@article {pmid40378938,
year = {2025},
author = {Feng, Y and Kim, JW and Xie, W},
title = {The intestinal functions of PXR and CAR.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107779},
doi = {10.1016/j.phrs.2025.107779},
pmid = {40378938},
issn = {1096-1186},
abstract = {Pregnane X receptor (PXR) and constitutive androstane receptor (CAR) are so-called xenobiotic nuclear receptors that play pivotal roles in xenobiotic metabolism and detoxification. Both receptors, highly expressed in the liver and intestine, also have endobiotic functions by regulating the homeostasis of endogenous chemicals. While their hepatic functions are well-documented, the functional roles of PXR and CAR in the gastrointestinal tract are less understood. This review highlights the intestinal functions of PXR and CAR, focusing on their involvement in colon cancer, host-microbiome interactions, inflammation, and gut barrier integrity. PXR exhibits dual roles in colon cancer, acting either as a tumor suppressor by inducing cell-cycle arrest or as a promoter of cancer aggressiveness through activating the FGF19 signaling. CAR, on the other hand, regulates intestinal barrier integrity and immune responses, particularly in the context of inflammatory bowel disease (IBD). Both PXR and CAR interact with gut microbiota, modulating microbial composition and the production of metabolites, such as indole-3-propionic acid (IPA) that influences the gut barrier function and inflammation. Activation of PXR also mitigates intestinal inflammation by antagonizing the NF-κB signaling, while CAR activation affects bile acid metabolism and T-cell homeostasis. These findings underscore the complex and context-dependent roles of PXR and CAR in the intestinal tracts, offering potential therapeutic targets for gastrointestinal diseases.},
}

@article {pmid40378921,
year = {2025},
author = {Wong, SY and Estevinho, MM and Heaney, T and Marshall, AA and Giselbrecht, E and Daniel, SG and Zhou, C and Rosas-Villegas, A and Jang, KK and Yang, H and Mabel Ko, H and Paulson, JD and Ding, Y and Bittinger, K and Cho, JH and Lewis, JD and Ramanan, D and Cadwell, K},
title = {Goblet cell loss linked to NOD2 and secondary resection in Crohn's disease is induced by dysbiosis and epithelial MyD88.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101533},
doi = {10.1016/j.jcmgh.2025.101533},
pmid = {40378921},
issn = {2352-345X},
abstract = {BACKGROUND & AIMS: The role of goblet cells in small intestinal inflammation in Crohn's disease is unknown. Polymorphisms of NOD2 confer risk for Crohn's disease (CD) and associate with small intestinal disease location. We previously showed in mice that Nod2 deficiency leads to overexpansion of Phocaeicola vulgatus in the gut and downstream goblet cell defects, which preceded small intestinal inflammation. In this study, we ask whether goblet cell defects occur in CD patients with NOD2 polymorphisms and investigate in mice how P. vulgatus signals through the intestinal epithelium.

METHODS: We performed a retrospective study of patients with CD to assess clinical outcomes and goblet cell histology by NOD2 status. We evaluated the contribution of microbiota and MyD88 signaling in the intestinal epithelium to goblet cell defects in the setting of Nod2 deficiency using genetic mouse models and germ-free mice.

RESULTS: In patients with CD who have undergone ileocolic resection, NOD2 risk alleles confer a risk for re-operation (OR 8.12, P = .047) and for increased pERK and goblet cell defects in uninflamed ileal tissue. We show that patients with CD with ileal involvement harbor P. vulgatus regardless of NOD2 risk allele status. We show that intestinal epithelial MyD88 and TLR4 are required for goblet cell defects in Nod2[-/-] mice harboring P. vulgatus. Finally, we show that P. vulgatus requires complex microbiota to exert its effects in Nod2-deficient mice.

CONCLUSIONS: Goblet cell defects may be a harbinger of small intestinal inflammation in CD patients, particularly in the postoperative setting. Our findings in mice show that small intestinal goblet cell loss associated with Nod2 mutation is induced by microbiome dysbiosis and epithelial MyD88, in part due to TLR4 signaling.},
}

@article {pmid40378786,
year = {2025},
author = {Chmolowska, D and Wasak-Sęk, K and Chroňáková, A and Bahram, M and Choczyński, M and Tedersoo, L},
title = {Soil and its microbiome in translocated meadows in the context of habitats in the receptor area.},
journal = {Journal of environmental management},
volume = {386},
number = {},
pages = {125714},
doi = {10.1016/j.jenvman.2025.125714},
pmid = {40378786},
issn = {1095-8630},
abstract = {Turf translocation, which is undertaken to mitigate the destruction of valuable habitats, can challenge the soil biota. We investigated translocated protected Molinion meadows in the context of the surrounding environments. Soil and soil microorganisms were examined in meadows translocated four years earlier to a habitat garden in recycled land. Neighbouring habitats, comprised of woodland, cropland and fallow, represented the receptor area, while meadows that remained near the donor area were treated as reference areas. The soil moisture, compaction, reactivity and nutrient availability were examined. The microbial properties studied included taxon-specific markers for a quantitative PCR and Fatty Acid Analysis, N transformation (nitrification potential and ammonia oxygenase gene quantification), as well as the composition and diversity of bacteria, archaea, fungi and protists through soil DNA metabarcoding. The translocated soils were more compacted and had smaller water retention, which impacted the soil communities. A switch from N immobilisation to ammonification and a high diversity of fungi, including a greater richness of saprotrophic and symbiotrophic species occurred, with a higher relative abundance of Ascomycota. Amendments in Stramenopila, Chlorophyta and Alveolata communities were present. A low ratio of ammonia oxidising archaea and bacteria (AOA:AOB; 0.4 translocated vs. 4.9 reference) indicated a degradation of the wet meadow status, which created a suitable environment for copiotrophs. The initial increase in biodiversity pointed out habitat deterioration leading to the loss of specific, protected communities. The use of 'omics' was a sensitive indicator of changes that occurred at the level of the microbiome structure rather than the biomass.},
}

@article {pmid40378579,
year = {2025},
author = {Davison, A and Reimann, F and Gribble, FM},
title = {Molecular mechanisms of stimulus detection and secretion in enteroendocrine cells.},
journal = {Current opinion in neurobiology},
volume = {92},
number = {},
pages = {103045},
doi = {10.1016/j.conb.2025.103045},
pmid = {40378579},
issn = {1873-6882},
abstract = {Enteroendocrine cells (EECs) secrete over 20 different gut hormones in response to changes to the gut environment. They detect a range of nutritional stimuli through activation of a host of nutrient-sensing G-protein-coupled receptors and electrogenic nutrient cotransport. These activate intracellular signalling pathways which converge on membrane depolarisation and action potential generation, which elicit secretion. Emerging evidence has demonstrated that EECs also respond to non-nutritional stimuli, including mechanosensation, pH changes, and metabolites produced by the gut microbiome. EECs are polyhormonal cells, in which hormone expression is plastic and dependent on location in the gut. Hormones and small-molecule neurotransmitters secreted by EECs can activate extrinsic vagal afferents, modulating central processes such as appetite and food preference. While neuronal afferents are sometimes found in close proximity to EECs, the extent to which EEC/neuronal connections recapitulate traditional synaptic connections remains undefined.},
}

@article {pmid40378468,
year = {2025},
author = {Siddiquee, M and Cornelius, S and Seo, Y and Bullerjahn, GS and Bridgeman, TB and Sudman, M and Kang, DW},
title = {Uncovering microbial interactions in a persistent Planktothrix bloom: Towards early biomarker identification in hypereutrophic lakes.},
journal = {Water research},
volume = {283},
number = {},
pages = {123683},
doi = {10.1016/j.watres.2025.123683},
pmid = {40378468},
issn = {1879-2448},
abstract = {Cyanobacterial harmful algal blooms pose significant threats to global water supplies, ecosystems, and economies. Among the harmful cyanobacteria, Planktothrix, a resilient and toxin-producing filamentous cyanobacterium, has garnered increasing attention. However, an understanding of the entire microbiome, particularly the phycosphere surrounding Planktothrix blooms, remains largely unexplored. To the best of our knowledge, this is the first comprehensive study combining 16S rDNA and fungal internal transcribed spacer amplicon sequencing and shotgun metagenomics to elucidate Planktothrix bloom microbiomes and identify potential microbial or functional biomarkers for CyanoHABs. Our observations revealed that a summer bloom in Grand Lake St. Marys was initiated with Dolichospermum and then shifted to Planktothrix dominance. This transition was associated with nitrogen metabolism genes, suggesting that nitrogen plays a key role in bloom persistence through interactions among nitrogen-fixing bacteria, ammonia-oxidizing archaea, anammox bacteria, and denitrifiers. Additionally, metagenomic data revealed a strong positive correlation of toxin concentration with carbohydrate-nitrogen-sulfur-fatty acid associated metabolic pathways and a strong negative correlation with pollutant degradation pathways. Intriguingly, diazotrophic methane-related microbes were detected, which opens discussion on potential symbiosis that couples nitrogen and carbon metabolism. Toxin-degrading bacteria, such as Polynucleobacter and Acidovorax, were positively correlated with fungi like Vishniacozyma, proposing their cooperative roles during bloom events. Notably, Rhodobacter, a photosynthetic purple non-sulfur bacterium, showed strong negative correlations with both Planktothrix and the toxin-producing gene mcyE, positioning it as a promising biomarker for early bloom detection. Overall, this study advances the understanding of Planktothrix-dominated bloom ecology and highlights microbial signatures for proactive CyanoHAB management in freshwater systems.},
}

@article {pmid40378358,
year = {2025},
author = {Yau, R and Pavloudi, C and Zeng, Y and Saw, J and Eleftherianos, I},
title = {Infection with the entomopathogenic nematodes Steinernema alters the Drosophila melanogaster larval microbiome.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0323657},
pmid = {40378358},
issn = {1932-6203},
mesh = {Animals ; *Drosophila melanogaster/microbiology/parasitology ; Larva/microbiology/parasitology ; *Microbiota ; *Rhabditida/physiology ; Xenorhabdus ; },
abstract = {The fruit fly Drosophila melanogaster is a vital model for studying the microbiome due to the availability of genetic resources and procedures. To understand better the importance of microbial composition in shaping immune modulation, we can investigate the role of the microbiota through parasitic infection. For this, we use entomopathogenic nematodes (EPN) of the genus Steinernema which exhibit remarkable ability to efficiently infect a diverse array of insect species, facilitated by the mutualistic bacteria Xenorhabdus found within their gut. To examine the microbiome changes in D. melanogaster larvae in response to Steinernema nematode infection, D. melanogaster late second to early third instar larvae were exposed separately to S. carpocapsae and S. hermaphroditum infective juveniles. We have found that S. carpocapsae infective juveniles are more pathogenic to D. melanogaster larvae compared to the closely related S. hermaphroditum. Our microbiome analysis also indicates substantial changes in the size and composition of the D. melanogaster larval microbiome during infection with either nematode species compared to the uninfected controls. Our results serve as a foundation for future studies to elucidate the entomopathogenic-specific effector molecules that alter the D. melanogaster microbiome and understand the role of the microbiome in regulating insect anti-nematode immune processes.},
}

Animals
*Drosophila melanogaster/microbiology/parasitology
Larva/microbiology/parasitology
*Microbiota
*Rhabditida/physiology
Xenorhabdus

@article {pmid40378286,
year = {2025},
author = {Fields, BD and Pascal, DG and Rando, OK and Huddleston, ME and Ingram, K and Hopton, R and Grogg, MW and Nelson, MT and Voigt, CA},
title = {Design of a Continuous GAA-Producing Probiotic as a Potential Mitigator of the Effects of Sleep Deprivation.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.4c00690},
pmid = {40378286},
issn = {2161-5063},
abstract = {Creatine is a popular athletic supplement that has also been shown to improve cognitive performance upon sleep deprivation. However, it is rapidly cleared from the gastrointestinal tract a few hours after consumption. Toward providing a persistent creatine dose, we engineered the human probiotic Escherichia coli Nissle (EcN) to produce guanidinoacetic acid (GAA), which is converted to creatine in the liver. We find GAA-producing enzymes present in the human microbiome and compare their activities to known enzymes. Three copies of arginine:glycine amidinotransferase (AGAT) from Actinokineospora terrae are expressed from the genome, and native gcvP, argR, and argA are edited or deleted to improve substrate availability without negatively impacting cell viability. A standard EcN dose (10[12] cells) produces 41 ± 7 mg GAA per hour under laboratory conditions. This work demonstrates that a probiotic bacterium can be engineered to produce sustained GAA titers known to impact cognitive performance.},
}

@article {pmid40378154,
year = {2025},
author = {Goszcz, A and Furtak, K and Stasiuk, R and Wójtowicz, J and Musiałowski, M and Schiavon, M and Dębiec-Andrzejewska, K},
title = {Bacterial osmoprotectants - a way to survive in saline conditions and potential crop allies.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf020},
pmid = {40378154},
issn = {1574-6976},
abstract = {Soil salinization, affecting 6.5% of arable land, deteriorates soil properties, reduces microbiota activity, hinders plant growth, and accelerates soil erosion. Excessive salt induces physiological drought and toxicity stress in plants, causing chlorosis, ion imbalances, and enzyme disruptions. This paper discusses microorganisms' resistance mechanisms, plant responses to salt stress and summarizes current knowledge on bacterial osmoprotectants and their functions. It also reviews emerging agrobiotechnological strategies using microbial osmoprotectants to remediate salinized soils and enhance plant growth and productivity under salt stress. Osmoprotectants stabilize proteins, buffer redox potential, and retain water, thus alleviating osmotic stress and promoting bacteria and plants growth. Their application improves soil properties by enhancing aggregate formation, water permeability, moisture content, cation exchange capacity, and ion availability. Despite extensive literature on the function of osmoprotectants, the knowledge about their role in soil environments and agrobiotechnology applications remains limited. This paper indicates proposed research perspectives, including discovering new osmoprotectants, their correlation with soil fertilization, interactions with the soil microbiome, and plant responses. It also identifies significant knowledge gaps in these areas, highlighting the need for further studies to consolidate existing data and assess the potential of this approach to enhance soil health and crop productivity in saline environments.},
}

