent a unique reservoir of probiotic strains and bioactive peptides. This study aimed to isolate and characterize a novel probiotic strain from the intestine of the insectivorous bat Hipposideros speoris and evaluate its probiotic attributes, antioxidant potential, safety traits, and bacteriocin production. The isolated strain was identified as Enterococcus hirae BNT6 through 16S rRNA sequencing. Probiotic properties including acid and bile tolerance, cell surface hydrophobicity, adhesion to SW480 epithelial cells, and antioxidant activities (DPPH and ABTS scavenging) were assessed. Safety traits were evaluated through hemolysis, DNase activity, and antibiotic susceptibility testing. Bacteriocin purification was carried out using ammonium sulfate precipitation, gel filtration chromatography and RP-HPLC. Antimicrobial activity was tested against pathogenic bacteria, while molecular characterization was performed by SDS-PAGE, MALDI-TOF MS, peptide mass fingerprinting, spectroscopic analysis, and 3D in silico modeling. E. hirae BNT6 survived at pH 3, tolerated 0.3% bile salts, showed high hydrophobicity (51.7%), and adhered efficiently to SW480 cells. It exhibited strong antioxidant activity (65.7% DPPH and 81.6% ABTS scavenging). Safety evaluation confirmed its non-hemolytic, DNase-negative phenotype and susceptibility to most clinically relevant antibiotics. The purified bacteriocin, Enterocin BNT6, displayed broad-spectrum antimicrobial activity against Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, and Bacillus subtilis, and remained stable under varying pH, temperature, and enzymatic conditions. Molecular analyses indicated a size of ~ 27 kDa (SDS-PAGE) and ~ 15 kDa (MALDI-TOF MS), with peptide mass fingerprinting showing 59% similarity to mammalian FAM216B protein. Structural studies revealed a predominantly α-helical conformation. Our findings establish Enterococcus hirae BNT6 as the first bat-derived probiotic strain producing a FAM216B-like bacteriocin with strong probiotic, antioxidant, and antimicrobial activities. In silico structural modeling revealed a predominantly α-helical, stable conformation with striking similarity to mammalian FAM216B, suggesting potential evolutionary mimicry. These unique attributes highlight its promise as a next-generation therapeutic and microbiome-based intervention.},
}

@article {pmid41026372,
year = {2025},
author = {Leiva-Castro, C and Múnera-Rodríguez, AM and Torres-Joya, G and Palomares-Jerez, F and López-Enríquez, S},
title = {Modulating inflammation and oxidative stress in rheumatoid arthritis: a systematic review of nutraceutical interventions.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {41026372},
issn = {1568-5608},
support = {Project-2022/00000421//VII Plan Propio de Investigación y Transferencia" from the University of Seville/ ; Project-2023/00000482//VII Plan Propio de Investigación y Transferencia" from the University of Seville/ ; RYC2021-031256-I//Ministry of Science and Innovation through research Ramon y Cajal program/ ; },
abstract = {Rheumatoid arthritis is a chronic autoimmune disease characterized by persistent synovial inflammation and progressive joint destruction. The gut microbiome has emerged as a key factor in the regulation of the immune system, and its dysbiosis has been implicated in the pathogenesis of rheumatoid arthritis. Nutraceuticals, including probiotics, omega-3 fatty acids, coenzyme Q10, vitamin D, and polyphenols, have shown potential in modulating the gut microbiota and inflammatory pathways. This review explores the interplay between nutraceuticals, gut microbiota, and immune function in rheumatoid arthritis, with attention to pharmacokinetics and safety. We discuss recent clinical evidence, elucidate molecular mechanisms of action, and highlight future research directions for integrating nutraceuticals into therapeutic strategies for rheumatoid arthritis.},
}

@article {pmid41026256,
year = {2025},
author = {Mohan, M and Abedien, ZU and Kaparaju, P},
title = {Thermophilic anaerobic digestion of polylactic acid, polyethylene and polypropylene microplastics: effect of inoculum-substrate ratio and microbiome.},
journal = {Biodegradation},
volume = {36},
number = {5},
pages = {95},
pmid = {41026256},
issn = {1572-9729},
mesh = {*Polyesters/metabolism ; *Polypropylenes/metabolism ; Anaerobiosis ; Biodegradation, Environmental ; *Microbiota ; *Polyethylene/metabolism ; *Microplastics/metabolism ; Bacteria/metabolism/classification/genetics ; Fatty Acids, Volatile/metabolism ; },
abstract = {Microplastics (MPs) generated from major plastic polymers have impacted the environment and formulation of an end-of-life scenario is a need of the hour. In the current study, the effects of inoculum to substrate ratios (ISR) 2, 4 and 6 on the MPs from polyethylene (PE), polypropylene (PP) and polylactic acid (PLA) under thermophilic and mesophilic anaerobic digestion (AD) conditions was studied. The results indicated thermophilic AD to be a prospective method for PLA degradation with a maximum cumulative biogas production of 894.08 NmL/gVSadded at ISR4 and 89.62% of volatile fatty acids (VFA) was utilised during 148 days of incubation. However, the thermophilic AD of PP and PE was observed to be highly inefficient with a maximum biogas production of 111.64 and 47.48 NmL/gVSadded and also resulted in VFA accumulation. Under mesophilic AD conditions, PLA degradation was highly inefficient due to long hydrolysis time, whilst inhibition was noticed with both PP and PE. The microbiological study revealed the abundance of Firmicutes and Synergistota, genus D8A-2, Thermovirga and Candidatus Caldatribacterium during thermophilic AD of PLA. An abundance of Methanothermobacter indicated hydrogenotrophic methane production as the major pathway for methanogenesis during thermophilic AD of MPs. An abundance of PWY-3781 associated with detoxification of reactive oxygen species was observed in the AD of PP and PE. Overall, the study provided insight into the prospects for improving thermophilic AD for PLA.},
}

*Polyesters/metabolism
*Polypropylenes/metabolism
Anaerobiosis
Biodegradation, Environmental
*Microbiota
*Polyethylene/metabolism
*Microplastics/metabolism
Bacteria/metabolism/classification/genetics
Fatty Acids, Volatile/metabolism

@article {pmid41026240,
year = {2025},
author = {Abdelali, SK and Aissaoui, L and Cano-Argüelles, AL and Piloto-Sardiñas, E and Abuin-Denis, L and Maitre, A and Foucault-Simonin, A and Mateos-Hernández, L and Kratou, M and Wu-Chuang, A and Obregon, D and Cabezas-Cruz, A},
title = {Seasonal Variations in the Microbiome of Hyalomma excavatum Ticks in Algeria.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {96},
pmid = {41026240},
issn = {1432-184X},
mesh = {Animals ; *Seasons ; Algeria ; *Microbiota ; *Ixodidae/microbiology ; Female ; *Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Rickettsia/isolation & purification/genetics ; Biodiversity ; },
abstract = {Ticks are key vectors of zoonotic diseases, with their microbiomes playing a critical role in tick physiology, survival, and vector competence. This study presents the first investigation of the microbiome in Hyalomma excavatum ticks from Algeria, focusing on seasonal variations in bacterial diversity, community composition, and pathogen interactions. Using next-generation sequencing (NGS), the microbiome of 21 female ticks collected during spring, summer, and autumn was analyzed. Beta diversity analysis revealed significant seasonal shifts in microbial community structure, while alpha diversity metrics showed no significant differences in richness and evenness. Co-occurrence network analysis demonstrated seasonal shifts in microbial interactions, particularly between symbionts and pathogens, highlighting Francisella as a key taxon in tick survival and pathogen dynamics. Rickettsia presence varied by season, influencing microbial network stability. These findings underscore the ecological determinants shaping the microbiome and its potential role in pathogen transmission. Understanding seasonal microbiome shifts provides valuable insights for managing tick-borne diseases and could inform the development of targeted, season-specific vector control strategies.},
}

Animals
*Seasons
Algeria
*Microbiota
*Ixodidae/microbiology
Female
*Bacteria/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
RNA, Ribosomal, 16S/genetics
Rickettsia/isolation & purification/genetics
Biodiversity