@article {pmid40377895,
year = {2025},
author = {Sharma, S and Kaur, I and Dubey, N and Goswami, N and Tanwar, SS},
title = {Berberine can be a Potential Therapeutic Agent in Treatment of Huntington's Disease: A Proposed Mechanistic Insight.},
journal = {Molecular neurobiology},
volume = {},
number = {},
pages = {},
pmid = {40377895},
issn = {1559-1182},
abstract = {Huntington's disease (HD) is a genetic neurodegenerative disorder caused by CAG repeat expansion in the HTT gene, producing mutant huntingtin (mHTT) protein. This leads to neuronal damage through protein aggregation, transcriptional dysregulation, excitotoxicity, and mitochondrial dysfunction. mHTT impairs protein clearance and alters gene expression, energy metabolism, and synaptic function. Therapeutic strategies include enhancing mHTT degradation, gene silencing via antisense oligonucleotides and RNAi, promoting neuroprotection through BDNF signaling, and modulating neurotransmitters like glutamate and dopamine. Berberine, a natural isoquinoline alkaloid, has emerged as a promising therapeutic option for HD due to its multifaceted neuroprotective properties. Research indicates that berberine can mitigate the progression of neurodegenerative diseases, including HD, by targeting various molecular pathways. It exhibits antioxidant, anti-inflammatory, and autophagy-enhancing effects, which are crucial in reducing neuronal damage and apoptosis associated with HD. These properties make berberine a potential candidate for therapeutic intervention in HD, as demonstrated in both cellular and animal models. Berberine activates the PI3K/Akt pathway, which is vital for cell survival and neuroprotection. It reduces oxidative stress and neuroinflammation, both of which are implicated in HD pathology. Berberine enhances autophagic processes, promoting the degradation of mutant huntingtin protein, a key pathological feature of HD. In transgenic HD mouse models, berberine administration has been shown to alleviate motor dysfunction and prolong survival. It effectively reduces the accumulation of mutant huntingtin in cultured cells, suggesting a direct impact on the disease's molecular underpinnings. Berberine's safety profile, established through its use in treating other conditions, supports its potential for clinical trials in HD patients. Its ability to modulate neurotransmitter levels and engage multiple signaling pathways further underscores its therapeutic promise. While berberine shows significant potential as a therapeutic agent for HD, further research is necessary to fully elucidate its mechanisms and optimize its clinical application. The current evidence in the review paper, primarily from preclinical studies, provides a strong foundation for future investigations into berberine's efficacy and safety in human HD patients.},
}

@article {pmid40377871,
year = {2025},
author = {Rahmati, R and Zarimeidani, F and Ghanbari Boroujeni, MR and Sadighbathi, S and Kashaniasl, Z and Saleh, M and Alipourfard, I},
title = {CRISPR-Assisted Probiotic and In Situ Engineering of Gut Microbiota: A Prospect to Modification of Metabolic Disorders.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40377871},
issn = {1867-1314},
abstract = {The gut microbiota, a substantial group of microorganisms residing in the human body, profoundly impacts various physiological and pathological mechanisms. Recent studies have elucidated the association between gut dysbiosis and multiple organ diseases. Gut microbiota plays a crucial role in maintaining gastrointestinal stability, regulating the immune system and metabolic processes not only within the gastrointestinal tract but also in other organs such as the brain, lungs, and skin. Dysbiosis of the gut microbiota can disrupt biological functioning and contribute to the development of metabolic disorders. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated proteins (Cas) modules are adaptive immune systems in numerous archaea and bacteria. CRISPR/Cas is a versatile gene-editing tool that enables modification of the genome in live cells, including those within the gut microbiota. This technique has revolutionized gene editing due to its simplicity and effectiveness. It finds extensive applications in diverse scientific arenas, facilitating the functional screening of genomes during various biological processes. Additionally, CRISPR has been instrumental in creating model organisms and cell lines for research purposes and holds great potential for developing personalized medical treatments through precise genetic alterations. This review aims to explore and discuss the possibilities of CRISPR/Cas and the current trends in using this technique for editing gut microbiota genes in various metabolic disorders. By uncovering the valuable potential of CRISPR/Cas in modifying metabolic disorders through the human gut microbiota, we shed light on its promising applications.},
}

@article {pmid40377870,
year = {2025},
author = {Amen, RA and Hassan, YM and Essmat, RA and Ahmed, RH and Azab, MM and Shehata, NR and Elgazzar, MM and El-Sayed, WM},
title = {Harnessing the Microbiome: CRISPR-Based Gene Editing and Antimicrobial Peptides in Combating Antibiotic Resistance and Cancer.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40377870},
issn = {1867-1314},
abstract = {The growing crisis of antibiotic resistance and the increasing incidence of cancer have prompted the exploration of innovative approaches, such as gene editing and antimicrobial peptides (AMPs). The human microbiome is integral to various aspects of health, disease, and therapeutic development, influencing metabolic pathways, immune function, and pathogen resistance. Recent advances in gene editing technologies, particularly CRISPR (clustered regularly interspaced short palindromic repeats), have opened new avenues for leveraging the microbiome to address complex medical challenges, including combating multidrug-resistant pathogens and cancer. The microbiome plays a crucial role in combating antibiotic resistance by modulating microbial communities, influencing pathogen survival and susceptibility to treatments. This review explores the microbiome's dynamic role in metabolic regulation, its contribution to cancer management, and how AMPs help maintain homeostasis and exhibit emerging anticancer properties, supported by both preclinical findings and clinical evidence. Additionally, CRISPR-based microbiome engineering offers potential to enhance host-microbiome interactions, optimizing therapeutic outcomes. The integration of microbiome metagenomics and proteomics has led to the discovery of novel AMPs with targeted anticancer effects. Innovative strategies, such as engineered probiotics and CRISPR-based microbiome engineering, present exciting prospects for next-generation therapies. Despite these advances, the translation of microbiome-based therapies into clinical settings remains challenging due to ethical, regulatory, and ecological hurdles. This review underscores the transformative potential of microbiome-based interventions, emphasizing the role of personalized medicine in maximizing therapeutic efficacy. Furthermore, we also address critical research gaps, limitations, and future directions, including optimizing AMP stability, delivery, and bioavailability, as well as overcoming the regulatory and ethical challenges in clinical translation.},
}

@article {pmid40377699,
year = {2025},
author = {Cobos-Uribe, C and Dhingra, R and Almond, MA and Alexis, NE and Peden, DB and Roach, J and Rebuli, ME},
title = {Human Sputum Microbiome Composition and Sputum Inflammatory Cell Profiles Are Altered with Controlled Wood Smoke Exposure as a Model for Wildfire Smoke.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
pmid = {40377699},
issn = {1535-4970},
abstract = {RATIONALE: Wood smoke exposure is increasing worldwide due to the rise in wildfire events. Various studies have associated exposure to wildfire-derived smoke with adverse respiratory conditions. However, the mechanism by which this occurs is unknown. Previous studies using wood smoke as a model of wildfire smoke have focused on the respiratory immune response and have reported increased neutrophil percentage and cytokine production in airway samples. The effect of wood smoke on the respiratory microbiome, however, has not been examined.

METHODS: Healthy volunteers (N=54) were subjected to controlled wood smoke exposure (500 µg/m3) for two hours, and induced sputum samples were collected and processed for microbiome analysis, immune mediators, and cell differentials at baseline, six- and 24-hours post-exposure. A negative binomial mixed model analysis examined associations between microbiome components and inflammatory cells in sputum.

MAIN RESULTS: Following wood smoke exposure, while sputum microbiome diversity remained unchanged, the microbiome composition was altered, particularly the abundance of several low-abundance bacteria, including Fretibacterium and Selenomonas, indicating that this inhalational exposure can alter the composition of the sputum microbiome. Additionally, a significant decrease in macrophage cells was observed at 24 hours without a significant change in neutrophils. We further found small but significant associations between different taxa and macrophages (per mg of sputum), including a negative association with Fretibacterium.

CONCLUSIONS: Together, these findings demonstrate that inhalational wood smoke exposure can modify several low-abundance bacteria within the respiratory microbiome and that these changes are associated with sputum inflammatory cell alterations, providing insights for future studies to focus on respiratory innate immune host-microbiome crosstalk in the context of environmental exposures.},
}

@article {pmid40377649,
year = {2025},
author = {Turov F, O and Yatsyk S, P and Krapivkin A, I and Vrublevsky S, G and Mamedov I, S and Perevezentsev O, A},
title = {[Current understanding of the urinary tract microbiome in children].},
journal = {Urologiia (Moscow, Russia : 1999)},
volume = {},
number = {1},
pages = {141-147},
pmid = {40377649},
issn = {1728-2985},
mesh = {Humans ; *Microbiota ; *Urinary Tract Infections/microbiology/drug therapy/diagnosis ; Child ; *Urinary Tract/microbiology ; Female ; Male ; },
abstract = {INTRODUCTION: The second most common reason for prescribing antibiotics in children is urinary tract infection (UTI). Since antimicrobial stewardship is a priority in the further development of strategies of the treatment of children with UTIs, the need to form an optimal model for its diagnosis and treatment is relevant in pediatric urology.

AIM: To analyze domestic and foreign publications devoted to the study of the urinary tract microbiome in children.

RESULTS: Cultivation or culturing methods continue to be considered the "gold standard" in many countries for the diagnosis of bacterial infections, although more sensitive and specific technologies are available. A urine sample was previously considered sterile if uropathogens did not grow using standard techniques. It remains unclear whether standard microbial culturing methods are adequate to determine species diversity and identify all microorganisms capable of causing UTIs. A study of the bladder microbiome and maintenance of its homeostasis to prevent inflammatory lower urinary tract diseases is an emerging area of research. It is known that the bladder of a healthy person contains non-uropathogenic bacteria, such as Lactobacillus, which are believed to function as an immune system and protect against the effects of uropathogens.},
}

Humans
*Microbiota
*Urinary Tract Infections/microbiology/drug therapy/diagnosis
Child
*Urinary Tract/microbiology
Female
Male

@article {pmid40377635,
year = {2025},
author = {Faniev M, V and Kadyrov Z, A and Druzhinina N, K and Stepanov V, S and Prokopiev Ya, V and Fedorenko T, V and Markelova M, I and Khusnutdinova D, R and Grigorieva T, V},
title = {[Characterization of the taxonomic structure of testicular and urethral microbiota in men with non-obstructive azoospermia with different outcomes in ART protocols].},
journal = {Urologiia (Moscow, Russia : 1999)},
volume = {},
number = {1},
pages = {47-53},
pmid = {40377635},
issn = {1728-2985},
mesh = {Humans ; Male ; *Azoospermia/microbiology/therapy ; *Microbiota ; Adult ; *Testis/microbiology ; *Urethra/microbiology ; Retrospective Studies ; *Bacteria/classification/genetics/isolation & purification ; *Reproductive Techniques, Assisted ; RNA, Ribosomal, 16S/genetics ; },
abstract = {AIM: To carry out a comparative analysis of the taxonomic structure of the testicular and urethral microbiota of patients with non-obstructive azoospermia (NOA) in ART protocols with positive (live birth) and negative outcomes.

MATERIALS AND METHODS: The samples of testicular tissue and urethra of infertile patients with NOA (n=62) were evaluated. To realize the reproductive potential, all patients underwent micro-TESE in the ART protocol. All patients were retrospectively divided into two groups. In group 1, there were patients with NOA and a positive ART result (n=16), while in group 2 patients had NOA and a negative ART result (n=46). To study the bacterial diversity of testicular tissue, an analysis of amplicons of the bacterial 16S rRNA gene was performed using high-throughput NGS.

RESULTS: A comparative analysis of the relative representation of bacterial taxa in the testicular tissue of patients with NOA with positive and negative ART outcomes revealed a number of significant differences. For example, significant differences (p<0.05) were found in the relative representation of the phylum Fusobacteriota, the Pasteurellaceae, Dialisteraceae, Porphyromonadaceae, Alcanivoracaceae, Neisseriaceae_563222, Ruminococcaceae, Acutalibacteraceae, Peptostreptococcaceae_256921, Marinilabiliaceae, Exiguobacteraceae, Coprobacillaceae, Bacillaceae_H_289398, Burkholderiaceae_A_595427 in patients of group 1. Significant differences (p<0.05) were also found in the frequency of occurrence of the phylum Fusobacteriota, the families Lactobacillaceae, Pasteurellaceae, Alcanivoracaceae, Acutalibacteraceae, Peptostreptococcaceae_256921, Exiguobacteraceae, Coprobacillaceae, Bacillaceae_H_289398, Burkholderiaceae_A_595427 in patients with positive ART outcomes. When analyzing the urethral microbiome using high-throughput sequencing, no significant differences in alpha-diversity indices were shown. We also found significant differences (p<0.05) in the frequency of occurrence of the Streptococcaceae family, and they were more common in patients with negative ART outcomes. Meanwhile, representatives of the Enterococcaceae and Brevibacteriaceae families were more common in patients with positive ART outcomes.

CONCLUSIONS: It is obvious that changes in the microbiota of the genital tract have a specific effect on the reproductive system, and correction of abnormal microbiomes can improve reproductive outcomes.},
}

Humans
Male
*Azoospermia/microbiology/therapy
*Microbiota
Adult
*Testis/microbiology
*Urethra/microbiology
Retrospective Studies
*Bacteria/classification/genetics/isolation & purification
*Reproductive Techniques, Assisted
RNA, Ribosomal, 16S/genetics

@article {pmid40377498,
year = {2025},
author = {Angendohr, C and Koppe, C and Herebian, D and Schneider, AT and Keysberg, L and Singer, MT and Gilljam, J and Dille, MA and Bode, JG and Doll, S and Conrad, M and Vucur, M and Luedde, T},
title = {The ferroptosis mediator ACSL4 fails to prevent disease progression in mouse models of MASLD.},
journal = {Hepatology communications},
volume = {9},
number = {6},
pages = {},
doi = {10.1097/HC9.0000000000000684},
pmid = {40377498},
issn = {2471-254X},
mesh = {Animals ; *Ferroptosis/genetics ; *Coenzyme A Ligases/genetics/metabolism ; Disease Progression ; Mice ; Disease Models, Animal ; Mice, Knockout ; Diet, High-Fat/adverse effects ; *Fatty Liver/metabolism/etiology ; Male ; Liver/metabolism/pathology ; Mice, Inbred C57BL ; Long-Chain-Fatty-Acid-CoA Ligase ; Metabolic Syndrome ; },
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is an increasingly prevalent condition and a major risk factor for chronic liver damage, potentially leading to steatohepatitis and HCC. It is already known that patients with MASLD show increased systemic and hepatic iron concentrations as well as perturbed lipid metabolism, suggesting the involvement of ferroptosis in the development and progression of MASLD. Consequently, inhibition of ferroptosis represents a potential therapeutic option for patients with MASLD.

METHODS: We investigated whether liver parenchymal cell-specific deletion (LPC-KO) of the pro-ferroptotic gene acyl-CoA synthetase long-chain family member 4 (ACSL4LPC-KO) reduces MASLD onset and progression in mice. ACSL4LPC-KO and wild-type littermates were fed a choline-deficient high-fat diet (CD-HFD) or a Western diet for 20 weeks (CD-HFD and Western diet) or 40 weeks (CD-HFD only) to monitor MASLD progression and metabolic syndrome development.