@article {pmid41026216,
year = {2025},
author = {Martin-Pozas, T and Fernandez-Cortes, A and Calaforra, JM and Sanchez-Moral, S and Saiz-Jimenez, C and Jurado, V},
title = {Aerobiology and Environmental Zonation in Gypsum Caves: A Comparative Study of Culturing and NGS Approaches.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {95},
pmid = {41026216},
issn = {1432-184X},
support = {PID2020-114978GB-I00 and PDI2023-146299OB-C22//Ministerio de Ciencia e Innovación/ ; },
mesh = {*Caves/microbiology ; *Calcium Sulfate/analysis ; *Bacteria/genetics/classification/isolation & purification/growth & development ; High-Throughput Nucleotide Sequencing/methods ; *Air Microbiology ; *Microbiota ; Spain ; *Fungi/isolation & purification/genetics/classification ; Geologic Sediments/microbiology ; Phylogeny ; Biodiversity ; },
abstract = {Classical aerobiological studies commonly use high-volume air samplers to quantify and identify cultivable airborne bacteria and fungi. However, this approach introduces a significant bias, as it overlooks the non-cultivable fraction, which likely constitutes a major component of the airborne microbiome. The advent of next-generation sequencing (NGS) has addressed this limitation, enabling a more comprehensive characterization of the cave aerobiome. This study analyzes both cultivable and non-cultivable airborne bacteria from Covadura and C3 caves, located in the Gypsum Karst of Sorbas (SE Spain). A total of 24 bacterial genera were identified using culture-based methods, whereas NGS revealed 749 genera. Culture-based methods using the surface air system (SAS) predominantly recovered Gram-positive spore-forming bacteria from the phyla Bacillota and Actinomycetota, which were largely absent or present in low relative abundances in the NGS datasets. In contrast, NGS revealed a broader diversity, including numerous Gram-negative and rare airborne bacteria not detected by culture. The NGS results from airborne samples showed greater similarity to the microbial communities found in cave biofilms and sediments, suggesting that a portion of airborne bacteria originates from within the cave and is influenced by microclimatic conditions such as ventilation and air stagnation. Although the short-read sequencing approach used in this study has limitations, such as reduced taxonomic resolution compared to the culture-based approach, it remains the most effective tool for capturing the diversity and ecological patterns of airborne microorganisms. The integration of gas tracers and other environmental data allowed the identification of zones within the cave with different ventilation patterns and degrees of isolation, which corresponded to different spatial distributions of airborne bacteria. Our findings underscore that reliable aerobiological studies in caves require the combination of non-culture dependent-based sequencing approaches and environmental monitoring to fully understand the origin, diversity, and ecological dynamics of airborne microbial communities.},
}

*Caves/microbiology
*Calcium Sulfate/analysis
*Bacteria/genetics/classification/isolation & purification/growth & development
High-Throughput Nucleotide Sequencing/methods
*Air Microbiology
*Microbiota
Spain
*Fungi/isolation & purification/genetics/classification
Geologic Sediments/microbiology
Phylogeny
Biodiversity

@article {pmid41026185,
year = {2025},
author = {Borja-Martínez, G and de León-Lorenzana, A and Yanez-Montalvo, A and Hernández-Canchola, G and Falcón, LI and Vázquez-Domínguez, E},
title = {Evolutionary and Ecological Drivers of Gut Microbiota in Wild Rodent Species from the Yucatán Peninsula.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {100},
pmid = {41026185},
issn = {1432-184X},
support = {887756//Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCyT)/ ; IV200421//Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica-DGAPA/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mexico ; *Rodentia/microbiology/classification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Biological Evolution ; Biodiversity ; Symbiosis ; },
abstract = {The host-microbiome association is considered a coevolutionary process, in which the microbiome provides important functions for host development, physiology and health. However, the ecological and evolutionary forces shaping the diversity and structure of the bacterial communities that form the microbiome are still being elucidated. We assessed the composition of gut microbiota in six rodent species from three geographic regions across the Yucatán peninsula, Mexico. We evaluated the contribution of host species identity, phylogenetic relationships, and geography to the rodents' gut microbiota, using 16S rRNA V4 sequences. We performed a comprehensive set of analytical approaches, including Hill numbers, machine learning, and phylogenetic comparative frameworks. Our results show that phylosymbiosis is one of the main mechanisms driving microbiota dissimilitude across species and specific microbiota diversity traits. Additionally, the microbial pool in each region was geographically differentiated, shaped by the rodent community ensemble, while ecological filtering rendered a microbial pool characteristic of each species. The environment also played a significant role for some species like Heteromys gaumeri, while dietary habits showed a stronger signal for Oryzomys couesi. Rodents with more specialized habits like Ototylomys phyllotis (semi-arboreal, folivorous) had higher bacterial diversity. The abundance of eight bacterial families determined key differences of the gut microbiota which, in addition to phylogeny and geography, are associated with distinct diet and metabolic functions among rodents. Distinct metabolic functions were related, among others, to toxins metabolism and digestion of complex food components. Overall findings show that both evolutionary and ecological drivers influence these rodents gut microbial structure and composition.},
}

Animals
*Gastrointestinal Microbiome/genetics
Mexico
*Rodentia/microbiology/classification
Phylogeny
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Biological Evolution
Biodiversity
Symbiosis

@article {pmid41026172,
year = {2025},
author = {Gao, H and Ma, X and Lu, M and Wang, Y and Liu, H and Hu, X and Nie, Y},
title = {Population and Spatial Features Impact the Gut Phageome-Bacteriome Structure and Interactions in a Mammal Species Living in Fragmented Habitats.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {98},
pmid = {41026172},
issn = {1432-184X},
support = {32225033//National Natural Science Foundation of China/ ; 2022YFF1301500//Ministry of Science and Technology of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/classification/physiology/isolation & purification ; *Bacteria/classification/genetics/isolation & purification/virology ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Antelopes/microbiology/virology ; Metagenome ; Feces/microbiology ; },
abstract = {The mammalian gut microbiome composition has been shown to promote host adaptation to ecological environments. However, the variation in the gut phageome and bacteriome composition at both the population level and spatial scale in wild animals has not been well investigated. Here, we used viral metagenomes and 16S rRNA gene sequencing to explore how these characteristics affect the gut microbiome of Przewalski's gazelle, an endangered group-living ungulate that lives in several fragmented habitats due to anthropogenic activities. The results revealed that population and habitat geographic characteristics collectively explained much more of the variation in phageome and bacteriome compositions than did host-associated factors. Both gut phage and bacterial diversity were positively associated with population size, and differentiation in gut microbiome diversity increased with geographic distance among populations. Additionally, the gut phage and the bacterial hosts displayed similar patterns in composition across habitats, indicating that the microbiome may exhibit complex interactions in response to the environment. For the first time, our study reveals the important roles of population and habitat geographic characteristics in driving spatial patterns of gut microbiome structures in wild animals and highlights the interactions between gut phages and the bacteriome in adaptation to living environments under the influence of human disturbances.},
}

Animals
*Gastrointestinal Microbiome
*Bacteriophages/genetics/classification/physiology/isolation & purification
*Bacteria/classification/genetics/isolation & purification/virology
*Ecosystem
RNA, Ribosomal, 16S/genetics
*Antelopes/microbiology/virology
Metagenome
Feces/microbiology

@article {pmid41026164,
year = {2025},
author = {Yeo, IC and Shim, KY and Min, JO and Kim, JH and Ha, SY and Jeong, CB},
title = {Vertical Structure and Functional Diversity of Microbial Communities in the Ross Sea, Antarctica.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {99},
pmid = {41026164},
issn = {1432-184X},
support = {KIMST RS-2022-KS221661//Korea Institute of Marine Science and Technology promotion/ ; NRF-2022R1C1C1010575//National Research Foundation of Korea/ ; },
mesh = {Antarctic Regions ; *Seawater/microbiology/chemistry ; *Microbiota ; *Biodiversity ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {The Ross Sea, Antarctica, encompasses distinct water masses, each characterized by unique physicochemical conditions influencing microbial community composition and functional diversity. This study examined microbial communities across five stations covering various water masses, including Antarctic Surface Water (AASW), Circumpolar Deep Water (CDW), and Shelf Water (SW). Despite limited horizontal variability, significant vertical structuring was observed, potentially driven by vertical microbial dispersal from surface waters. Surface communities exhibited lower alpha diversity due to abundant labile organic matter favoring fast-growing heterotrophic taxa, whereas deeper communities displayed increased microbial richness, reflecting adaptation to more refractory organic matter. Functional diversity revealed distinct depth-related patterns, with metabolic pathways associated with organic matter predominantly enriched in surface layers. Concurrently, rare taxa became more abundant with depth, emphasizing their potential role as keystone organisms in deep-ocean nutrient cycling. These findings highlight the critical role of vertical microbial connectivity and organic matter composition in shaping microbial community structure and functional specialization, contributing significantly to our understanding of microbial-mediated biogeochemical processes in polar marine ecosystems.},
}