RESULTS: In contrast to the recently published studies by Duan et al, our results show no significant differences between ACSL4LPC-KO and wild-type mice with regard to the development of MASLD or the progression of metabolic syndrome. Furthermore, no differences were observed in metabolic parameters (ie, weight gain, glucose tolerance test, hepatic steatosis) or MASLD-associated inflammatory response.

CONCLUSIONS: Our analyses, therefore, suggest that loss of ACSL4 has no effect on the progression of MASLD induced by CD-HFD or the Western diet. The discrepancy between our and previously published results could be due to differences in the diets or the influence of a distinct microbiome, so the results obtained with hepatocyte-specific ACSL4LPC-KO should be taken with caution.},
}

Animals
*Ferroptosis/genetics
*Coenzyme A Ligases/genetics/metabolism
Disease Progression
Mice
Disease Models, Animal
Mice, Knockout
Diet, High-Fat/adverse effects
*Fatty Liver/metabolism/etiology
Male
Liver/metabolism/pathology
Mice, Inbred C57BL
Long-Chain-Fatty-Acid-CoA Ligase
Metabolic Syndrome

@article {pmid40377331,
year = {2025},
author = {Heil, JA and Bernardin, JR and Galla, SJ and Bittleston, LS},
title = {A framework for utilizing leaf-associated microbes to achieve conservation and restoration goals.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0108224},
doi = {10.1128/msphere.01082-24},
pmid = {40377331},
issn = {2379-5042},
abstract = {Plant-associated microbiomes have profound effects on ecosystem functioning and play a role in the success of plants at both small and large scales. As key components of healthy plants and ecosystems, plant microbiomes should be considered in conservation and ecosystem management strategies. Many knowledge gaps and logistical barriers exist that increase the difficulty of employing microbes in conservation; however, some success has been achieved by manipulating the root microbiome and in agricultural contexts. In contrast with the root microbiome, the role of the leaf microbiome in conservation remains largely unexplored. In this perspective, we posit that the leaf microbiome plays an essential role in plant and ecosystem health and should be considered in conservation strategies. We include a framework for approaching leaf microbiome management, including identification of sources of disturbance, identifying mechanisms to address resulting plant stress, types of microbial inoculation to achieve desired outcomes, and co-producing plans of management with interest groups and rights holders.},
}

@article {pmid40377302,
year = {2025},
author = {Jourdain, L and Gu, W},
title = {Designing synthetic microbial communities for enhanced anaerobic waste treatment.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0040425},
doi = {10.1128/aem.00404-25},
pmid = {40377302},
issn = {1098-5336},
abstract = {Synthetic microbial communities (SynComs) are powerful tools for investigating microbial interactions and community assembly by focusing on minimal yet functionally representative members. Here, we will highlight key principles for designing SynComs, specifically emphasizing the anaerobic digestion (AD) microbiome for waste treatment and upcycling. The AD process has traditionally been used to reduce organic waste volume while producing biogas as a renewable energy source. Its microbiome features well-defined trophic layers and metabolic groups. There has been growing interest in repurposing the AD process to produce value-added products and chemical precursors, contributing to sustainable waste management and the goals of a circular economy. Optimizing the AD process requires a better understanding of microbial interactions and the influence of both biotic and abiotic parameters, where SynComs offer great promise. Focusing on AD microbiomes, we review the principles of SynComs' design, including keystone taxa and function, cross-feeding interactions, and metabolic redundancy, as well as how modeling approaches could guide SynComs design. Furthermore, we address practical considerations for working with AD SynComs and examine constructed SynComs designed for anaerobic waste digestion. Finally, we discuss the challenges associated with designing and applying SynComs to enhance our understanding of the AD process. This review aims to explore the use of synthetic communities in studying anaerobic digestion and highlights their potential for developing innovative biotechnological processes.},
}

@article {pmid40377187,
year = {2025},
author = {Veseli, I and Chen, YT and Schechter, MS and Vanni, C and Fogarty, EC and Watson, AR and Jabri, B and Blekhman, R and Willis, AD and Yu, MK and Fernàndez-Guerra, A and Füssel, J and Eren, AM},
title = {Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.89862},
pmid = {40377187},
issn = {2050-084X},
support = {1746045//National Science Foundation Graduate Research Fellowship Program/ ; R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM128716/NH/NIH HHS/United States ; RC2 DK122394/NH/NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Stress, Physiological ; Metagenome ; *Bacteria/metabolism/genetics/classification ; },
abstract = {A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health vs IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.},
}

Humans
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/microbiology
*Stress, Physiological
Metagenome
*Bacteria/metabolism/genetics/classification

@article {pmid40376856,
year = {2025},
author = {Takyi, E and Nirmalkar, K and Adams, J and Krajmalnik-Brown, R},
title = {Interventions targeting the gut microbiota and their possible effect on gastrointestinal and neurobehavioral symptoms in autism spectrum disorder.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2499580},
doi = {10.1080/19490976.2025.2499580},
pmid = {40376856},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Autism Spectrum Disorder/therapy/microbiology ; Probiotics/therapeutic use/administration & dosage ; Fecal Microbiota Transplantation ; Prebiotics/administration & dosage ; *Gastrointestinal Diseases/therapy/microbiology ; Gastrointestinal Tract/microbiology ; Child ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Autism spectrum disorder (ASD) is a developmental disorder that is characterized by deficits in social communication and restricted, repetitive, and stereotyped behaviors. In addition to neurobehavioral symptoms, children with ASD often have gastrointestinal symptoms (e.g. constipation, diarrhea, gas, abdominal pain, reflux). Several studies have proposed the role of gut microbiota and metabolic disorders in gastrointestinal symptoms and neurodevelopmental dysfunction in ASD patients; these results offer promising avenues for novel treatments of this disorder. Interventions targeting the gut microbiota - such as fecal microbiota transplant (FMT), microbiota transplant therapy (MTT), probiotics, prebiotics, synbiotics, antibiotics, antifungals, and diet - promise to improve gut health and can potentially improve neurological symptoms. The modulation of the gut microbiota using MTT in ASD has shown beneficial and long-term effects on GI symptoms and core symptoms of autism. Also, the modulation of the gut microbiota to resemble that of typically developing individuals seems to be the most promising intervention. As most of the studies carried out with MTT are open-label studies, more extensive double-blinded randomized control trials are needed to confirm the efficacy of MTT as a therapeutic option for ASD. This review examines the current clinical research evidence for the use of interventions that target the microbiome - such as antibiotics, antifungals, probiotics/prebiotics, synbiotics, and MTT - and their effectiveness in changing the gut microbiota and improving gastrointestinal and neurobehavioral symptoms in ASD.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Autism Spectrum Disorder/therapy/microbiology
Probiotics/therapeutic use/administration & dosage
Fecal Microbiota Transplantation
Prebiotics/administration & dosage
*Gastrointestinal Diseases/therapy/microbiology
Gastrointestinal Tract/microbiology
Child
Anti-Bacterial Agents/therapeutic use

@article {pmid40376801,
year = {2025},
author = {Prisco, SZ and Blake, M and Kazmirczak, F and Moon, R and Kremer, BP and Hartweck, LM and Kim, M and Vogel, N and Mendelson, JB and Moutsoglou, D and Thenappan, T and Prins, KW},
title = {Lactobacillus Restructures the Micro/Mycobiome to Combat Inflammation-Mediated Right Ventricular Dysfunction in Pulmonary Arterial Hypertension.},
journal = {Circulation. Heart failure},
volume = {},
number = {},
pages = {e012524},
doi = {10.1161/CIRCHEARTFAILURE.124.012524},
pmid = {40376801},
issn = {1941-3297},
abstract = {BACKGROUND: Inflammation suppresses right ventricular (RV) function in pulmonary arterial hypertension (PAH). In particular, we showed GP130 (glycoprotein-130) signaling promotes pathological microtubule remodeling and RV dysfunction in rodent PAH. Emerging data demonstrate the intestinal microbiome regulates systemic inflammation, but the impact of modulating the gut microbiome on the GP130-microtubule axis in RV failure is unknown.

METHODS: Two weeks following monocrotaline injection, rats were administered daily Lactobacillus rhamnosus (4×10[7] colony-forming units) via oral gavage for 10 days. Next-generation metagenomics and internal transcribed spacer 2 sequencing delineated fecal bacterial and fungal compositions. SomaScan proteomics measured levels of 7596 serum proteins. RV immunoblots quantified protein abundances. Light or super resolution confocal microscopy assessed RV, lung, and jejunal morphology. Echocardiography and invasive closed-chest pressure-volume loops evaluated PAH severity and RV function. The relationship between Lactobacillus abundance and RV function was assessed in 65 patients with PAH.

RESULTS: Lactobacillus administration restructured both the intestinal micro- and mycobiome. The alteration in the gut ecosystem improved intestinal health as demonstrated by increased jejunal villus length and glycocalyx thickness and diminished intestinal permeability biomarkers. Serum proteomics revealed Lactobacillus modulated systemic inflammation and decreased circulating GP130 ligands. Lactobacillus-mediated suppression of GP130 signaling blunted pathological microtubule remodeling in RV cardiomyocytes. Microtubule-associated phenotypes, including RV cardiomyocyte and nuclear hypertrophy, transverse tubule integrity, and connexin-43 localization, were all corrected with Lactobacillus. These cellular changes manifested as improved RV function despite no significant alteration in PAH severity. Finally, patients with PAH and detectable fecal Lactobacillus had superior RV function despite similar mean pulmonary arterial pressure and pulmonary vascular resistance as compared with those without detectable Lactobacillus.

CONCLUSIONS: Lactobacillus supplementation restructures the gut micro/mycobiome, restores intestinal health, dampens systemic inflammation, and reduces GP130 ligands and associated RV cardiomyocyte microtubule remodeling. These data identify a novel microbiome-inflammation-microtubule axis that has therapeutic relevance for RV dysfunction.},
}

@article {pmid40376566,
year = {2025},
author = {},
title = {Correction to "Gut Microbiome and Metabolome Changes in Chronic Low Back Pain Patients With Vertebral Bone Marrow Lesions".},
journal = {JOR spine},
volume = {8},
number = {2},
pages = {e70074},
doi = {10.1002/jsp2.70074},
pmid = {40376566},
issn = {2572-1143},
abstract = {[This corrects the article DOI: 10.1002/jsp2.70042.].},
}

@article {pmid40376006,
year = {2025},
author = {Ma, J and Fang, Y and Li, S and Zeng, L and Chen, S and Li, Z and Ji, G and Yang, X and Wu, W},
title = {Interpretable machine learning algorithms reveal gut microbiome features associated with atopic dermatitis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1528046},
pmid = {40376006},
issn = {1664-3224},
mesh = {*Dermatitis, Atopic/microbiology/diagnosis ; Humans ; *Gastrointestinal Microbiome ; *Machine Learning ; RNA, Ribosomal, 16S/genetics ; Algorithms ; Support Vector Machine ; },
abstract = {BACKGROUND: The "gut-skin axis" has been proposed to play an important role in the development and symptoms of atopic dermatitis. Therefore, we have constructed an interpretable machine learning framework to quantitatively screen key gut flora.

METHODS: The 16S rRNA dataset, after applying the centered log-ratio transformation, was analyzed using five different machine learning models: random forest, light gradient boosting machine, extreme gradient boosting, support vector machine with radial kernel, and logistic regression. Interpretable machine learning methods, such as SHAP values, were used to identify significant features associated with atopic dermatitis.

RESULTS: Random forest performed better than the other "tree" models in the validation partitions. The SHAP global dependency plot indicated that Bifidobacterium ranked as the strongest predictive factor across all prediction horizons, although the SHAP values for some features were still higher in support vector machine and logistic regression models. The SHAP partial dependency plot for "tree" models showed that the best segmentation point for Bifidobacterium was further from the origin compared to other features in the respective models, quantitatively reflecting differences in gut microbiota.

CONCLUSION: Machine learning models combined with SHAP could be used to quantitatively screen key gut flora in atopic dermatitis patients, providing doctors with an intuitive understanding of 16S rRNA sequencing data to support precision medicine in care and recovery.},
}

*Dermatitis, Atopic/microbiology/diagnosis
Humans
*Gastrointestinal Microbiome
*Machine Learning
RNA, Ribosomal, 16S/genetics
Algorithms
Support Vector Machine

@article {pmid40375898,
year = {2025},
author = {Xu, C and Zhao, LY and Ye, CS and Xu, KC and Xu, KY},
title = {The application of machine learning in clinical microbiology and infectious diseases.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1545646},
pmid = {40375898},
issn = {2235-2988},
mesh = {Humans ; *Machine Learning ; *Communicable Diseases/diagnosis/microbiology ; *Microbiology ; Artificial Intelligence ; Algorithms ; },
abstract = {With the development of artificial intelligence(AI) in computer science and statistics, it has been further applied to the medical field. These applications include the management of infectious diseases, in which machine learning has created inroads in clinical microbiology, radiology, genomics, and the analysis of electronic health record data. Especially, the role of machine learning in microbiology has gradually become prominent, and it is used in etiological diagnosis, prediction of antibiotic resistance, association between human microbiome characteristics and complex host diseases, prognosis judgment, and prevention and control of infectious diseases. Machine learning in the field of microbiology mainly adopts supervised learning and unsupervised learning, involving algorithms from classification and regression to clustering and dimensionality reduction. This Review explains crucial concepts in machine learning for unfamiliar readers, describes machine learning's current applications in clinical microbiology and infectious diseases, and summarizes important approaches clinicians must be aware of when evaluating research using machine learning.},
}

Humans
*Machine Learning
*Communicable Diseases/diagnosis/microbiology
*Microbiology
Artificial Intelligence
Algorithms

@article {pmid40375894,
year = {2025},
author = {Li, Q and Zhang, Y and Wang, X and Dai, L and Zhao, W},
title = {Gut microbiota of patients with post-stroke depression in Chinese population: a systematic review and meta-analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1444793},
pmid = {40375894},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Stroke/complications/microbiology ; *Depression/microbiology/etiology ; China/epidemiology ; *Bacteria/classification/genetics/isolation & purification ; Asian People ; East Asian People ; },
abstract = {BACKGROUND: Evidence of changes in the composition and function of the gut microbiota (GM) in post-stroke depression (PSD) patients is gradually accumulating. This study aimed to systematically evaluate the relationship between PSD and GM.

METHODS: We searched in PubMed, Web of Science, Embase, Cochrane databases, Wangfang, VIP, CBM, and CNKI from the establishment of the database to April 17, 2024, and systematic review and meta-analysis were performed to investigate the differences of GM between patients with PSD spectrum and healthy controls (HC) or stroke spectrum.

RESULT: There were 14 studies consisting a total of 1,556 individuals included in the meta-analysis. The pooled results showed that PSD spectrum demonstrated significantly increased α diversity as indexed by Chao1 index, ACE indexes, Shannon index, and Simpson index as compared to HC. Additionally, stroke spectrum significantly increased α diversity as indexed by Simpson index compared to PSD. Furthermore, the pooled estimation of relative abundance showed that Bacteroidota, Fusobacteriota, and Pseudomonadota in PSD patients were significantly higher than those in the HC group, while the abundance of Bacillota was higher in the HC group. Moreover, significant differences in GM were observed between PSD patients and HC at the family and genus levels.

CONCLUSION: This study found that the α diversity of PSD patients was higher than that of HC. Moreover, there were also differences in the distribution of GM at the phylum, family, and genus levels, respectively. At the same time, the level of Lachnospira in PSD patients was lower than that in the stroke group.

https://www.crd.york.ac.uk/PROSPERO/, identifier CRD42024582708.},
}

Humans
*Gastrointestinal Microbiome
*Stroke/complications/microbiology
*Depression/microbiology/etiology
China/epidemiology
*Bacteria/classification/genetics/isolation & purification
Asian People
East Asian People

@article {pmid40375709,
year = {2025},
author = {Kumar, A and Bawa, Y and Pramanik, J and Batta, K and Prajapati, B and Mehra, R and Menkinoska, M and Petkoska, AT},
title = {Unveiling the Role and Mechanism of Mycoprotein for Reducing Cardiovascular Risk.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010347951250416140136},
pmid = {40375709},
issn = {1873-4316},
abstract = {Cardiovascular diseases (CVDs) have the highest mortality rates worldwide. To reduce the risk of CVDs, dietary interventions are a potential approach. This review explores the potential of mycoprotein, a fungal-derived protein, as a dietary approach for maintaining cardiovascular health. A comprehensive literature search was conducted using various databases (Web of Science, Medline, Scopus, Google Scholar, EBSCO, PubMed) and government websites (WHO, CDC) to identify relevant studies. Mycoprotein provides essential amino acids with high bioavailability (0.996) while containing minimal saturated fat (1.5 grams) and high fiber (6 grams). Clinical studies have shown that mycoprotein consumption reduces cholesterol, improves lipid profiles, and potentially lowers blood pressure, possibly due to its impact on gut microbiota (GM) and short-chain fatty acids (SCFAs) production. The intestinal fermentation of mycoprotein fiber increases the abundance of beneficial gut bacteria, binds to Gprotein coupled receptors like GPR41 and 43 to promote vasodilation, inhibits the angiotensinconverting enzyme, and reduces hepatic cholesterol production. Chitin and beta-glucan, the primary fiber of mycoprotein, exhibit anti-inflammatory properties that may contribute to overall cardiovascular health. The study concludes that mycoprotein is a sustainable and nutritious alternative, and its consumption promotes cardiovascular health and reduces CVD risks.},
}

@article {pmid40375701,
year = {2025},
author = {Tiwari, R and Tiwari, G and Singh, A and Dhas, N},
title = {Pharmacological Foundation and Novel Insights of Resveratrol in Cardiovascular System: A Review.},
journal = {Current cardiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.2174/011573403X343252250502045328},
pmid = {40375701},
issn = {1875-6557},
abstract = {Research into drugs that can enhance cardiovascular health has been sparked by the rising prevalence of cardiovascular illnesses (CVDs). In addition to its anti-inflammatory and antioxidant qualities, Resveratrol (RES) is well known for its capacity to increase endothelial NO synthase (eNOS) activity. This page summarises RES's wide effects on energy metabolism, resilience to stress, exercise mimicking, circadian rhythm, lifespan control, and microbiome composition. This article addresses the poor and contradictory results shown in preclinical and clinical trials provides an update on the cardiovascular preventive properties of RES. The activation of AMP-activated protein kinase (AMPK), silent information regulator 1 (SIRT1), and natural antioxidant enzymes is associated with some of the positive effects of RES on the cardiovascular system. A microarray data summary indicates a strong correlation between the heart's reaction to calorie restriction and the transcriptional responses to RES. RES has been demonstrated to reduce contractile dysfunction, cardiac remodelling, and hypertrophy in several animal models of heart failure. Its preventive properties are believed to be due to several molecular pathways, including the suppression of prohypertrophic signalling molecules, enhancement of cardiac Ca2+ handling, control of autophagy, and decreases in inflammation. RES thus has the potential to be used in several novel therapeutic approaches for treating diseases such as atherosclerosis, ischemia/reperfusion damage, metabolic syndrome, heart failure, and inflammatory changes associated with ageing.},
}

@article {pmid40375477,
year = {2025},
author = {Hagel, JM and Chang, L and Li, J and Chen, X and Yu, L and Gallant, JA and Facchini, PJ},
title = {Bioproduction of a Large-Scale Library of Tryptamine Derivatives for Neuropsychiatric Drug Screening.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.4c00857},
pmid = {40375477},
issn = {1554-8937},
abstract = {Drug screening programs targeting novel indolethylamines with pharmacological properties suitable for the treatment of psychiatric and central nervous system disorders benefit from the availability of large compound libraries normally prepared using synthetic chemistry. Bioproduction strategies based on microbial metabolic engineering and fermentation generally fail to achieve the throughput, scale, or versatility of synthetic chemistry owing, in part, to a lack of efficient and promiscuous enzymes. Moreover, synthetic biology rarely extends to the purification of targeted products, which is an essential component of synthetic chemistry and drug screening regimes. A lattice of biosynthetic routes beginning with endogenous tryptophan or exogenous indole derivatives were engineered in Escherichia coli using heterologous genes encoding enzymes sourced from plants, mushrooms, microbes and animals. Twelve tryptophan decarboxylase candidates were screened and highly versatile top-performers from Bacillus atrophaeus and the gut microbiome species Clostridium sporogenes were identified. Seven halogenases, three tryptophan synthase β-subunits, six N-methyltransferases, five regioselective prenyltransferases, a cytochrome P450 oxidoreductase 5-hydroxylase, an N-acetyltransferase, a 4-O-kinase and various accessory proteins were also tested. These enzymes were used in various combinations and permutations to build E. coli strains capable of 344 putative biotransformations, which resulted in the formation of 279 products with only 63 targeted compounds not detected. A set of 17 novel N-acetylated derivatives were selected for upscaled culturing and purification to ≥95% from 0.5 to 1 L of the fermentation broth, which yielded ∼6-80 mg of each molecule. The potential of each compound for bioactivity at 14 different receptors or transporters with established or purported involvement in neuropsychiatric diseases was tested using a single ligand concentration. Nearly all the N-acetylated compounds showed interaction with the melatonin (MT1) receptor, and several molecules showed interaction with serotonergic receptors 5-HT2B, 5-HT2C, and 5-HT7. Overall, we show that bio-fermentation is useful in the large-scale screening of molecules with potential in drug development.},
}

@article {pmid40375452,
year = {2025},
author = {Hutchings, B and López-Legentil, S and Stefaniak, L and Nydam, M and Erwin, PM},
title = {Microbial Distortion? Impacts of Delayed Preservation on Microbiome Diversity and Composition in a Marine Invertebrate.},
journal = {MicrobiologyOpen},
volume = {14},
number = {2},
pages = {e70019},
doi = {10.1002/mbo3.70019},
pmid = {40375452},
issn = {2045-8827},
support = {//This research was supported by the Ruth D. Turner Foundation and National Science Foundation (DEB-2122475)./ ; },
mesh = {Animals ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Urochordata/microbiology ; *Preservation, Biological/methods ; Biodiversity ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; Belize ; Time Factors ; DNA, Ribosomal/genetics/chemistry ; Phylogeny ; },
abstract = {Field collections of marine invertebrates are often accompanied by delays in preservation, which may impact microbiome composition. Here, we tested the effects of delayed preservation and relaxation methods on microbiome diversity and composition in the colonial ascidian Trididemnum solidum using 16S rRNA amplicon sequencing. Replicate samples collected from Belizean reefs were either (1) immediately preserved in ethanol ("control"), (2) held in ambient seawater for 3 h before preservation ("SW"), or (3) held in ambient seawater with menthol (a common pre-preservation relaxation technique for ascidian identification) for 3 h before preservation ("SW + M"). All T. solidum microbiomes were different from ambient seawater bacterioplankton and dominated by the same microbial taxa, including the genera Thalassobaculum, Tistrella, and Synechocystis. However, the 3-h delay in sample preservation (SW) significantly reduced microbiome richness compared to controls (p = 0.028), while menthol treatment (SW + M) mitigated this diversity loss (p = 0.208). Microbial composition at the community level did not differ significantly for either delayed preservation method compared to controls (SW p = 0.054, SW + M p = 0.052). Taxon-level shifts were rare but did occur, most notably a bloom of the facultatively anaerobic gammaproteobacterium Catenococcus that was 37x (SW) and 197x (SW + M) more abundant in delayed preservations. After a 3-h preservation delay (SW), only 122 microbial taxa (1.85% of total) exhibited significantly differential abundances with controls, with menthol treatment (SW + M) reducing taxon-level shifts to 65 taxa (0.98%). Our results showed that brief delays in preservation did not significantly alter community-level microbiome composition and dominant taxa, with menthol exposure counteracting minor microbiome shifts associated with preservation delays.},
}

Animals
*Microbiota
RNA, Ribosomal, 16S/genetics
Seawater/microbiology
*Bacteria/classification/genetics/isolation & purification
*Urochordata/microbiology
*Preservation, Biological/methods
Biodiversity
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA
Belize
Time Factors
DNA, Ribosomal/genetics/chemistry
Phylogeny

@article {pmid40375390,
year = {2025},
author = {Mauvais, FX and van Endert, PM},
title = {Type 1 Diabetes: A Guide to Autoimmune Mechanisms for Clinicians.},
journal = {Diabetes, obesity & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.16460},
pmid = {40375390},
issn = {1463-1326},
abstract = {Type 1 diabetes (T1D) results from the destruction of pancreatic beta cells by autoreactive T lymphocytes, leading to insulin deficiency and lifelong insulin dependence. It develops in genetically predisposed individuals, triggered by environmental or immunological factors. Although the exact causes of T1D remain unknown, the autoimmune pathogenesis of the disease is clearly indicated by the genetic risk conferred by allelic human leukocyte antigens (HLA), the almost obligatory presence of islet cell autoantibodies (AAbs) and immune cell infiltration of pancreatic islets from patients. At the same time, epidemiological data point to a role of environmental factors, notably enteroviral infections, in the disease, although precise causative links between specific pathogens and T1D have been difficult to establish. Studies of human pancreas organs from patients made available through repositories and the advent of high-dimensional high-throughput technologies for genomic and proteomic studies have significantly elucidated our understanding of the disease in recent years and provided mechanistic insights that can be exploited for innovative targeted therapeutic approaches. This short overview will summarise current salient knowledge on immune cell and beta cell dysfunction in T1D pathogenesis. PLAIN LANGUAGE SUMMARY: Type 1 diabetes (T1D) is a chronic disease where the body's own immune system attacks and destroys the insulin-producing beta cells in the pancreas. This leads to a lack of insulin, a hormone essential for regulating blood sugar, which means people with T1D need insulin for life. The disease can develop at any age but is most diagnosed in children and young adults. Despite advances in treatment, T1D still significantly reduces life expectancy, especially in countries with fewer healthcare resources. T1D develops in people with a genetic predisposition, often triggered by environmental factors such as viral infections or changes in the gut microbiome. The disease progresses silently through three stages: Stage 1: Autoantibodies to beta cell components appear, signalling the immune system is reacting against the pancreas, but there are no symptoms; Stage 2: Beta cell function starts to decline, but fasting blood sugar is still normal; Stage 3: Enough beta cells are destroyed that fasting blood sugar rises, and symptoms of diabetes appear. The risk of progressing from stage 1 to full-blown diabetes is about 35-50% within five years, and even higher from stage 2. Over 60 genes are linked to T1D risk, most of which affect how the immune system works. The strongest genetic risk comes from specific versions of histocompatibility genes, which help the immune system distinguish between the body's own cells and invaders. Some types of these genes make it easier for the immune system to mistakenly attack beta cells. However, 90% of people diagnosed with T1D have no family member with T1D, showing that genetics is only part of the story. Environmental factors also play a big role. For example, certain viral infections, especially with viruses infecting the intestine, are associated with a higher risk of developing T1D. The gut microbiome - the community of bacteria living in our intestines - also influences risk, with healthier, more diverse microbiomes appearing to offer some protection. In T1D, immune cells - especially so-called T lymphocytes - mistake beta cells in the pancreas for threats and destroy them. This process is called autoimmunity. The attack is often reflected by the presence of autoantibodies against proteins found in beta cells. Over time, as more beta cells are lost, the body can no longer produce enough insulin, leading to the symptoms of diabetes. Interestingly, not all people with T1D have the same pattern of disease. For example, children diagnosed before age 7 often have more aggressive disease, more autoantibodies, and stronger genetic risk factors than those diagnosed later. Much of our understanding of T1D has come from studying animal models, but new technologies now allow researchers to study human pancreas tissue and blood immune cells in greater detail. Scientists are also exploring how the gut microbiome, diet, and environmental exposures contribute to T1D risk and progression. Treatment currently focuses on replacing insulin, but researchers are working on therapies that target the immune system or aim to protect or replace beta cells. Strategies include immunotherapy, gene therapy, and even modifying the gut microbiome. The goal is to prevent or reverse the disease, not just manage its symptoms. In summary, T1D is a complex autoimmune disease influenced by both genes and the environment. It progresses silently before symptoms appear, and while insulin therapy is life-saving, new research is paving the way for treatments that could one day halt or even prevent the disease.},
}

@article {pmid40375187,
year = {2025},
author = {Bai, XJ and Mei, YC and Zhao, JT and Chen, ZR and Yang, CX and Dong, XJ and Yu, JW and Xiang, LB and Zhou, EZ and Chen, Y and Hao, JY and Zhang, ZJ and Liuyang, YX and Ren, L and Yao, YM and Zhang, L and Lv, Y and Lu, Q},
title = {Changes in microbiome composition after fecal microbiota transplantation via oral gavage and magnetic navigation technology-assisted proximal colon/cecum enema in antibiotic knock-down rats: a comparative experimental study.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {295},
pmid = {40375187},
issn = {1471-2180},
support = {92048202//Major Research Plan of the National Natural Science Foundation of China/ ; 2021GXLH-Z-047//Key R&D Plan of Shaanxi Province/ ; },
mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; Rats ; Feces/microbiology ; *Gastrointestinal Microbiome ; Rats, Sprague-Dawley ; *Colon/microbiology ; *Enema/methods ; Male ; *Cecum/microbiology ; Anti-Bacterial Agents ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Administration, Oral ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) transfers fecal matter from a donor into the gastrointestinal tract of a recipient to induce changes to the gut microbiota for therapeutic benefit; however, differences in the composition of gut microbiota after FMT via different donor material delivery routes are poorly understood. In this study, we first developed a novel technique for FMT, magnetic navigation technology(MAT)-assisted proximal colon enemas, in healthy Sprague-Dawley rats. Besides, the difference in fecal microbiota composition after FMT via oral gavage and proximal colon/cecum enemas was determined in antibiotic knock-down rats, in addition to the impact on intestinal barrier function.