Antarctic Regions
*Seawater/microbiology/chemistry
*Microbiota
*Biodiversity
*Bacteria/classification/genetics/isolation & purification/metabolism
Ecosystem
RNA, Ribosomal, 16S/genetics
Phylogeny

@article {pmid41026097,
year = {2025},
author = {Patyka, M and Wang, R and Honchar, A and Patyka, T and Khablak, S},
title = {Modulation of the rhizosphere microbiome structure and optimization of beneficial functions in winter wheat induced by Bacillus subtilis: a metagenomic and phenotypic study.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf097},
pmid = {41026097},
issn = {1574-6941},
abstract = {The rhizosphere microbiome critically determines plant health and productivity. This study investigated the impact of Bacillus subtilis H38 on the taxonomic and functional profiles of the winter wheat (Triticum aestivum L.) rhizosphere microbiome under typical chernozem conditions using 16S rRNA gene sequencing and shotgun metagenomics, complemented by plant phenotypic evaluation and targeted metabolite analysis. Inoculation with B. subtilis H38 significantly restructured the rhizosphere bacterial community, increasing alpha-diversity (Shannon index from 5.8 to 6.7) and showing distinct clustering in beta-diversity analysis. The relative abundance of putative plant-beneficial genera, including Bacillus, Pseudomonas, Azotobacter, and Streptomyces, was significantly elevated. Shotgun metagenomic analysis revealed enrichment of functional genes associated with nitrogen fixation, phosphorus mobilization, phytohormone biosynthesis, siderophore production, and synthesis of antimicrobial compounds. Targeted metabolomic analysis confirmed elevated levels of indole-3-acetic acid (IAA) and key siderophores. Concurrently, treated wheat plants exhibited an 18.0% increase in above-ground biomass and a 25.0% increase in root length under field conditions. These findings underscore the potential of B. subtilis to beneficially reshape the rhizosphere microbiome and its metagenome, leading to enhanced plant growth, and highlight its utility as a potent biofertilizer for improving wheat productivity. This research reinforces the potential of harnessing beneficial plant-microbe interactions to enhance agricultural productivity while minimizing dependence on synthetic agrochemicals.},
}

@article {pmid41025937,
year = {2025},
author = {Garvey, SM and Blonquist, TM and Brutscher, LM and Walsh, DM and Kaden, VN and Beckman, DB and Zeng, M and Bruno, RS and Cook, CM and Spears, JL},
title = {Dietary Supplementation with the Probiotic Bacillus velezensis BV379 Decreases Abdominal Bloating Without Perturbing the Commensal Gut Microbiota: A Randomized, Double-Blind, Placebo-Controlled Trial in Healthy Adults.},
journal = {Journal of the American Nutrition Association},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/27697061.2025.2563894},
pmid = {41025937},
issn = {2769-707X},
abstract = {OBJECTIVE: Various bacterial Bacillaceae and Bacillus strains have demonstrated health benefits, but less is known about probiotic characteristics of strains of Bacillus velezensis. In this randomized, double-blind, placebo-controlled clinical trial, we investigated the safety and efficacy of B. velezensis BV379 supplementation for 8 weeks (2 × 10[9] colony-forming units (CFU)/day).

METHODS: During the baseline and final weeks, GI symptoms were recorded daily using the 8-item Gastrointestinal Tolerance Questionnaire (GITQ). The primary outcome was the proportion of participants showing an improvement from baseline to week 8 in the 7-day, 3-item composite score for abdominal distention/bloating, burping, and gas/flatulence. Plasma chemistry, hematology, intestinal permeability, and fecal metagenomes were also investigated.

RESULTS: Eighty participants (54% female; age: 50.3 ± 10.1 years) were randomized to BV379 (n = 39) or placebo (n = 41). At end of study, no significant difference was observed in the percentage of participants with improvement in the 3-item composite GITQ score (BV379: 36.1%; placebo: 28.2%; p = 0.46). Analysis of individual GI symptoms showed that more participants experienced improvement in abdominal distention/bloating with BV379 compared to placebo (38.9% vs 17.9%; p = 0.044). There were no clinically meaningful changes in plasma chemistry, hematology, or intestinal permeability between groups. Fecal metagenomic analyses showed no overall shifts in microbial composition between groups. In addition to B. velezensis, a few commensal species such as Lacticasei bacillus casei were significantly enriched in the BV379 group.

CONCLUSION: Despite not significantly improving the composite GITQ score of distention/bloating, burping, and gas/flatulence, BV379 supplementation was a well-tolerated approach to specifically lower abdominal bloating.},
}

@article {pmid41025824,
year = {2025},
author = {Li, Z and Li, S and Han, C and Chen, Y and Zhen, H and Sun, Y and Zhou, X and Chen, Y and Zheng, Y and Han, L and Krutmann, J and Nie, C and Wang, J and Xia, J},
title = {A comprehensive reference catalog of human skin DNA virome reveals novel viral diversity and microenvironmental influences.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0117825},
doi = {10.1128/spectrum.01178-25},
pmid = {41025824},
issn = {2165-0497},
abstract = {UNLABELLED: Human skin serves as a dynamic habitat for a diverse microbiome, including a complex array of viruses whose diversity and roles are not fully understood. A total of 2,760 skin metagenomes from 6 published skin studies were collected. A skin virome catalog was constructed using standard methods in the viromics field. Viral characteristics were identified through cross-cohort meta-analysis and used to characterize viral features across different skin environments. We identified 20,927 viral sequences, which clustered into 2,873 viral operational taxonomic units (vOTUs), uncovering a substantial breadth of viral diversity on human skin. The results also highlight significant differences in viral communities that are associated with varying skin microenvironments. The oily skin is enriched in Papillomaviridae, the dry skin area is enriched in Autographiviridae and Inoviridae, and the moist skin is enriched in Herelleviridae. We also investigated the relationship between bacteriophages and bacteria on the skin surface. We found that skin bacteria such as Pseudomonas, Klebsiella, and Staphylococcus are predicted to be infected by phages from the class Caudoviricetes. This comprehensive skin DNA viral catalog significantly advances our understanding of the virome's role within the skin ecosystem.

IMPORTANCE: This study presents a comprehensive reference catalog of the human skin DNA virome, constructed from 2,760 metagenomic datasets collected globally. It identified 20,927 viral sequences, with 90.85% representing previously unknown viruses, greatly expanding our understanding of skin viral diversity. The findings reveal significant differences in viral communities between distinct skin microenvironments (oily, dry, and moist) and highlight close interactions between bacteriophages and their bacterial hosts, suggesting a potential role for the virome in maintaining microbial balance and skin health. This extensive skin viral catalog constitutes a crucial resource for future epidemiological and therapeutic research, potentially facilitating the development of novel phage therapies and diagnostic markers for skin disorders.},
}

@article {pmid41025821,
year = {2025},
author = {Jablonska, S and Nelson, L and Finger, G and Kula, A and Putonti, C},
title = {Draft genome sequences of Staphylococcus species isolated from urine samples from asymptomatic females.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0081225},
doi = {10.1128/mra.00812-25},
pmid = {41025821},
issn = {2576-098X},
abstract = {The female urinary tract is host to several different Staphylococcus species, both uropathogens and commensals. To further investigate these species, we sequenced the genomes of four isolates from voided urine samples collected from asymptomatic ("healthy") females: Staphylococcus aureus U215, Staphylococcus haemolyticus U117, and Staphylococcus hominis strains U224 and U226.},
}