METHODS: A device consisting of an external magnet and a magnet-tipped 6 Fr tube was used in the MAT group (n = 6), and the control group (n = 6) where fecal matter was delivered without magnetic navigation. The feasibility and safety of this method were assessed by angiography and histology. Next, the fecal microbiota of donor rats was transplanted into antibiotic knock-down rats via oral gavage (n = 6) and MAT-assisted proximal colon/cecum enema (n = 6) for a week. Analysis of fecal 16 S rRNA was conducted to determine differences in the composition of gut microbiota between different groups. The rat intestinal barrier integrity were evaulated by H&E and ZO-1/MUC2 immunofluorescence staining.

RESULTS: The end of the fecal tube could be placed in the cecum or proximal colon of rats in MAT group; however, this was rarely achieved in the control group. No colon perforation or bleeding was detected in either group. After fecal microbiota transplantation, the microbiota α-diversity and β-diversity were comparable among the different delivery routes.At the family level, the relative abundances of Muribaculaceae, Oscillospiraceae, and Erysipelotrichaceae were higher in the gavage treatment group, whereas Lactobacillaceae and Saccharimonadaceae were higher in the enema treatment group (all p < 0.05). FMT by enema was superior to gavage in maintaining the integrity of the rat intestinal barrier, as assessed by an elevation in the density of goblet cells and increased expression of mucin-2.

CONCLUSIONS: Fecal microbiota tube placement using magnetic navigation was safe and feasible in rats.Different delivery route for FMT affects the gut microbiota composition and the integrity of the rat intestinal barrier. Future experimental designs should consider the colonization outcomes of critical microbial taxa to determine the optimal FMT delivery routes in scientific research as well as clinical practise.},
}

Animals
*Fecal Microbiota Transplantation/methods
Rats
Feces/microbiology
*Gastrointestinal Microbiome
Rats, Sprague-Dawley
*Colon/microbiology
*Enema/methods
Male
*Cecum/microbiology
Anti-Bacterial Agents
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Administration, Oral

@article {pmid40374795,
year = {2025},
author = {Mizutani, H and Fukui, S and Oosuka, K and Ikeda, K and Kobayashi, M and Shimada, Y and Nakazawa, Y and Nishiura, Y and Suga, D and Moritani, I and Yamanaka, Y and Inoue, H and Nakagawa, H and Dohi, K and Kaiju, H and Takaba, K and Wada, H and Shiraki, K},
title = {Biliary microbiome profiling via 16 S rRNA amplicon sequencing in patients with cholangiocarcinoma, pancreatic carcinoma and choledocholithiasis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16966},
pmid = {40374795},
issn = {2045-2322},
mesh = {Humans ; *Cholangiocarcinoma/microbiology ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; Middle Aged ; *Microbiota/genetics ; *Pancreatic Neoplasms/microbiology ; *Choledocholithiasis/microbiology ; Aged ; *Bile Duct Neoplasms/microbiology ; Bacteria/genetics/classification ; *Bile/microbiology ; },
abstract = {Recent studies have revealed that oral, gut, and intratumoral microbial dysbiosis significantly affects tumor progression, therapy resistance, and prognosis in cholangiocarcinoma (CCA) and pancreatic ductal adenocarcinoma (PDAC) patients. However, the biliary microbiome, which directly interacts with malignant tissues, remains poorly understood. In this study, we analyzed the bile microbiota from 17 CCA, 15 PDAC, and 40 choledocholithiasis (CDL) patients using bacterial 16 S rRNA and fungal ITS sequencing. Principal coordinate analysis revealed significant differences in microbial communities between the cancer and CDL groups. The microbial community structure in each group demonstrated a specific pattern. Linear discriminant analysis revealed Streptococcus, Sphingomonas, and Bacillus enrichment in CCA patients, Neisseria, Sphingomonas, and Caulobacter in PDAC patients were more prevalent compared with CDL patients. Caulobacter was more prevalent, wheares Campylobacter was less in PDAC patients than in CCA patients. Fungal DNA was detected in ~ 50% of the samples, with CCA and PDAC patients. KEGG pathway analysis revealed altered metabolic pathways, including peptidoglycan, sphingolipid, and fatty acid metabolism and bile acid metabolism, in CCA and PDAC patients. These findings highlight the potential role of the biliary microbiome in CCA and PDAC pathogenesis, offering new insights into disease mechanisms and biomarkers.},
}

Humans
*Cholangiocarcinoma/microbiology
*RNA, Ribosomal, 16S/genetics
Female
Male
Middle Aged
*Microbiota/genetics
*Pancreatic Neoplasms/microbiology
*Choledocholithiasis/microbiology
Aged
*Bile Duct Neoplasms/microbiology
Bacteria/genetics/classification
*Bile/microbiology

@article {pmid40374534,
year = {2025},
author = {Lee, MS and Son, MY and Cho, HS},
title = {The Gut Microbiome in Hepatocellular Carcinoma: Proliferation, Inhibition, Diagnosis, and Immunotherapy.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2412075},
doi = {10.4014/jmb.2412.12075},
pmid = {40374534},
issn = {1738-8872},
mesh = {Humans ; *Carcinoma, Hepatocellular/therapy/diagnosis/microbiology ; *Gastrointestinal Microbiome/physiology ; *Liver Neoplasms/therapy/diagnosis/microbiology ; Immunotherapy ; Cell Proliferation ; Animals ; },
abstract = {Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. Major causes of HCC include hepatitis B and C viral infections, alcoholic hepatitis, and liver cirrhosis. Additionally, conditions such as obesity, diabetes, and metabolic syndrome have been identified as contributing factors to HCC development. In recent years, research on gut microbiota has expanded significantly, resulting in numerous studies exploring the relationship between HCC and gut microbiota. Thus, in this review, we highlight the association between gut microbiota and HCC, focusing on microbiota-related proliferation, inhibition, diagnosis, and immunotherapy. The gut microbiota is proposed to play a crucial role in both the diagnosis and treatment of HCC, paving the way for the development of novel diagnostic and therapeutic approaches for this disease.},
}

Humans
*Carcinoma, Hepatocellular/therapy/diagnosis/microbiology
*Gastrointestinal Microbiome/physiology
*Liver Neoplasms/therapy/diagnosis/microbiology
Immunotherapy
Cell Proliferation
Animals

@article {pmid40374457,
year = {2025},
author = {Laaraj, J and Lachance, G and Bergeron, A and Fradet, Y and Robitaille, K and Fradet, V},
title = {New insights into gut microbiota-prostate cancer crosstalk.},
journal = {Trends in molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molmed.2025.03.015},
pmid = {40374457},
issn = {1471-499X},
abstract = {Recent evidence underscores a reciprocal relationship between the gut microbiota and prostate cancer (PCa). Dysbiosis, often driven by Western dietary habits and antibiotic use, can heighten systemic inflammation and hinder antitumor immunity, thereby fostering PCa onset and progression. Conversely, certain gut microbes and their metabolites may protect against tumor growth by modulating immune and hormonal pathways that impact therapeutic responses, including androgen deprivation therapy (ADT). Emerging evidence links gut microbial shifts to PCa aggressiveness, potentially sustaining local androgen production and promoting resistance. In this review, we explore current understanding of the gut-PCa interplay, highlighting key knowledge gaps and the need for further research to clarify how targeting the microbiome might influence PCa outcomes.},
}

@article {pmid40374164,
year = {2025},
author = {Hu, FB and Drescher, G and Trichopoulou, A and Willett, WC and Martínez-González, MA},
title = {Three Decades of the Mediterranean Diet Pyramid: A Narrative Review of Its History, Evolution, and Advances.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2025.04.036},
pmid = {40374164},
issn = {1938-3207},
abstract = {The Mediterranean Diet Pyramid was officially published in the American Journal of Clinical Nutrition in 1995. Since then, our understanding of the role of the Mediterranean diet (MedDiet) and its role in reducing risk of chronic diseases has grown substantially. The aim of this article is to provide a narrative review of the historical context of the MedDiet and its environmental impact, summarize health-related evidence from the past three decades, and explore its practical applications and cultural adaptations. A large body of evidence from prospective cohort studies, randomized controlled trials, and mechanistic studies consistently supports the benefits of the MedDiet for the prevention of chronic diseases, particularly cardiometabolic diseases and improving healthy aging. Growing evidence demonstrates that the MedDiet promotes favorable changes in circulating metabolites and gut microbiome composition, providing novel insights into biological mechanisms underlying its health benefits and informing the development of precision nutrition strategies. The MedDiet aligns with the principles of the Planetary Health Diet recommended by the EAT-Lancet Commission, which aims to promote both human health and environmental sustainability. The development of the MedDiet pyramid 30 years ago inspired the creation of the Asian, African, and Latin American Heritage Diet Pyramids. Despite robust evidence, further studies are needed to evaluate the long-term effectiveness and adaptability of the MedDiet across diverse populations, cultural settings, and food environments.},
}

@article {pmid40374162,
year = {2025},
author = {Zhao, J and Miao, D},
title = {Precision Oncology in Colorectal Cancer: An Anatomical Revolution Through Molecular-Clinical Integration Across Colonic Subsites.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {},
number = {},
pages = {102613},
doi = {10.1016/j.clinre.2025.102613},
pmid = {40374162},
issn = {2210-741X},
abstract = {Colorectal cancer (CRC) exhibits significant heterogeneity across different colonic subsites, which vary in embryological origin, microbiome, metabolome, and molecular profiles, affecting tumorigenesis, treatment response, and prognosis. We emphasize the importance of this subsite heterogeneity to advance precision medicine in CRC. Colorectal cancer (CRC) is a major public health crisis worldwide, with significant morbidity and mortality. Despite its prevalence, the majority of clinical and basic research studies have historically simplified CRC into broad categories such as right-sided colon cancer, left-sided colon cancer, and rectal cancer [1]. This oversimplification overlooks the critical differences among the distinct colonic subsites: cecum, ascending colon, hepatic flexure, transverse colon, splenic flexure, descending colon, and sigmoid colon [2,3]. Each of these subsites exhibits unique embryological origins, vascular supply, neural innervation, and microbial colonization, which drive spatially defined heterogeneity in tumorigenesis, treatment response, and survival [4]. This commentary calls for a paradigm shift in CRC research, advocating for a molecular-clinicopathological framework that recognizes the distinct characteristics of each colonic subsites.},
}

@article {pmid40374084,
year = {2025},
author = {Jung, YS and Song, NE and Oh, SY and Park, YK and Kim, YJ and Seong, H and You, SM and Jung, DH and Shin, D and Lee, MG and Lim, MC and Han, NS},
title = {Advances in in vitro cultivation techniques for comprehensive analysis of human gut microbiome.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108595},
doi = {10.1016/j.biotechadv.2025.108595},
pmid = {40374084},
issn = {1873-1899},
abstract = {The role of gut microbiota in human health and disease is becoming increasingly recognized. Historically, the impact of human gut microbiota on health has been studied using clinical trials and animal models. However, clinical studies often struggle with controlling variables and pinpointing disease-causing factors, while animal models fall short of accurately replicating the human gut environment. Additionally, continuous sample collection for gut microbiota analysis in vivo presents significant ethical and technical challenges. To address these limitations, in vitro fermentation models have emerged as promising alternatives. These models aim to simulate the structural and functional characteristics of the human gut in a controlled setting, offering valuable insights into microbial behavior. This review highlights current knowledge and technological advances in in vitro cultivation systems for human gut microbiota, focusing on key elements such as three-dimensional scaffolds, culture media, fermentation systems, and analytical techniques. By examining these components, the review establishes a framework for improving methods to cultivate and study human gut microbiota, enhancing research methodologies for better understanding microbial interactions, behavior, and adaptation in diverse environments.},
}

@article {pmid40374065,
year = {2025},
author = {Aathira, NS and Kaur, A and Kumar, A and Dar, GM and Nimisha, and Sharma, AK and Bera, P and Mahajan, B and Chatterjee, A and Saluja, SS},
title = {The genetic risk factors, molecular pathways, microRNAs, and the gut microbiome in Alzheimer's disease.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2025.05.021},
pmid = {40374065},
issn = {1873-7544},
abstract = {Alzheimer's disease (AD) is the most prevalent form of dementia worldwide. It is a multifaceted condition resulting from interplay of genetic mutations (e.g., APP, PSEN1, PSEN2) that account for less than 5% of cases, several genetic risk variants such as APOE4, TREM2, CD33, CLU, SORL1, and CR1 contribute to disease susceptibility and epigenetic factors, which may mediate the influence of environmental and lifestyle factors over time. Other critical contributors such as aging, protein misfolding and aggregation (amyloid-β and tau), molecular and transcriptomic dysregulation affecting neuronal function, and modifiable lifestyle factors like diet, physical activity, and environmental exposures presents challenges in accurate diagnosis and management. Research has predominantly focused on the diverse molecular pathways in the pathogenesis of AD, with particular attention given to the amyloidogenic pathways, tau pathology, calcium signalling, endolysosomal pathways, and others, whether they are directly or indirectly involved. Apart from these known molecular pathways, miRNAs are gaining attention as important regulators, which have been implicated in moderating the expression of mRNA targets involved in various processes associated with the clearance of pathogenic β-amyloid proteins. A mounting body of research suggests the possible role of gut microbiota in AD which regulates inflammation, neurotransmitters, and the blood-brain barrier. Gut dysbiosis can trigger neuroinflammation and amyloid-beta aggregation, making microbiome composition a potential early AD biomarker. This review aims to explore briefly the diverse risk encompassing genetic polymorphisms, altered molecular pathways implicated in AD pathogenesis, miRNA regulatory mechanisms, and the potential impact of gut microbiota on AD risk.},
}

@article {pmid40373957,
year = {2025},
author = {Patra, V and Trajanoski, S and Joshi, A and Lenief, V and Goyet, C and Cornu, A and Golob-Schwarzl, N and Somlapura, M and Mosnier, A and Zarfl, M and Eichmann, T and Köefeler, H and Norval, M and Nicolas, JF and Wolf, P and Vocanson, M},
title = {Urocanase-positive skin resident bacteria metabolize cis-urocanic acid and in turn reduce the immunosuppressive properties of UV radiation.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.03.035},
pmid = {40373957},
issn = {1523-1747},
abstract = {The skin microbiome plays an important role in health and disease. We have recently shown that microbes living on the skin regulate the immunomodulatory properties of ultraviolet (UV) radiation, but the underlying mechanisms remain to be uncovered. Using a pre-clinical model of immunosuppression against the chemical allergen 2,4-dinitrofluorobenzene (DNFB), 16S microbiome sequencing, in vitro cultures, HPLC-MS, as well as the generation of gnotobiotic-like mice, we report that acute UVB radiation induces a transient and significant restructuring of bacterial communities on the skin via one of its major photoproducts, cis-urocanic acid (cis-UCA). Certain bacteria, such as Staphylococcus epidermidis, use urocanase (HutU) to metabolize cis-UCA in order to proliferate. This in turn affects the concentration of cis-UCA, limiting its ability to suppress adaptive immune responses and induce tolerance to DNFB. Interestingly, addition of a topical urocanase inhibitor restricts the metabolism of cis-UCA by HutU+ bacteria and restores immunosuppression. Overall, these results illustrate how, by harnessing a unique nutrient produced in response to solar UV radiation, urocanase-positive skin resident bacteria can fine-tune immune responses to environmental antigens. They should open new avenues to enhance the beneficial effects of phototherapy protocols, as well as sun protection.},
}

@article {pmid40373943,
year = {2025},
author = {Bhuiya, S and Kaushik, S and Logheeswaran, J and Karthika, P and Prathiviraj, R and Selvin, J and Kiran, GS},
title = {Emergence of Recurrent Urinary Tract Infection: Dissecting the mechanism of Antimicrobial Resistance, Host-Pathogen Interaction, and Hormonal Imbalance.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107698},
doi = {10.1016/j.micpath.2025.107698},
pmid = {40373943},
issn = {1096-1208},
abstract = {Urinary tract infection is one of the most common infections worldwide, causing numerous deaths every year. The gut-bladder axis has been recently found to be a key factor in initiating UTI pathogenesis, along with the imbalance in the gut microbiome, which is associated with advanced susceptibility to rUTI. The patients who suffer from UTIs are, more often than not, the ones who have the lowest levels of butyrate-producing gut bacteria. Antibiotics cause dysbiosis in the gut and increase the growth of uropathogenic strains. Moreover, the gut-vagina and vagina-bladder axes are involved in UTIs by transferring microbial species, modulating the immune response, and developing intracellular bacterial reservoirs in the bladder. The rising usage of antibiotics has raised antimicrobial resistance (AMR) worldwide and recently worsened the treatment of UTIs. Resistance mechanisms include enzymatic hydrolysis of antibiotics, efflux systems, biofilm formation, horizontal gene transfer, and a weakened host's immune system, allowing bacteria to escape from the treatments. Besides, in pregnant women and adolescents, the alterations in sex hormone levels increase the risk of rUTIs. Knowledge of microbiota that harbor in the gut-vagina and vagina-bladder axes might lead to the invention of nonantibiotic preventive and therapeutic techniques in the future. In conclusion, this review emphasizes the need for a study to understand the host-microbe interactions, gut health, and AMR to effectively deal with and prevent recurrent UTIs. Also, the review explores a comprehensive analysis of the epigenetic network between host UTIs and marker genes in E. coli.},
}

@article {pmid40373900,
year = {2025},
author = {Yin, CY and Sadiq, H and Liao, WH and Wang, HN and Fu, Z and Yu, WG and Han, F},
title = {Identification and functional characterization of two novel hyaluronate lyases BxHly33 and BiHly33, from the human gut microbiome.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {144153},
doi = {10.1016/j.ijbiomac.2025.144153},
pmid = {40373900},
issn = {1879-0003},
abstract = {Hyaluronic acid (HA) is a key glycosaminoglycan in the extracellular matrix, essential for cellular signaling, hydration, and tissue homeostasis. This study identified two novel polysaccharide lyase family 33 (PL33) hyaluronate lyases, BxHly33 and BiHly33, from the human gut microbiome using metagenomic screening. These enzymes demonstrated high specificity and stability in degrading HA, with optimal activity at pH 6.6-7.6 and temperatures of 35-40 °C. Furthermore, structural and biochemical analyses revealed their catalytic mechanisms, highlighting key residues responsible for their function. Notably, specific alanine substitutions significantly enhanced their enzymatic activity. BxHly33 and BiHly33 present promising alternatives to conventional hyaluronidases, which are often costly and immunogenic, for drug delivery and tissue engineering applications. This study will provide novel insights into exploring their therapeutic potential in HA degradation therapies.},
}

@article {pmid40373750,
year = {2025},
author = {Goepp, M and Milburn, JV and Zhang, B and Dong, Y and Tyrrell, V and Zheng, X and Marshall, JM and Bolsega, S and Basic, M and Glendinning, L and Ho, GT and Satsangi, J and Breyer, RM and Narumiya, S and McSorley, HJ and Schwarze, JKJ and Anderson, CJ and Dockrell, DH and Rossi, AG and Bleich, A and Lucas, CD and O'Donnell, VB and Mole, D and Arends, MJ and Zhou, Y and Yao, C},
title = {Age-related impairment of intestinal inflammation resolution through an eicosanoid-immune-microbiota axis.},
journal = {Cell host & microbe},
volume = {33},
number = {5},
pages = {671-687.e6},
doi = {10.1016/j.chom.2025.04.014},
pmid = {40373750},
issn = {1934-6069},
mesh = {Animals ; *Eicosanoids/metabolism/immunology ; *Gastrointestinal Microbiome/immunology ; Mice ; *Inflammation/immunology/microbiology ; Dysbiosis/immunology/microbiology ; *Aging/immunology ; Mice, Inbred C57BL ; Intestinal Mucosa/microbiology/immunology ; Receptors, Prostaglandin E, EP4 Subtype/metabolism/genetics ; *Intestines/immunology/microbiology/pathology ; T-Lymphocytes/immunology ; Male ; },
abstract = {Aging manifests a decline of immune function, induces microbiome dysbiosis, drives organ inflammation, and impedes the resolution of inflammation. However, the mechanisms underlying age-related intestinal inflammation remain poorly described. Here, we find that the resolution of T cell-initiated intestinal inflammation is impaired with aging. This impairment is mediated by disrupting the immune-microbiota interplay, controlled by intestinal eicosanoid metabolism. Pharmacologically inhibiting eicosanoid biosynthesis, blocking the prostaglandin E receptor subtype 4 (EP4), or genetically ablating EP4 diminishes age-related impairment of intestinal inflammation resolution. Mechanistically, mononuclear phagocyte-intrinsic eicosanoid-EP4 signaling impedes the resolution of intestinal inflammation through fostering gut microbial dysbiosis and, more importantly, interrupting segmented filamentous bacterial adhesion to the intestinal epithelium. Colonization with EP4-ablated mouse microbiota or segmented filamentous bacteria improves the resolution of intestinal inflammation. These findings reveal that eicosanoid-dependent immune-microbiota interactions impair inflammation resolution in the aged intestine, highlighting potential intervention strategies for improving age-related gut health.},
}

Animals
*Eicosanoids/metabolism/immunology
*Gastrointestinal Microbiome/immunology
Mice
*Inflammation/immunology/microbiology
Dysbiosis/immunology/microbiology
*Aging/immunology
Mice, Inbred C57BL
Intestinal Mucosa/microbiology/immunology
Receptors, Prostaglandin E, EP4 Subtype/metabolism/genetics
*Intestines/immunology/microbiology/pathology
T-Lymphocytes/immunology
Male

@article {pmid40373748,
year = {2025},
author = {Kublin, JG},
title = {Antibiotics fire up inflammation to cool vaccine responsiveness.},
journal = {Cell host & microbe},
volume = {33},
number = {5},
pages = {618-620},
doi = {10.1016/j.chom.2025.04.015},
pmid = {40373748},
issn = {1934-6069},
mesh = {Humans ; *Anti-Bacterial Agents/adverse effects ; *Inflammation/chemically induced/immunology ; *Rabies Vaccines/immunology/administration & dosage ; *Gastrointestinal Microbiome/drug effects/immunology ; Vaccination ; Animals ; },
abstract = {In this issue of Cell Host & Microbe, Feng et al. find that broad-spectrum antibiotics perturbed the ecology of the gut microbiome in individuals receiving a rabies vaccine, resulting in systemic inflammatory responses. Such inflammation is hypothesized to alter immune homeostasis with consequences for immunological responsiveness to vaccination.},
}

Humans
*Anti-Bacterial Agents/adverse effects
*Inflammation/chemically induced/immunology
*Rabies Vaccines/immunology/administration & dosage
*Gastrointestinal Microbiome/drug effects/immunology
Vaccination
Animals

@article {pmid40373747,
year = {2025},
author = {Li, Z and Xia, J and Wang, J},
title = {Unveiling strain-level dynamics in the human skin microbiome.},
journal = {Cell host & microbe},
volume = {33},
number = {5},
pages = {615-617},
doi = {10.1016/j.chom.2025.03.014},
pmid = {40373747},
issn = {1934-6069},
mesh = {Humans ; *Skin/microbiology ; *Microbiota ; Symbiosis ; *Bacteria/classification ; Skin Microbiome ; },
abstract = {Species-level uniformity on the skin surface masks substantial strain-level diversity modulated by ecological dynamics. In this issue of Cell Host & Microbe, Jacob et al. uncover dynamic intraspecies behaviors, revealing different patterns of colonization and persistence for two important skin commensals.},
}

Humans
*Skin/microbiology
*Microbiota
Symbiosis
*Bacteria/classification
Skin Microbiome

@article {pmid40373743,
year = {2025},
author = {Anantharaman, K and Martin, C},
title = {Genetic keys to microbial gut colonization.},
journal = {Cell host & microbe},
volume = {33},
number = {5},
pages = {605-607},
doi = {10.1016/j.chom.2025.04.016},
pmid = {40373743},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; Humans ; *Host Microbial Interactions/genetics ; *Gastrointestinal Tract/microbiology ; *Bacteria/genetics/growth & development ; },
abstract = {What enables certain microbes to successfully colonize the mammalian gut? In a recent issue of Cell, Liu et al. present a microbial cross-species genomic framework that identifies conserved genetic determinants of gut residency. This study provides a roadmap for developing more effective microbiome-based therapeutics, advancing our understanding of host-microbe interactions.},
}

*Gastrointestinal Microbiome/genetics
Animals
Humans
*Host Microbial Interactions/genetics
*Gastrointestinal Tract/microbiology
*Bacteria/genetics/growth & development

@article {pmid40373649,
year = {2025},
author = {Rosa-Masegosa, A and Vilchez-Vargas, R and Gorrasi, S and Monteoliva-García, A and Gonzalez-Martinez, A and Gonzalez-Lopez, J and Muñoz-Palazon, B},
title = {Unraveling the composition and succession of the microbial community in aerobic granular sludge treating urban wastewater with high load from hospital effluent.},
journal = {Chemosphere},
volume = {381},
number = {},
pages = {144483},
doi = {10.1016/j.chemosphere.2025.144483},
pmid = {40373649},
issn = {1879-1298},
abstract = {The treatment of wastewater containing high concentrations of pharmaceutical compounds is a challenge that has not yet been fully resolved. In this study, the occurrence of pharmaceutical and the bacterial and fungal communities were investigated during the treatment of urban wastewater including the hospital effluents using aerobic granular sludge technology. The physic-chemical results pointed out the capability of this technology to remove high rates of organic matter (97 %), total suspended solids (90 %), and nitrogen (85 %) without compromising the granular integrity and properties. The obtained data of pharmaceuticals remarked that the influent concentration had a strong effect on the removal ratio. The better average pharmaceutical removal performances were for carbamazepine (60-85 %), ketoprofen(50-60 %), cyclophosphamide(∼70 %), and trimethoprim(70 %), while the most recalcitrant compound was diclofenac. The molecular analysis exposed the relevance of endogenous microbial loads in the raw wastewater, especially in the start-up period. The mature granules demonstrated the strong selection of granules-forming bacteria, whereas the fungal populations took a longer period to be stable in granular biomass. Once the reactor was stable, the system was able to compete successfully with the influent microorganisms and avoid the spreading of pathogen microorganisms in the effluent, achieving excellent macro-pollutant and micro-pollutant removal ratios.},
}

@article {pmid40373419,
year = {2025},
author = {Orsi, AS and Lemos Junior, WJF and Alegbeleye, OO and Muniz, DC and Horita, CN and Sant'Ana, AS},
title = {Sodium chloride reduction in meat processing: Microbial shifts, spoilage risks, and metagenomic insights.},
journal = {Meat science},
volume = {226},
number = {},
pages = {109848},
doi = {10.1016/j.meatsci.2025.109848},
pmid = {40373419},
issn = {1873-4138},
abstract = {This review evaluated the impact of sodium chloride (NaCl) reduction or substitution on the microbial ecology of meat products, with a focus on how these changes affect shelf life and safety. Reducing NaCl in fresh meat products promotes the growth of psychrotrophic spoilage bacteria, such as Pseudomonas sp., which thrive at low temperatures, and mesophilic pathogens like Escherichia coli and Staphylococcus aureus, particularly under inadequate storage conditions. In cured and fermented meats, such as salami, lowering NaCl levels disrupts the balance of salt-tolerant microorganisms, notably lactic acid bacteria (LAB) and coagulase-negative staphylococci, potentially leading to increased spoilage and pathogen proliferation. In smoked meats, the combination of reduced NaCl and altered microbial ecology, including a shift toward LAB dominance, may weaken the inhibitory effects on spore-forming bacteria like Clostridium botulinum. Additionally, using metagenomics, we explore the shifts in microbial communities observed in studies involving meat, revealing critical insights into the composition and diversity of bacteria in meat products, as well as the gaps in research on the impact of NaCl reduction and/or substitution on the microbiota. This review provides a comprehensive understanding of these microbial shifts, highlighting the distinct responses of psychrotrophic, mesophilic, and LAB groups to NaCl modification and the need to understand the effects of these alternatives on the meat product microbiome, as well as the neglected microorganisms that can affect the quality and safety of these products.},
}