@article {pmid41025799,
year = {2025},
author = {Buckner, AM and Glendinning, L and Palma Hidalgo, JM and van Munster, JM and Stevens, M and Watson, M and Newbold, CJ},
title = {The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0056325},
doi = {10.1128/spectrum.00563-25},
pmid = {41025799},
issn = {2165-0497},
abstract = {Ruminants play an important part in global food security, but also emit methane, which contributes to global warming. Rumen microbes strongly influence the energy retention efficiency from the host's plant-based diet and produce methane as a by-product. While thousands of novel microbial genomes have been assembled from metagenomic sequence data, their culturability is ill-defined. Here, different media (Med10, Med2, and MedTC) were used to isolate co-cultures of microbes from rumen fluid. Thirty-four OTUs were identified belonging to the phyla Bacillota (75.28 ± 6.34%), Bacteroidota (19.99 ± 4.85%), Pseudomonadota (2.46 ± 2.01%), and Actinomycetota (2.09 ± 1.07%). The most abundant genera were Selenomonas (28.08 ± 11.71%), Streptococcus (22.67 ± 6.06%), Prevotella (18.71 ± 4.02%), and unclassified Lachnospiraceae (11.50 ± 2.54%), and 31 significantly enriched on at least one medium, with each medium successfully culturing a distinct range of microbes. The composition of the source rumen fluid was vastly different from those cultured. Bacteroidota (52.53 ± 5.10%) predominated, with Bacillota (41.00 ± 3.96%), Methanobacteriota (5.12 ± 1.94%), Pseudomonadota (1.22 ± 0.78%), and Actinomycetota (0.12 ± 0.08%) comprising the rest. The most abundant genera were Prevotella (29.13 ± 4.16%), Butyrivibrio (18.21 ± 2.08%), Succiniclasticum (15.57 ± 5.03%), unclassified Bacteroidetes (13.91 ± 1.67%), and unclassified Prevotellaceae (9.50 ± 2.01%). These data further emphasize the importance of using defined media to select for different microbial taxa. This is essential to understand the complex workings of the rumen microbes to enhance digestion efficiency and reduce the loss of energy that could potentially be utilized by the host.IMPORTANCEThis research demonstrates that using a range of culture media, containing a wide variety of substrates, can lead to the culture of key rumen microbes. The knowledge of which of these microbes is selectively enriched on each medium is essential to understand how to grow these microbes in co-culture and isolate them in pure culture for further investigation. In addition, this research shows the stark disparity between the population of rumen microbes grown in co-culture and those found in the rumen itself. This further demonstrates the need for a targeted approach to growing and isolating these microbes. Learning how these microbes respond to culture media with different nutritional compositions will lead to a better understanding of the rumen microbiota, and this research provides a valuable insight into how selective media can target the enrichment of different microbes. This knowledge will contribute to increasing ruminant digestion efficiency and reducing methane production.},
}

@article {pmid41025782,
year = {2025},
author = {Boyd, AI and Kafer, LA and F Escapa, I and Kambal, A and Tariq, H and Hilsenbeck, SG and Nguyen-Phuc, H and Rajan, A and Lensmire, JM and Patras, KA and Piedra, PA and Blutt, SE and Lemon, KP},
title = {Nasal microbionts differentially colonize and elicit cytokines in human nasal epithelial organoids.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0049325},
doi = {10.1128/msphere.00493-25},
pmid = {41025782},
issn = {2379-5042},
abstract = {UNLABELLED: Nasal colonization by Staphylococcus aureus or Streptococcus pneumoniae is associated with an increased risk of infection by these pathobionts, whereas nasal colonization by Dolosigranulum species is associated with health. Human nasal epithelial organoids (HNOs) differentiated at air-liquid interface (ALI) physiologically recapitulate human nasal respiratory epithelium with a robust mucociliary blanket. Due to their natural stem-like properties, HNO lines are a long-term experimental resource that offers genetic diversity based on the different donors. To develop HNOs as a new model system for bacterial nasal colonization, we reproducibly monocolonized HNOs differentiated at ALI with S. aureus, S. pneumoniae, or Dolosigranulum pigrum for up to 48 h with varying kinetics across species. HNOs tolerated bacterial monocolonization with localization of bacteria to the mucus layer and with minimal cytotoxicity compared to uncolonized HNOs. Human nasal epithelium exhibited both species-specific and general cytokine responses, without induction of type I interferons, which is consistent with colonization rather than infection. Only live S. aureus colonization robustly induced epithelial cell production of interleukin-1 family cytokines, suggestive of inflammasome signaling. D. pigrum and live S. aureus decreased CXCL10, whereas S. pneumoniae increased CXCL11, chemokines involved in antimicrobial responses to both viruses and bacteria. Overall, HNOs are a new model system for uncovering microbe-epithelial cell dynamics at the human nasal mucosa.

IMPORTANCE: Human nasal microbiota often includes highly pathogenic members, many of which are antimicrobial resistance threats, e.g., methicillin-resistant Staphylococcus aureus and drug-resistant Streptococcus pneumoniae. Preventing colonization by nasal pathobionts decreases infections and transmission. In contrast, nasal microbiome studies identify candidate beneficial bacteria that might resist pathobiont colonization, e.g., Dolosigranulum pigrum. Learning how these microbionts interact with the nasal epithelium and identifying new means to reduce pathobiont colonization are key goals in the field. As a tool to advance this research, we developed human nasal epithelial organoids (HNOs) differentiated at an air-liquid interface as a new model system of bacterial nasal colonization. HNOs accurately represent the mucosal surface of the human nasal passages, enabling exploration of bacterial-epithelial interactions, which is important since the epithelium is an instigator of the initial innate immune response to bacteria. Here, we identified differential epithelial cytokine responses to these three bacteria, setting the stage for future research.},
}

@article {pmid41025644,
year = {2025},
author = {Saito, D and Saito, CPB and Cannavan, FDS and Tsai, SM},
title = {Draft genome sequences of six Rothia mucilaginosa strains assembled from the human oral microbiome.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0050825},
doi = {10.1128/mra.00508-25},
pmid = {41025644},
issn = {2576-098X},
abstract = {We report draft metagenome-assembled genomes (MAGs) of six Rothia mucilaginosa strains recovered from the oral microbiome of distinct human subjects. MAGs were retrieved according to a species-specific genome mapping approach, displaying high average nucleotide identities (≥95.85%) to R. mucilaginosa ATCC 25296's genome and minimal contamination levels (≤3.75%).},
}

@article {pmid41025606,
year = {2025},
author = {Helliwell, JA and Chilton, CH and Young, C and Clark, EV and Wilkinson, L and Fuentes Balaguer, A and Bottomley, D and Croft, J and Corrigan, N and Kirby, A and Quirke, P and Stocken, DD and Jayne, DG and Wood, HM},
title = {Perioperative changes in the microbiome during rectal cancer surgery: exploratory analysis of the National Institute for Health and Care Research (NIHR) IntAct trial.},
journal = {The British journal of surgery},
volume = {112},
number = {9},
pages = {},
pmid = {41025606},
issn = {1365-2168},
support = {14/150/62//National Institute for Health and Care Research/ ; NIHR303267//National Institute for Health and Care Research/ ; JSPS CLSG 2020 10 03//Jean Shanks Foundation/ ; NIHR213331//Jean Shanks Foundation/ ; NIHR302439//Jean Shanks Foundation/ ; NIHR213331//Jean Shanks Foundation/ ; NIHR205280//Jean Shanks Foundation/ ; /CRUK_/Cancer Research UK/United Kingdom ; },
mesh = {Humans ; Male ; *Rectal Neoplasms/surgery/microbiology ; Female ; Aged ; *Gastrointestinal Microbiome ; Middle Aged ; Anastomotic Leak/microbiology ; *Rectum/microbiology/surgery ; Postoperative Complications/microbiology ; Perioperative Period ; },
abstract = {BACKGROUND: The gut microbiome may influence postoperative outcomes after rectal cancer surgery, including anastomotic leak. However, perioperative microbiome dynamics and their association with outcomes remain poorly understood. The aim of this study was to characterize changes in the rectal microbiome in patients undergoing rectal cancer surgery within the National Institute for Health and Care Research (NIHR) IntAct trial.

METHODS: Rectal swabs were collected at baseline, day of surgery, and postoperative day 3-5. DNA was extracted for 16S ribosomal RNA (rRNA) sequencing and collagenase-producing organisms were identified by culture. Associations between microbiome composition and clinical variables were analysed.