@article {pmid40372916,
year = {2025},
author = {Ramar, M and Wiscovitch-Russo, R and Yano, N and Singh, H and Lamere, E and Short, M and Gonzalez-Juarbe, N and Fedulov, AV},
title = {Live bacteria in gut microbiome dictate asthma onset triggered by environmental particles via modulation of DNA methylation in dendritic cells.},
journal = {Cell reports},
volume = {44},
number = {5},
pages = {115684},
doi = {10.1016/j.celrep.2025.115684},
pmid = {40372916},
issn = {2211-1247},
abstract = {Despite broad knowledge of the pathogenesis, our understanding of the origin of allergy and asthma remains poor, preventing etiotropic treatments. The gut microbiome is seen to be altered in asthmatics; however, proof of causality of the microbiome alterations is lacking. We report on gut microbiome transplantation (GMT) from mice predisposed to asthma by maternal exposure to pro-allergy environmental particles into naive recipients. This GMT confers asthma predisposition, and the effect is abrogated by gamma sterilization of the transplant material or by co-administration of antibacterials, indicating that viable bacteria are mediating the effect. Metagenomics identifies key changes in the "pro-asthma" microbiome, and metabolomics links the identified species to altered production of butyrate known to act on immune cells and epigenetic mechanisms. We further show that transplant recipients develop DNA methylation alterations in dendritic cells. Finally, dendritic cells with an altered methylome present allergen to T cells, and this effect is abrogated by an epigenetically acting drug in vitro.},
}

@article {pmid40372689,
year = {2025},
author = {Seton, KA and Carding, SR},
title = {Profiling Antibody Reactivity to Gut Microbes in ME/CFS Patients.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2920},
number = {},
pages = {279-293},
pmid = {40372689},
issn = {1940-6029},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Fatigue Syndrome, Chronic/immunology/microbiology ; *Immunoglobulin G/immunology ; Feces/microbiology ; Dysbiosis/immunology/microbiology ; *Antibodies, Bacterial/immunology ; },
abstract = {The gut microbiome plays a vital role in physiological functions including metabolism, immune regulation, and gut-brain communication. Alterations in gut microbe makeup and function, termed microbial dysbiosis, are associated with various metabolic, inflammatory, and neurological disorders. Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) patients often display gut microbial dysbiosis and increased intestinal barrier permeability ("leaky gut"). This "leaky gut" allows for microbial products and toxins, such as lipopolysaccharides (LPS), to enter the bloodstream, triggering systemic inflammation and immune dysregulation. ME/CFS patients exhibit altered immune responses, including production of antibodies reactive with gut microbial antigens, although the significance of these antibodies in promoting pathogenic or protective immune responses remains unclear. This chapter outlines methodologies for quantifying antibody reactivity to intestinal microbes and identifying stool-bound IgG in ME/CFS patients and healthy same household controls, to further investigate the role of anti-microbial IgG in ME/CFS pathogenesis.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Fatigue Syndrome, Chronic/immunology/microbiology
*Immunoglobulin G/immunology
Feces/microbiology
Dysbiosis/immunology/microbiology
*Antibodies, Bacterial/immunology

@article {pmid40372527,
year = {2025},
author = {Bressa, C and González-Soltero, R and Tabone, M and Clemente-Velasco, S and Gálvez, BG and Larrosa, M},
title = {Exploring the relationship between APOEε4 allele and gut microbiota composition and function in healthy adults.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {77},
pmid = {40372527},
issn = {2191-0855},
support = {2018/UEM4//Universidad Europea de Madrid/ ; 2022/UEM28//Universidad Europea de Madrid/ ; grant 2012_11910//Ministerio de Ciencia, Innovación y Universidades/ ; },
abstract = {The APOE ε4 allele (APOE4) is a known risk factor for neurodegenerative and cardiovascular diseases, but its link to body composition and metabolism remains debated. The gut microbiota influences host metabolism and immunity, yet its relationship with APOE genotype in healthy individuals is not well understood. The objective of this work was to examine associations between APOE genotype and gut microbiota composition and function in healthy adults, focusing on microbial and metabolic differences related to the APOE4 allele. Seventy-seven healthy Spanish adults were genotyped for APOE. Fecal microbiota profiles were assessed by 16 S rRNA gene sequencing, and predicted functions were inferred using PICRUSt2. Body composition (DEXA) and physical activity (accelerometry) were also measured. APOE4 carriers exhibited subtle shifts in microbiota composition, including a five-fold reduction in Megamonas and lower abundance of the Eubacterium brachy group-both linked to energy harvest and adiposity-compared to APOE3 homozygotes. An uncharacterized Puniceicoccaceae genus was enriched in APOE4 carriers. Although E. brachy group abundance correlated with adiposity, no significant differences in body composition were observed. Functional predictions showed APOE4-associated microbiota enriched in pathways for carotenoid biosynthesis and trehalose metabolism, and depleted in tryptophan biosynthesis, propionate production, and multidrug resistance mechanisms. APOE4 carriers harbor gut microbiota with distinct taxonomic and functional features, potentially reflecting adaptations to metabolic and oxidative challenges. These findings underscore the relevance of the gut microbiome in shaping APOE4-associated phenotypes and warrant further investigation into its mechanistic contributions to health and disease.},
}

@article {pmid40372056,
year = {2025},
author = {Kok, CR and Thissen, JB and Cerroni, M and Tribble, DR and Cancio, A and Tran, S and Schofield, C and Colombo, RE and Troth, T and Joya, C and Lalani, T and Be, NA},
title = {Field expedient stool collection methods for gut microbiome analysis in deployed military environments.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0081824},
doi = {10.1128/msphere.00818-24},
pmid = {40372056},
issn = {2379-5042},
abstract = {Field expedient devices and protocols for the collection, storage, and shipment of stool samples in deployed settings are needed for the advancement of microbiome research in military health. Relevant assessments include the evaluation of microbiome signatures associated with susceptibility to travelers' diarrhea and recovery of gut function following infection. However, inherent biases in microbial measurements due to preservatives and sampling methods are unclear and should be assessed for an accurate evaluation of the microbiome. We performed shotgun metagenomic sequencing and compared the microbiome composition in paired fecal samples collected using Flinters Technology Associates (FTA) cards and OMNIgene (OG) Gut tubes, prior to and during international travel, from 49 adult participants, 39 of whom remained asymptomatic and 10 experienced travelers' diarrhea. Higher concentrations of nucleic acid and sequencing libraries were observed in OG samples. A majority of genera (82.9%) were detected with both methods, and detections of genera limited to one collection method were not highly prevalent across samples and were present in extremely low relative abundances (<0.01%). Differences in beta diversity were largely explained by inter-individuality of microbiome composition, followed by the effect of collection method and timepoint-disease states. Differential abundance analysis indicated that Corynebacterium and Blautia were consistently higher in abundance across all groups with FTA and OG collection, respectively. The observed differences in microbiome composition between methods suggest the need for consistent and standardized protocols within a study. Overall, the data presented here could help guide the future design of fecal microbiome study protocols in field and military deployment settings.IMPORTANCEThe assessment of field-deployable methods for fecal sample collection and storage is required to reliably capture samples collected in remote and austere locations. This study describes a comparative metagenomics analysis between samples collected by two different commercially available methods in a military-deployed setting. The results presented here are foundational for the future design of fecal microbiome study protocols in an operational context.},
}

@article {pmid40372053,
year = {2025},
author = {Mandolini, E and Probst, M and Telagathoti, A and Frey, B and Rodriguez-R, LM and Fornasier, F and Praeg, N and Illmer, P and Peintner, U},
title = {Determinism and stochasticity drive microbial community assembly and microbial interactions in calcareous glacier forefields.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0030225},
doi = {10.1128/aem.00302-25},
pmid = {40372053},
issn = {1098-5336},
abstract = {Calcareous glacier forefields challenge prevailing ecological frameworks on microbial biodiversity and community assembly due to their unique bedrock. Early stages of soil development in these environments are notorious for their high turnover rates, demanding a high degree of replication for obtaining conclusive data. However, studies across different calcareous glaciers are still missing. Here, we robustly investigated both bacterial and fungal diversity, association networks, and assembly processes in four calcareous glacier forefields of the Alps, focusing on the earliest soil developmental stages (<25 years) early in the snow-free season. We found a diverse community of bacteria and fungi, potentially involved in P and N nutrient cycling. A core microbiome existing across all four locations suggests that certain microbes might be more successful colonizers of these ecosystems than others. Nearest taxon index revealed phylogenetically clustered microbial communities. These findings suggest that the distribution and colonization of some microbes were influenced by selective forces such as geography and climate during the early stages of soil development in calcareous glaciers. Interestingly, there were no common bacterial-fungal associations across the four locations, indicating that this habitat does not select for specific bacterial-fungal associations and that associations were driven by neutral processes. We discuss microbial communities and their interactions in these special calcareous glacier forefield habitats. Moreover, we present innovative approaches for studying microbial assembly that address both deterministic, intrinsic drivers, like specific microbial traits, and stochastic, extrinsic drivers, such as the opportunistic behavior of microbes.IMPORTANCEOur study is based on three fundamental and unique approaches: (i) we utilize the early stages of soil development in four glacier forefields across the Alpine range. This design implies high replicability in a natural setting, which is crucial for drawing general conclusions. (ii) Our study investigates glacier forefields with calcareous bedrock directly after snowmelt. These habitats and periods remain surprisingly underexplored. (iii) Our results underline the relevance of bacterial-fungal associations in microbial community assembly alongside dispersal, drift, and natural selection. Taken together, our study provides new insights into the development of complex microbial communities, their stabilization and predictability, including ecological implications.},
}

@article {pmid40372041,
year = {2025},
author = {Mason, CJ and Nelson, RC and Weaver, M and Simmonds, TJ and Geib, SM and Shikano, I},
title = {Assessing the impact of diet formulation and age on targeted bacterial establishment in laboratory and mass-reared Mediterranean fruit fly using full-length 16S rRNA sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0288124},
doi = {10.1128/spectrum.02881-24},
pmid = {40372041},
issn = {2165-0497},
abstract = {UNLABELLED: Insect gut microbiota play important roles in host health and interactions with the environment. In laboratory and mass-reared insects, gut microbiomes can differ in composition and function compared to wild conspecifics. For fruit flies, such as the Mediterranean fruit fly (medfly; Ceratitis capitata), these changes can influence male performance and behavior. Overall, understanding factors that influence the ability of bacteria to establish in hosts is important for the establishment of lost or novel microbiota in mass-reared insects. The goal of this study was to evaluate how host age and diet-inoculation method influenced bacterial establishment in laboratory and mass-reared medflies. We used an Enterobacter strain with antibiotic resistance and coupled it with full-length PacBio Kinnex 16S rRNA sequencing to track the establishment of the specific isolates under different adult dietary conditions. We also used two longstanding reared lines of medfly in our study. Our results identified that diet had a strong interaction with age. The target bacterial isolate was detected in medfly when inoculated with liquid diet regardless of age, but those fed a slurry-based diet and a separate water source had less establishment. This was consistent for both fly rearing lines used in the study. 16S rRNA sequencing corroborated the establishment of the specific strain but also revealed some species/strain-level variation of Enterobacter sequences associated with the flies. Additionally, our study illustrates that long-read 16S rRNA sequencing may afford improved characterization of species- and strain-level distribution of Enterobacteriaceae in insects.

IMPORTANCE: Insects form intimate relationships with gut microorganisms that can help facilitate several important roles. The goal of our study was to evaluate factors that influence microbial establishment in lines of the Mediterranean fruit fly (medfly), an important pest species worldwide. Mass-reared insects for the sterile insect technique often possess gut microbiomes that substantially differ from wild flies, which can impact their performance in pest control contexts. Here, we show that liquid-based formulations can be utilized to manipulate the gut microbiota of mass-reared medflies. Furthermore, using near full-length 16S rRNA metabarcoding sequencing, we uncovered strain-level diversity that was not immediately obvious using other approaches. This is a notable finding, as it suggests that full-length 16S rRNA approaches can have marked improvements for some taxa compared to fewer hypervariable regions at approximately the same cost. Our results provide new avenues for exploring and interrogating medfly-microbiome interactions.},
}

@article {pmid40372034,
year = {2025},
author = {Leong, C and Chua, W and Chong, C-S and Lee, SM and Maurer-Stroh, S and Jung, WH and Dawson, TL},
title = {Non-synonymous ERG11 mutations in M. restricta and M. arunalokei: impact on azole susceptibility.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0000725},
doi = {10.1128/spectrum.00007-25},
pmid = {40372034},
issn = {2165-0497},
abstract = {UNLABELLED: Malassezia are commensal lipid-dependent yeasts and opportunistic pathogens that cause superficial mycoses and systemic infection. Azole antifungals target cell wall ergosterol synthesis and are the first line of antifungal treatment. ERG11 gene mutations and overexpression are major mechanisms conferring azole resistance and resulting in antifungal therapy failure. Malassezia restricta is found ubiquitously on healthy and diseased skin, with azole-resistant isolates described. Malassezia arunalokei is a relatively new, closely related common skin species. Ketoconazole and itraconazole were the most effective at inhibiting both species. Isolates of M. restricta and M. arunalokei from healthy skin of Singapore subjects were cultured, evaluated, and generally susceptible to common over-the-counter azoles, including clotrimazole, except for select less-susceptible strains. Some less-susceptible strains have novel or reported non-synonymous mutations in the ERG11 gene, such as R88C. The QK178RQ ERG11 sequence variation was observed to be associated with differences in M. restricta and M. arunalokei as independent species. In the absence of identified ERG11 mutations, strains with elevated MICs were observed to have elevated ERG11 expression and drug efflux pump expression/activity. We conclude that antifungal susceptibility is determined by a combination of intrinsic (e.g., mutations, gene expression, efflux pump activity) and extrinsic (e.g., skin condition, prior antifungal exposure) factors and that the skin microbiome serves as a reference for the emergence of new mutations and strain phenotypes.

IMPORTANCE: Malassezia over colonization is associated with conditions such as dandruff and seborrheic dermatitis, which give rise to unpleasant itching and swelling on the skin. Azole antifungals such as ketoconazole, clotrimazole, and miconazole are the primary treatments of choice available as over-the-counter creams or shampoos. However, the emergence of antifungal resistance leads to a loss of treatment efficacy and persistent fungal infection. To understand the mechanisms underlying antifungal resistance, we profiled the susceptibility profiles of commensal Malassezia isolates from the skin and identified novel ERG11 mutations. Our results indicate that antifungal susceptibility is determined by a combination of factors (mutations, efflux pump activity, gene expression, copy number) and suggest that the healthy skin microbiome serves as a reference for the emergence of new mutations and strain phenotypes.},
}

@article {pmid40371961,
year = {2025},
author = {McCagherty, J and Pollock, J and Maddox, TW and Paterson, GK and Hall, JL},
title = {Diagnostic value of a point of care bacterial fluorescence imaging device for detecting wound infections in dogs and cats.},
journal = {Veterinary surgery : VS},
volume = {},
number = {},
pages = {},
doi = {10.1111/vsu.14266},
pmid = {40371961},
issn = {1532-950X},
support = {//European College of Veterinary Surgeons/ ; },
abstract = {OBJECTIVE: To determine if a hand-held point of care imaging device would improve the detection of bacteria on the surface of wounds in dogs and cats in postoperative and traumatic wounds.

STUDY DESIGN: Clinical prospective study.