RESULTS: A total of 202 patients were included (mean age 65 years; 69.8% male). At baseline, smoking status explained 3.2% of variation in beta-diversity (P = 0.046). On the day of surgery, beta-diversity was associated with hospital site (11.1%; P = 0.033), mechanical bowel preparation (2.6%; P = 0.024), and preoperative oral antibiotics (1.0%; P = 0.020). After surgery, hospital site (16.3%; P < 0.001), a defunctioning stoma (2.9%; P = 0.003), and preoperative oral antibiotics (1.6%; P = 0.006) influenced beta-diversity. Alpha-diversity decreased over time, with postoperative increases in Enterococcus and Prevotella. A defunctioning stoma was associated with lower alpha-diversity and increased Pseudomonas and Streptococcus. No significant difference in alpha- or beta-diversity was observed between patients with and without anastomotic leak, although subtle differences in taxa of low abundance were detected and 43.6% of postoperative samples demonstrated collagenase activity.

CONCLUSION: This is the largest study to date describing perioperative microbiome changes in patients undergoing rectal cancer surgery. Measurable shifts in the microbiome were observed, with small differences between patients with and without anastomotic leak. Further research is needed to explore the clinical significance of these microbiome changes.},
}

Humans
Male
*Rectal Neoplasms/surgery/microbiology
Female
Aged
*Gastrointestinal Microbiome
Middle Aged
Anastomotic Leak/microbiology
*Rectum/microbiology/surgery
Postoperative Complications/microbiology
Perioperative Period

@article {pmid41025564,
year = {2025},
author = {Zeng, S and Wang, H and Zhang, L and Li, S and Yuan, Y and Tian, M and Qu, Y and Ying, J and Zhou, M and Hu, Y and Huang, J and Zou, R and Zhao, F and Su, X and Liu, Q and He, Y and Feng, J and Huang, W and Luo, Y and Zhou, Z and Shen, W and Mu, D and Wang, S},
title = {The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e05154},
doi = {10.1002/advs.202505154},
pmid = {41025564},
issn = {2198-3844},
support = {2021YFC2701704//National Key Research and Development Program/ ; 2021YFC2701700//National Key Research and Development Program/ ; 82402025//National Natural Science Foundation of China/ ; 82241036//National Natural Science Foundation of China/ ; 82271749//National Natural Science Foundation of China/ ; 82371717//National Natural Science Foundation of China/ ; 82201905//National Natural Science Foundation of China/ ; 82571980//National Natural Science Foundation of China/ ; 82530056//National Natural Science Foundation of China/ ; 2025ZNSFSC1677//Department of Science and Technology of Sichuan Province/ ; SCU2023D006//Fundamental Research Funds for the Central University/ ; SZSM202311027//Sanming Project of Medicine in Shenzhen/ ; },
abstract = {The accelerating threat from antimicrobial resistance (AMR) has become a global health issue. The properties of AMR in the gut microbiome of preterm infants and its clinical relevance with necrotizing enterocolitis (NEC) remain unknown. In-depth integrative analyses of 5,684 gut metagenomes are performed to build an AMR genes (ARGs) landscape. A subset of 107 preterm infants who developed NEC is sampled to examine the trajectory and predictive potential of ARGs preceding NEC onset. The variation and core set of ARGs, their higher burden and diversity, and potential ARGs-enriched gut bacteria in preterm infants compared to full-term infants are comprehensively discovered, reflecting a strain shift in genomic functions. Moreover, the gut resistome converged over 9 days before NEC onset is observed, which is driven by 24 ARGs. Machine learning analysis reveals potential usage of the gut resistome as an indicator for predicting NEC onset in an external validation preterm birth cohort (the area under the receiver operating characteristic curve, AU-ROC = 0.823), which is significantly higher than that based on the bacterial species (AU-ROC = 0.727). Overall, the findings can be referenced to mitigate the burden and spread of ARGs, and specific ARGs have potential for disease risk stratification to improve clinical management.},
}

@article {pmid41025524,
year = {2025},
author = {Santi, MM and Genovese, E and Schou, TM and da Silva, M and Erhardt, S and Schwieler, L and Weidenfors, JA and Marino, G and Paludan, SR and Joca, S and Wegener, G and Reinert, L and Bay-Richter, C},
title = {Neuropsychiatric- and cognitive post-acute sequelae of SARS-CoV-2 infection - evidence from K18-hACE C57BL/6 J mice.},
journal = {The international journal of neuropsychopharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1093/ijnp/pyaf072},
pmid = {41025524},
issn = {1469-5111},
abstract = {BACKGROUND: Survivors of COVID-19 frequently report psychiatric and cognitive sequelae. The origin of such sequelae has not been determined, as it has been a challenge to resolve whether these symptoms have a viral origin or are related to the contextual stressors associated with the pandemic. In the current study, we used a mouse model of post-acute sequelae of SARS-CoV-2 infection (PASC) to evaluate the neurobiological nature of the sequelae without the interference of the contextual effects on behavior following SARS-CoV-2 infection.

RESULTS: SARS-CoV-2 infection resulted in behavioral deficits related to cognition but not anxiety- or depression-like behavior. The cognitive deficits were affected by the severity of the acute disease. Cytokine and chemokine levels as well as kynurenine pathway metabolites were significantly altered in the brains of infected mice. Both cytokine/chemokine levels and kynurenine pathway metabolites correlated with the severity of the acute disease. Microbiome taxonomic profiling revealed significant differences between groups, suggesting that specific bacterial species may be associated with the development of PASC.

CONCLUSIONS: These results suggest that SARS-CoV-2 infection leads to cognitive deficits in PASC, influenced by the severity of the acute disease. In contrast, PASC anxiety- and depression-like behavior was not related to the viral infection itself. This could indicate that PASC anxiety and depression is more linked to contextual stressors related to the pandemic, rather than the viral infection per se. Additionally, our results points to a role of cytokines and in particular metabolites of the kynurenine pathway in PASC, suggesting their potential as biomarkers and targets for pharmacological treatment.},
}

@article {pmid41025437,
year = {2025},
author = {Brockway, MM and Khalid, M and Khalil, Y and Rusi, HC and Asbury, MR and Arrieta, MC and Keys, E and Ou, C and Festival, J},
title = {Comparing Impacts of Donor Human Milk to Formula Supplementation on the Gut Microbiome of Full-Term Infants Born Via Cesarean Section: Protocol for a Pilot Randomized Controlled Trial.},
journal = {Journal of human lactation : official journal of International Lactation Consultant Association},
volume = {},
number = {},
pages = {8903344251369442},
doi = {10.1177/08903344251369442},
pmid = {41025437},
issn = {1552-5732},
abstract = {BACKGROUND: A disrupted gut microbiome during an infant's first 1000 days of life can lead to long-lasting negative effects on child health. Cesarean delivery and formula feeding are two factors that can detrimentally impact infant microbiome development as well as maternal mental health. Donor human milk may be a superior supplementation alternative to formula.

RESEARCH AIM: To examine donor human milk supplementation compared to formula supplementation in full-term infants born via Cesarean section and the impact on the infant gut microbiome, infant health outcomes, breastfeeding outcomes, and maternal mental health.Methods and Planned Analyses:We are conducting a pilot clinical randomized controlled trial, comparing donor human milk to formula supplementation for 187 full-term infants born via Cesarean section who are breastfeeding and require supplementation in the first postnatal week of life. Infant stool samples, breastfeeding outcomes, maternal mental health, and child health outcomes will be measured at 1-week, 3-, 6-, and 12-months postpartum. Additionally, child health and maternal mental health are being assessed at 18- and 36-months postpartum.

DISCUSSION: This study will generate essential data on the association between supplementation types and the full-term infant microbiome, breastfeeding exclusivity and duration, and infant health. It will also provide preliminary data to inform a multi-site, longitudinal mixed-methods randomized controlled trial that will assess longer term child health outcomes. This evidence may be used to inform guidelines and policies that will increase accessibility to and raise awareness of donor human milk as a supplementation option in this population.},
}

@article {pmid41025248,
year = {2025},
author = {Park, YJ and Lim, JK and Lee, YJ and Kwon, KK},
title = {Protocol for efficient recovery of high-quality DNA from microbiome of marine invertebrates.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {9},
pages = {e2507003},
doi = {10.71150/jm.2507003},
pmid = {41025248},
issn = {1976-3794},
support = {EA0311//Ministry of Oceans and Fisheries/ ; KIMST 20210469//Ministry of Oceans and Fisheries/ ; },
mesh = {Animals ; *Microbiota/genetics ; *DNA, Bacterial/isolation & purification/genetics ; *Aquatic Organisms/microbiology ; *Bacteria/genetics/isolation & purification/classification ; *Porifera/microbiology ; Symbiosis ; Republic of Korea ; *Invertebrates/microbiology ; Anthozoa/microbiology ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; },
abstract = {Marine organisms often form symbiotic relationships with various microorganisms to adapt and thrive in harsh environments. These symbiotic microbes contribute to host survival by providing nutrition, modulating the hosts' immune system, and supporting overall physiological stability. Advances in high-throughput sequencing technologies have enabled a deeper understanding of the structure and function of symbiotic microbial communities, as well as host-microbe interactions. Notably, symbiotic bacteria associated with marine invertebrates such as corals and sponges are recognized as a potential source of useful bioactive compounds, including antibiotics and enzymes. However, obtaining high-quality microbial DNA from host tissues still remains a technical challenge due to the presence of unknown substances. This study focuses on optimizing sample preparation and DNA extraction procedures and additional purification to improve the recovery of microbial DNA while minimizing host DNA contamination. Comparison between several methods was conducted using sponge samples to evaluate DNA quality and microbial recovery. A sample designated as 2110BU-001 was collected from the east coast of the Republic of Korea and used for culture-independent microbial cell isolation. Total bacterial DNA was extracted by using a manual Phenol-Chloroform protocol and three commercial kits. DNA extracted using the standard manual method showed both the highest yield and the largest fragment size. However, PCR (Polymerase chain reaction) test showed that quality of manually extracted DNA was not enough for sequencing. Therefore, the quality of DNA was improved through additional purification steps. Briefly, host eukaryotic cells were removed by mechanical process and almost only bacterial DNA was successfully obtained by combination of manual extraction method and further purification processes. The established protocol was successfully introduced to extraction of metagenomic DNA from mussel and jellyfish microbiomes, indicating that it can be widely applied to various marine organisms.},
}

Animals
*Microbiota/genetics
*DNA, Bacterial/isolation & purification/genetics
*Aquatic Organisms/microbiology
*Bacteria/genetics/isolation & purification/classification
*Porifera/microbiology
Symbiosis
Republic of Korea
*Invertebrates/microbiology
Anthozoa/microbiology
RNA, Ribosomal, 16S/genetics
High-Throughput Nucleotide Sequencing
Polymerase Chain Reaction

@article {pmid41025090,
year = {2025},
author = {Gavkare, AM and Nanaware, NL and Sonar, MN and Dhotre, SV and Mumbre, SS and Nagoba, BS},
title = {Gut microbiome and viral infections: A hidden nexus for immune protection.},
journal = {World journal of virology},
volume = {14},
number = {3},
pages = {111912},
pmid = {41025090},
issn = {2220-3249},
abstract = {The gut microbiome plays a crucial role in regulating immune responses, influencing susceptibility to viral infections, shaping disease progression, and its outcomes. Emerging research highlights the intricate relationship between gut microbial communities and viral pathogenesis, demonstrating that dysbiosis can compromise antiviral defenses while a balanced microbiome enhances immune resilience. This review explores key microbial mechanisms, including microbiome-mediated immune modulation, interactions with viral replication, and the impact of microbiome on systemic inflammation, highlighting how dietary interventions, such as probiotics, prebiotics, and bioactive compounds, offer potential strategies to modulate gut microbiota and mitigate viral infections. Special emphasis is placed on viruses affecting the gastrointestinal and respiratory systems, including severe acute respiratory syndrome coronavirus 2, norovirus, and influenza. Furthermore, we explore how nutrition-driven microbiome interventions may serve as adjunct therapeutic strategies, improving vaccine efficacy and post-viral recovery. Understanding the role of gut microbiome in viral infections can pave the way for microbiome-driven strategies to combat viral diseases and improve overall health outcomes.},
}

@article {pmid41025008,
year = {2025},
author = {Akpoveta, ED and Okpete, UE and Byeon, H},
title = {Unraveling the gut-liver axis in autoimmune liver disease overlap syndrome: A multi-omics perspective.},
journal = {World journal of gastroenterology},
volume = {31},
number = {37},
pages = {112298},
pmid = {41025008},
issn = {2219-2840},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/genetics ; *Hepatitis, Autoimmune/immunology/microbiology/metabolism ; *Liver Cirrhosis, Biliary/immunology/microbiology/metabolism ; *Liver/immunology/microbiology/metabolism ; *Dysbiosis/immunology/microbiology ; Metabolomics/methods ; Syndrome ; RNA, Ribosomal, 16S/genetics ; Multiomics ; },
abstract = {Autoimmune liver disease overlap syndrome (OS) is a rare and clinically significant condition that has received limited attention in microbiome research. In their recent study, Wang et al combined 16S rRNA sequencing with untargeted metabolomics to characterize the gut-liver axis in OS, identifying shared features of dysbiosis in autoimmune hepatitis (AIH) and primary biliary cholangitis (PBC), and unique signatures, including enrichment of Klebsiella and Escherichia and depletion of aromatic amino acids. In this letter, we critically appraise these findings, emphasizing that OS should be considered a distinct immunometabolic phenotype rather than a simple mixture of AIH and PBC. We discuss the potential mechanistic relevance of the Fusicatenibacter-tyrosine relationship, highlight the clinical implications of integrating microbiota-metabolite analyses, and outline the limitations that future studies must address.},
}

Humans
*Gastrointestinal Microbiome/immunology/genetics
*Hepatitis, Autoimmune/immunology/microbiology/metabolism
*Liver Cirrhosis, Biliary/immunology/microbiology/metabolism
*Liver/immunology/microbiology/metabolism
*Dysbiosis/immunology/microbiology
Metabolomics/methods
Syndrome
RNA, Ribosomal, 16S/genetics
Multiomics

@article {pmid41024986,
year = {2025},
author = {Singla, N and Singla, K and Attauabi, M and Aggarwal, D},
title = {Gut-skin axis: Emerging insights for gastroenterologists-a narrative review.},
journal = {World journal of gastrointestinal pathophysiology},
volume = {16},
number = {3},
pages = {108952},
pmid = {41024986},
issn = {2150-5330},
abstract = {The gut-skin axis (GSA) embodies a complex, bidirectional interaction between the gastrointestinal (GI) system and skin, driven by immune modulation, systemic inflammation, and gut microbiota dynamics. Disruptions in gut homeostasis, including dysbiosis and increased intestinal permeability, are increasingly recognized as contributing factors to dermatological conditions such as acne, psoriasis, and atopic dermatitis. For gastroenterologists, appreciating this interplay is essential, as diseases and their treatments frequently present with cutaneous manifestations, offering diagnostic and therapeutic insights. This review explores the underlying mechanisms of the GSA, focusing on the microbiome and its metabolites as key regulators of inflammation and immunity. It underscores the clinical importance of microbiome-targeted therapies, such as probiotics, prebiotics, and dietary modifications, in addressing both GI and dermatological disorders. Furthermore, the review examines the influence of GI conditions, including inflammatory bowel disease and celiac disease on skin health. This article seeks to equip gastroenterologists with practical insights for identifying, diagnosing, and managing skin conditions associated with GI health. The article also highlights the current limitations in knowledge regarding the GSA. The GSA represents a promising avenue for therapeutic advancements, encouraging interdisciplinary collaboration between gastroenterology and dermatology to optimize patient care.},
}

@article {pmid41024841,
year = {2025},
author = {Chang, H and Perez-Losada, J and Mao, JH},
title = {Emerging multifaceted roles of the microbiome in cancer susceptibility.},
journal = {World journal of clinical oncology},
volume = {16},
number = {9},
pages = {111379},
pmid = {41024841},
issn = {2218-4333},
abstract = {Identifying the factors that contribute to individual susceptibility to cancer is essential for both prevention and treatment. The advancement of biotechnologies, particularly next-generation sequencing, has accelerated the discovery of genetic variants linked to cancer susceptibility. While hundreds of cancer-susceptibility genes have been identified, they only explain a small fraction of the overall cancer risk, a phenomenon known as "missing heritability". Despite progress, even considering factors such as epistasis, epigenetics, and gene-environment interactions, the missing heritability remains unresolved. Recent research has revealed that an individual's microbiome composition plays a significant role in cancer susceptibility through several mechanisms, such as modulating immune cell activity and influencing the presence or removal of environmental carcinogens. In this review, we examine the multifaceted roles of the microbiome in cancer risk and explore gene-microbiome and environment-microbiome interactions that may contribute to cancer susceptibility. Additionally, we highlight the importance of experimental models, such as collaborative cross mice, and advanced analytical tools, like artificial intelligence, in identifying microbial factors associated with cancer risk. Understanding these microbial determinants can open new avenues for interventions aimed at reducing cancer risk and guide the development of more effective cancer treatments.},
}

@article {pmid41024833,
year = {2025},
author = {Tahri, A and Amedei, A},
title = {Unraveling the links between estrogen and gut microbiota in sex-hormone driven cancers.},
journal = {World journal of clinical oncology},
volume = {16},
number = {9},
pages = {108819},
pmid = {41024833},
issn = {2218-4333},
abstract = {Estrogens are a group of steroid hormones produced by ovary, placenta, and other organs. They have historically been associated with female reproduction, but according to current evidence estrogens regulate also male reproductive and nonreproductive organs. Estrogens play a crucial role in female reproductive development and maintenance either directly by increasing glycogen levels, epithelial thickness and mucus secretion or indirectly, by decreasing vaginal pH through the maintenance of lactobacilli dominance and lactic acid production. Several studies demonstrated that dysbiosis and/or specific bacteria could have impact on the development of sex-hormone driven cancers such as endometrial, cervical, ovarian, breast and prostate cancers, through mechanisms involving modulation of estrogen metabolism. This modulation is realized through secretion of β-glucuronidase which deconjugates estrogens into their active forms. When gut dysbiosis occurs, microbial diversity decreases and so the deconjugation diminishes leading to a decrease of circulating estrogens. Low levels of circulating estrogen may adversely affect a wide range of physiological factors, with clinical implications especially for gut health. In this review, we discuss the different aspects of the critical interplay between gut microbiome and estrogens in sex-hormone driven cancers and the potential outcomes on their clinical management.},
}

@article {pmid41024803,
year = {2025},
author = {Lin, XJ and Xu, JZ and Hu, Q and Chen, J},
title = {Effects of enhanced recovery after surgery on postoperative intestinal function and intestinal flora during laparoscopic gastric cancer surgery.},
journal = {World journal of gastrointestinal surgery},
volume = {17},
number = {9},
pages = {106286},
pmid = {41024803},
issn = {1948-9366},
abstract = {BACKGROUND: Enhanced recovery after surgery (ERAS) protocols have emerged as a promising approach in perioperative care. This study evaluated ERAS's impact on gastrointestinal recovery and microbiota composition following laparoscopic gastric cancer surgery.

AIM: To evaluate the impact of ERAS protocols on postoperative gastrointestinal function recovery and intestinal microbiota composition in patients undergoing laparoscopic gastric cancer surgery, and to identify factors associated with improved clinical outcomes and microbial diversity preservation.

METHODS: We conducted a retrospective analysis of 80 patients who underwent laparoscopic D2 gastrectomy, comparing ERAS (n = 40) vs traditional care (n = 40). Primary outcomes included postoperative gastrointestinal function recovery and complications. Intestinal microbiota was analyzed using 16S rRNA sequencing at multiple timepoints perioperatively.

RESULTS: ERAS patients demonstrated faster recovery of bowel function, with earlier return of bowel sounds (16.25 ± 6.41 hours vs 22.3 ± 6.49 hours), first flatus (23.95 ± 6.02 hours vs 28.45 ± 7.12 hours), and defecation (34.95 ± 9.34 hours vs 48.1 ± 15.64 hours), all P < 0.05. Complication rates, including antibiotic-associated diarrhea and surgical site infections, were comparable between groups. Microbial diversity indices and probiotic populations showed better preservation in the ERAS group postoperatively (P < 0.05), though neither group achieved complete restoration to preoperative levels at one month.

CONCLUSION: These results support tailoring ERAS protocols to prioritize gut microbiome resilience through early feeding and shortened antibiotic courses, with particular benefits for younger patients.},
}

@article {pmid41024787,
year = {2025},
author = {Qu, HD and Gao, X and Xiao, P and Jiao, Y},
title = {Microsatellite instability and its impact on nutritional and inflammatory profiles in colorectal cancer.},
journal = {World journal of gastrointestinal surgery},
volume = {17},
number = {9},
pages = {108215},
pmid = {41024787},
issn = {1948-9366},
abstract = {Microsatellite instability (MSI) is a critical molecular feature in colorectal cancer (CRC) that not only determines response to immunotherapy but also influences systemic nutritional and inflammatory status. MSI-high (MSI-H) CRC is characterized by heightened systemic inflammation, altered cytokine profiles, and unique gut microbiota compositions. Concurrently, MSI-H patients often exhibit poorer nutritional status, as reflected by lower body mass index, decreased serum albumin, and metabolic dysregulation. These immunonutritional alterations influence patient outcomes by affecting prognosis, response to therapy, and overall survival. This editorial summarizes current evidence linking MSI status with inflammatory and nutritional markers, highlighting the clinical implications of integrating nutritional assessment and inflammatory modulation into the maagement of CRC patients.},
}

@article {pmid41024767,
year = {2025},
author = {Ezzat, WM},
title = {Machine learning as an artificial intelligence application in management of chronic hepatitis B virus infection.},
journal = {World journal of gastroenterology},
volume = {31},
number = {35},
pages = {109776},
pmid = {41024767},
issn = {2219-2840},
mesh = {Humans ; *Hepatitis B, Chronic/therapy/microbiology/diagnosis/virology ; *Machine Learning ; *Gastrointestinal Microbiome ; *Hepatitis B virus/pathogenicity ; Algorithms ; Artificial Intelligence ; Antiviral Agents/therapeutic use ; Supervised Machine Learning ; },
abstract = {Let's review the role of gut microbiota in pathogenesis of chronic hepatitis B infection as addressed in by Zhu et al. Zhu et al used high-throughput technology to characterize the microbial ecosystems, which led to an explosion of various types of molecular profiling data, such as metagenomics, metatranscriptomics, and metabolomics. To analyze such data, machine learning (ML) algorithms have shown to be useful for identifying key molecular signatures, discovering potential patient stratifications, and, particularly, for generating models that can accurately predict phenotypes. Strong evidence suggests that such gut microbiome-based stratification could guide customized interventions to benefit human health. Supervised learning includes designing an algorithm to fix a pre-identified problem. To get an answer, ML software must access data that have been nominated. On the other hand, unsupervised learning does not address any pre-defined problems. Bias should be eliminated as much as possible. In unsupervised learning, an ML algorithm works to identify data patterns without any prior operator input. This can subsequently lead to elements being identified that could not be conceived by the operator. At the intersection between supervised and unsupervised learning is semi-supervised ML. Semi-supervised learning includes using a partially labeled data set. The ML algorithm utilizes unsupervised learning to label data (that has not yet been labelled) by drawing findings from the labeled data. Then, supervised techniques can be used to solve defined problems involving the labeled data. Reinforcement learning, which is similar to supervised learning in the meaning, is goal-oriented. Reinforcement learning does not need labeled data, instead, it is provided with a set of regulations on a problem. An algorithm will carry out operations to try to answer questions involving the problem. Based on obtained data of gut microbiota, various therapeutic modalities can be applied: Prebiotics, probiotics, postbiotics, engineered bacteria, bacteriophage, and novel microbe-materials therapeutic system and fecal transplantation. In conclusion, ML is an artificial intelligence application that helps in providing new perspectives on tailored therapy. Furthermore, assessing the impact of gut microbiota modification is a critical step in advanced liver disease management. These new artificial intelligence techniques although promising, still require further analysis and validation in future studies.},
}

Humans
*Hepatitis B, Chronic/therapy/microbiology/diagnosis/virology
*Machine Learning
*Gastrointestinal Microbiome
*Hepatitis B virus/pathogenicity
Algorithms
Artificial Intelligence
Antiviral Agents/therapeutic use
Supervised Machine Learning

@article {pmid41024758,
year = {2025},
author = {Al-Beltagi, M and Saeed, NK and Mani, PKC and Bediwy, AS and Elbeltagi, R},
title = {Inflammatory bowel disease in paediatrics: Navigating the old challenges and emerging frontiers.},
journal = {World journal of gastroenterology},
volume = {31},
number = {35},
pages = {111934},
pmid = {41024758},
issn = {2219-2840},
mesh = {Humans ; Child ; Precision Medicine/methods/trends ; *Colitis, Ulcerative/therapy/epidemiology/diagnosis ; Gastrointestinal Microbiome/immunology ; *Crohn Disease/therapy/diagnosis/epidemiology ; *Inflammatory Bowel Diseases/therapy/diagnosis/epidemiology ; Pediatrics/trends ; },
abstract = {Pediatric inflammatory bowel disease (IBD), encompassing Crohn's disease, ulcerative colitis, and IBD-unclassified, has become increasingly prevalent worldwide, including in previously low-incidence regions. Children often present with more extensive and aggressive disease, creating unique diagnostic and management challenges that differ significantly from adult-onset IBD. This review aims to synthesize current knowledge on pediatric IBD, highlighting historical challenges while exploring emerging frontiers in diagnosis, treatment, and long-term care strategies. A narrative synthesis of global and regional epidemiological data, clinical classifications, diagnostic advancements, management approaches, and psychosocial considerations was conducted, with a particular emphasis on innovations in precision medicine, microbiome-targeted therapy, and multidisciplinary care models. Pediatric IBD continues to rise globally, driven by environmental and genetic interactions, especially in rapidly industrializing regions. Novel diagnostic tools, age-specific treatment protocols, biologics, nutritional strategies, and psychosocial support are reshaping care. Emphasis on very early-onset IBD, transition care, and regional policy adaptations underscores the evolving complexity of managing pediatric IBD. The landscape of pediatric IBD care is rapidly evolving. Addressing the distinct pathophysiology, developmental impact, and healthcare challenges of pediatric patients requires an integrated, child-centered approach. Ongoing research into genetics, immune pathways, and the microbiome will be essential in tailoring precision therapies and improving outcomes globally.},
}

Humans
Child
Precision Medicine/methods/trends
*Colitis, Ulcerative/therapy/epidemiology/diagnosis
Gastrointestinal Microbiome/immunology
*Crohn Disease/therapy/diagnosis/epidemiology
*Inflammatory Bowel Diseases/therapy/diagnosis/epidemiology
Pediatrics/trends

@article {pmid41024692,
year = {2025},
author = {Pike, WA and Stephens, J and Donohue, M and Rajandran, K and Treanore, ED and Sher, A and Croteau, E and Rittschof, CC},
title = {Do honey phytochemicals modulate forager aggression and the gut microbiome in the honey bee (Apis mellifera L.)?.},
journal = {Biology open},
volume = {},
number = {},
pages = {},
doi = {10.1242/bio.062233},
pmid = {41024692},
issn = {2046-6390},
support = {IOS-2049501//National Science Foundation/ ; 1012993//National Institute of Food and Agriculture/ ; Graduate Research Fellowship Program//National Science Foundation/ ; //Commonwealth Undergraduate Research Experience Fellowship/ ; //The Bill Gatton Foundation/ ; },
abstract = {Plant phytochemicals found in nectar impact bee learning and memory and plant pollination success. Especially for generalist pollinators, dietary changes that alter phytochemical consumption could be common sources of behavioral variation. For honey bee (Apis mellifera L.) foragers, a major potential change in phytochemical consumption occurs when individuals switch from collecting nectar from flowers to collecting honey from neighboring colonies, a phenomenon known as honey robbing. In this study we investigated whether phytochemicals dominant in honey compared to nectar act as a short-term trigger of robbing behaviors in honey bee, which include increased aggression. We fed forager honey bees sucrose diets containing different phytochemicals found in nectar and honey and tested aggression using a lab-based assay. We found no evidence that phytochemicals altered forager behavior. We also compared the microbiome composition for foragers fed different phytochemicals and again found no effects. Our results suggest that neither direct effects of neuroactive phytochemicals, nor indirect effects through the structure or function of the gut microbiome, trigger honey robbing behaviors.},
}

@article {pmid41024685,
year = {2025},
author = {De Simone Carone, L and Barra, G and Cirella, R and Ziaco, M and Mercogliano, M and Olmeo, F and Andretta, E and Mazziotti, V and Fusco, C and D'Ippolito, G and Duda, KA and Farquharson, FM and Louis, P and Fontana, A and Silipo, A and Molinaro, A and Chiodo, F and Di Lorenzo, F},
title = {Decoding a Gut Commensal Signal: Structural and Immunological Profiling of Segatella Copri Lipopolysaccharide.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e202512947},
doi = {10.1002/anie.202512947},
pmid = {41024685},
issn = {1521-3773},
support = {/ERC_/European Research Council/International ; 101039841//Horizon Europe program/ ; 2022SHW3KY//Italian Ministry of University and Research/ ; P202293ZMC//Italian Ministry of University and Research/ ; PGR12361//Italian Ministry of Foreign Affairs and International Cooperation/ ; },
abstract = {The immunological effects of lipopolysaccharides (LPSs) from gut microbiota remain poorly explored, overshadowed by the longstanding view of LPS as a prototypical pro-inflammatory molecule. Herein, we report the first comprehensive chemical and immunological characterization of LPS from Segatella copri DSM 18205, a prominent member of the human oral and intestinal microbiota. This LPS features a unique chemical architecture, including a mannose- and glucose-rich oligosaccharide (OS) and a highly heterogeneous, hypo-acylated lipid A domain, as elucidated by advanced mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. Functionally, S. copri LPS displayed attenuated TLR4 activation and weak pro-inflammatory activity. Strikingly, high-dimensional cytometry by time-of-flight (CyTOF) revealed a selective preservation of CD14[+]CD16[+] monocytes, immune subsets typically depleted by canonical enterobacterial LPSs. These findings identify S. copri LPS as a chemically and functionally distinct microbial signature, offering new insights into host-microbiota immune crosstalk and highlighting its potential for microbiome-informed immunomodulatory strategies.},
}

@article {pmid41024580,
year = {2025},
author = {Deng, S and Hussain, T and Bartelli, TF and Sebastian, MM and Zarghooni, M and Velasco, WV and Somerville, B and Phan, L and Savage, MI and Song, Y and Clifford, JL and Kadara, H and McAllister, F and Brown, PH and Moghaddam, SJ and Aldaz, CM},
title = {Repurposing of the Macrolide Antibiotic Clarithromycin for the Prevention of Lung Cancer.},
journal = {Molecular cancer therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1158/1535-7163.MCT-25-0392},
pmid = {41024580},
issn = {1538-8514},
abstract = {Drug repurposing is the process of reusing existing pharmaceuticals for novel clinical purposes, which offers advantages such as streamlined clinical trial access and reduced drug development costs. Clarithromycin (CAM), a member of the macrolide antibiotics family, is a promising candidate for repurposing in cancer therapy due to its known preclinical and clinical immunomodulatory and anti-cancer properties. In the current study, we investigated whether CAM could be repurposed as a preventive treatment for KRAS-mutant lung cancer, a subtype of lung adenocarcinoma that is strongly associated with heavy smoking. CCSPCre; LSL-KrasG12D mice at an early stage of tumor development were treated with different doses of CAM for 10 weeks. While exhibiting an excellent safety profile, CAM was able to prevent the development of premalignant and malignant lung lesions in a dose-dependent manner. In addition, CAM significantly reduced the infiltration of neutrophils/PMN-MDSCs and inhibited the mRNA expression of pro-tumor inflammatory cytokines IL-6, TNFα, and IL-1β, as well as M2 macrophage markers Fizz1 and Arginase1 in the lung tumor microenvironment (TME). Moreover, we investigated the effect of CAM in reshaping the intestinal and lung microbiome. Long-term CAM usage decreased intestinal microbiome diversity, but more notably, significantly increased the abundance of the probiotic genus Muribaculaceae while decreasing the abundance of Desulfovibrioi, a genus associated with the promotion of various malignancies. Taken together, we conclude that CAM could provide promising cancer prevention efficacy in KRAS-mutant lung cancer due to its immunomodulatory properties on the TME, and its regulatory effects on the microbiome.},
}