SAMPLE POPULATION: Three cats and 15 dogs.

METHODS: Wounds were swabbed without and with the point of care wound imaging device (WID). Quantitative bacterial culture (QBC), polymerase chain reaction (PCR) and microbiome analysis were performed to assess for any significant difference in the findings of image-guided and non-guided sampling methods.

RESULTS: A total of four feline and 17 canine wounds were evaluated. Bacterial fluorescence was detected in all wounds using the point of care WID. Bacterial infections of wounds in dogs and cats was detected by the fluorescent imaging device. No significant difference was identified between the results of QBC and PCR for image-guided and non-guided wound swabs (p > .05).

CONCLUSION: The WID was able to detect bacteria on the surface of wounds in dogs and cats, accurately confirming the presence of a clinically relevant wound infection at the time of wound evaluation in all wounds but there was no significant difference in the bacterial yield with guided and non-guided swabs.

CLINICAL SIGNIFICANCE: The WID device was able to confirm the presence of a clinically relevant wound infection in real-time, enabling the clinician to initiate appropriate systemic and/or topical antibacterial treatment immediately. This study provides proof of concept of the point of care WID in dogs and cats upon which further studies can be based.},
}

@article {pmid40371957,
year = {2025},
author = {Brożek-Mądry, E and Burska, Z and Sosnowska-Turek, E},
title = {Nasal rinsing with probiotics in rhinosinusitis - analysis of symptoms and safety assessment.},
journal = {Otolaryngologia polska = The Polish otolaryngology},
volume = {79},
number = {3},
pages = {1-8},
doi = {10.5604/01.3001.0055.0503},
pmid = {40371957},
issn = {2300-8423},
mesh = {Humans ; *Probiotics/administration & dosage/therapeutic use ; *Sinusitis/therapy/drug therapy ; Female ; *Rhinitis/therapy/drug therapy ; Male ; Adult ; Middle Aged ; *Nasal Lavage/methods ; Chronic Disease ; Treatment Outcome ; Aged ; Rhinosinusitis ; },
abstract = {Introduction: In the pathophysiology of chronic upper respiratory tract inflammation, an important role is attributed to the disturbances of the patient's microbiome in terms of diversity and functioning, to the decreased abundance of commensal bacteria and the increase of pathogenic bacteria. In recent years, there has been growing scientific interest in the role of probiotics - administered both locally and orally - in the management of various diseases, particularly inflammatory conditions such as chronic rhinosinusitis.

Aim: To assess the use of nasal rinsing with probiotics in patients with rhinitis and rhinosinusitis (primary and secondary).

Material and methods: A total of 51 patients (31 women and 20 men) were included in the study, including 24 patients with granulomatosis with polyangiitis during immunosuppressive therapy (12 women and 12 men) and 27 patients (19 women and 8 men) with rhinitis (chronic rhinosinusitis with polyps, chronic rhinosinusitis without nasal polyps, atrophic rhinitis with nasal septum perforation, and allergic rhinitis). Exclusion criteria were: cystic fibrosis, primary ciliary dyskinesia, pregnancy, severe lung, heart, kidney disease, use of oral probiotics, use of intranasal probiotics in the last 6 months, sinus surgery in the last 6 months, lack of consent to participate in the study, antibiotic therapy in the last 2 months. Patients were scheduled to undergo nasal rinsing with a probiotic solution, with the following parameters assessed before and after the procedure: SNOT-22 scores and the severity of nasal lesions according to the Lund-Kennedy scale. In the group of patients with rhinitis, the ENS-6 questionnaire was also conducted and symptoms assessed on the VAS scale (visual analogue scale): nasal discharge, nasal obstruction, facial pain, impaired sense of smell, nasal irritation, nasal itching, and severity of crusting.

Results: The study showed that nasal rinsing with a probiotic solution is well tolerated and does not cause any adverse effects. In both groups, a reduction in symptoms was observed based on the SNOT-22 questionnaire (p = 0.002 in GPA, ns - in rhinitis/ rhinosinusitis). According to the Lund-Kennedy scale, the reduction in the intensity of changes in both groups was statistically significant. In addition, patients with primary rhinitis or rhinosinusitis also experienced a reduction in nasal mucosa irritation and crusting intranasal (p<0.05).

Conclusions: Probiotic nasal rinsing appears to have a beneficial effect on the condition of the nasal mucosa in patients with both primary and secondary (GPA-related) rhinosinusitis and is generally well tolerated.},
}

Humans
*Probiotics/administration & dosage/therapeutic use
*Sinusitis/therapy/drug therapy
Female
*Rhinitis/therapy/drug therapy
Male
Adult
Middle Aged
*Nasal Lavage/methods
Chronic Disease
Treatment Outcome
Aged
Rhinosinusitis

@article {pmid40371892,
year = {2025},
author = {Metris, A and Walker, AW and Showering, A and Doolan, A and McBain, AJ and Ampatzoglou, A and Murphy, B and O'Neill, C and Shortt, C and Darby, EM and Aldis, G and Hillebrand, GG and Brown, HL and Browne, HP and Tiesman, JP and Leng, J and Lahti, L and Jakubovics, NS and Hasselwander, O and Finn, RD and Klamert, S and Korcsmaros, T and Hall, LJ},
title = {Assessing the safety of microbiome perturbations.},
journal = {Microbial genomics},
volume = {11},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001405},
pmid = {40371892},
issn = {2057-5858},
mesh = {Humans ; *Microbiota/genetics ; Gastrointestinal Microbiome ; Skin/microbiology ; Mouth/microbiology ; },
abstract = {Everyday actions such as eating, tooth brushing or applying cosmetics inherently modulate our microbiome. Advances in sequencing technologies now facilitate detailed microbial profiling, driving intentional microbiome-targeted product development. Inspired by an academic-industry workshop held in January 2024, this review explores the oral, skin and gut microbiomes, focussing on the potential long-term implications of perturbations. Key challenges in microbiome safety assessment include confounding factors (ecological variability, host influences and external conditions like geography and diet) and biases from experimental measurements and bioinformatics analyses. The taxonomic composition of the microbiome has been associated with both health and disease, and perturbations like regular disruption of the dental biofilm are essential for preventing caries and inflammatory gum disease. However, further research is required to understand the potential long-term impacts of microbiome disturbances, particularly in vulnerable populations including infants. We propose that emerging technologies, such as omics technologies to characterize microbiome functions rather than taxa, leveraging artificial intelligence to interpret clinical study data and in vitro models to characterize and measure host-microbiome interaction endpoints, could all enhance the risk assessments. The workshop emphasized the importance of detailed documentation, transparency and openness in computational models to reduce uncertainties. Harmonisation of methods could help bridge regulatory gaps and streamline safety assessments but should remain flexible enough to allow innovation and technological advancements. Continued scientific collaboration and public engagement are critical for long-term microbiome monitoring, which is essential to advancing safety assessments of microbiome perturbations.},
}

Humans
*Microbiota/genetics
Gastrointestinal Microbiome
Skin/microbiology
Mouth/microbiology

@article {pmid40371722,
year = {2025},
author = {Paramasivan, S and Bassiouni, A and Bokulich, NA and Ramezanpour, M and Cooksley, C and Caporasso, JG and McColl, SR and Wormald, PJ and Psaltis, AJ and Vreugde, S},
title = {Tertiary Lymphoid Organs Are Associated With Bacterial Dysbiosis in Chronic Rhinosinusitis.},
journal = {International forum of allergy & rhinology},
volume = {},
number = {},
pages = {e23608},
doi = {10.1002/alr.23608},
pmid = {40371722},
issn = {2042-6984},
}

@article {pmid40371708,
year = {2025},
author = {Attaye, I and Bird, JK and Nieuwdorp, M and Gül, S and Seegers, JFML and Morrison, S and Hofkens, S and Herrema, H and Bui, N and Puhlmann, ML and de Vos, WM},
title = {Anaerobutyricum soehngenii improves glycemic control and other markers of cardio-metabolic health in adults at risk of type 2 diabetes.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2504115},
doi = {10.1080/19490976.2025.2504115},
pmid = {40371708},
issn = {1949-0984},
mesh = {Humans ; *Diabetes Mellitus, Type 2/metabolism/microbiology/prevention & control ; Middle Aged ; Male ; Female ; Double-Blind Method ; *Glycemic Control ; Adult ; Glycated Hemoglobin/analysis/metabolism ; Blood Glucose/metabolism ; Aged ; Prediabetic State/therapy ; Biomarkers/blood ; Blood Pressure ; Gastrointestinal Microbiome ; Europe ; },
abstract = {Anaerobutyricum soehngenii (previously Eubacterium hallii) is a butyrate-producing next-generation beneficial microbe generally recognized as safe. Several short-term intervention trials by A. soehngenii L2-7 have shown improvement of insulin sensitivity in prediabetic subjects and type 2 diabetes patients. To determine the long-term cardiometabolic benefits and safety, we performed a 3-month double-blind, randomized placebo-controlled intervention in 98 prediabetic insulin-resistant adults in Europe and U.S. with daily administration of encapsulated cells of A. soehngenii CH-106, a tetracycline-sensitive isogenic derivative of strain L2-7. Compared to placebo, A. soehngenii-treated subjects showed significantly reduced glycemic variability (1% reduction in the coefficient of variation; p = 0.01) and improved glycemic control (6% reduction in the overall net glycemic action-1; p < 0.05), including reduced serum glycated hemoglobin (HbA1c) levels when including the 4-week washout period (1 mmol/mol reduction; p < 0.05). Moreover, diastolic blood pressure was significantly reduced in all A. soehngenii-treated subjects (3 mm Hg; p < 0.05). The study product was well-tolerated and had no effect on the global intestinal microbiota composition, including alpha and beta-diversity, besides an increased abundance of A. soehngenii in the treatment group, indicative of compliance. The U.S. participants, compared to those in Europe, responded best, notably in the oral glucose tolerance tests (15% improvement in the area-under-the curve of plasma glucose levels; p = 0.039) or coefficient of variation (reduction of 3.1%; p < 0.05). This potentially relates to a more severe prediabetic state in U.S. subjects, associated with significantly reduced (1.5-3.5-fold) relative abundance of Bifidobacterium, Coprococcus, Ruminococcus spp. and two-fold increased relative abundance of Lachnoclostridium spp. In conclusion, daily oral supplementation with A. soehngenii was safe and improved various markers of glycemic control, reduced HbA1c levels and diastolic blood pressure, indicating a novel microbiome-based approach to improve cardio-metabolic health in adults at risk for developing type 2 diabetes.Clinical trial reg. no. NCT04529473, clinicaltrials.govSocial media summary 120 characters: Anaerobutyricum soehngenii supplementation improves #cardio-metabolic health in subjects at risk for type 2 #diabetes.},
}

Humans
*Diabetes Mellitus, Type 2/metabolism/microbiology/prevention & control
Middle Aged
Male
Female
Double-Blind Method
*Glycemic Control
Adult
Glycated Hemoglobin/analysis/metabolism
Blood Glucose/metabolism
Aged
Prediabetic State/therapy
Biomarkers/blood
Blood Pressure
Gastrointestinal Microbiome
Europe

@article {pmid40371617,
year = {2025},
author = {Rodrigues, IG and Moreno-Navarrete, J and Fernández-Real, JM},
title = {Gut microbiota and iron homeostasis: implications for glycemic control.},
journal = {Minerva medica},
volume = {},
number = {},
pages = {},
doi = {10.23736/S0026-4806.25.09706-X},
pmid = {40371617},
issn = {1827-1669},
abstract = {The gut microbiome, comprised of diverse microorganisms, plays a critical role in maintaining metabolic, immune, and digestive health. This dynamic ecosystem is highly influenced by external factors such as diet, genetics, environmental factors, and even medication use, including antibiotics. Iron, already bioavailable in the Archean Ocean, is one of the most abundant elements on Earth. All organisms compete or collaborate to obtain iron, demonstrating its relevance in the biological and physiological processes essential to the maintenance of metabolic homeostasis. The bidirectional relationship between the intestinal microbiota, and the host organism in obtaining iron influences both the metabolism of the host, and that of the microbiota. Bacteria in microbiota affects the absorption of iron by the organism, while factors such as iron deficiency or excess in the host modify bacterial biodiversity, its taxonomic composition and its functions. These changes impact bacterial virulence, influencing systemic iron levels, tissue storage and glucose metabolism in the host organism. Patients with changes in glucose metabolism and insulin resistance often present imbalances in iron regulation and alterations in the profile of their intestinal microbiota. The interaction between microbiota, iron and glycemia represents an emerging field of research, standing out as a promising area for nutritional and therapeutic interventions to promote metabolic health. This review explores the relationship between iron metabolism and gut microbiota, highlighting its impact on glucose metabolism.},
}

@article {pmid40371613,
year = {2025},
author = {Wang, M and Ma, G and Li, Y and Li, J and Xie, J and He, J and He, C and He, Y and Jia, K and Feng, X and Tian, T and Li, H and Liao, X and Liu, X},
title = {Potential Modulatory Roles of Gut Microbiota and Metabolites in the Associations of Macronutrient-to-Physical Activity Ratios With Dyslipidemia.},
journal = {Journal of the American Heart Association},
volume = {},
number = {},
pages = {e040042},
doi = {10.1161/JAHA.124.040042},
pmid = {40371613},
issn = {2047-9980},
abstract = {BACKGROUND: Lifestyle factors toward diet and physical activity (PA) may directly influence the pathophysiology of dyslipidemia. However, the associations of the specific macronutrient-to-PA ratio with dyslipidemia, and the underlying mechanisms regarding gut microbiota and metabolites, remain largely unexplored.

METHODS: Dietary and PA information from 273 participants with or at risk of metabolic syndrome was collected via a food frequency questionnaire and the International Physical Activity Questionnaire. Gut microbial genera and fecal metabolites were profiled through 16S rRNA sequencing and untargeted LC-MS metabolomics, respectively. Machine-learning algorithms were applied to identify gut microbiome features of macronutrient-to-PA ratios and to construct microbiome risk score.

RESULTS: Higher macronutrient-to-PA ratios, especially for high saturated fatty acid intake, were associated with increased risks of dyslipidemia, with adjusted odds ratio (95% CIs) of 2.87 (1.41-5.99) for hypercholesteremia, 2.21 (1.11-4.48) for hypertriglyceridemia, and 2.52 (1.26-5.16) for high low-density lipoprotein cholesterol. Microbiome risk scores were significantly associated with elevated levels of total cholesterol, triglycerides, and low-density lipoprotein cholesterol. Additionally, for each macronutrient-to-PA ratio, a core group of gut microbial genera were identified (eg, Phocaeicola, Lachnoclostridium, Limosilactobacillus, and Tyzzerella), exhibiting positive associations with lipid disorders and superior discrimination capacities for hypercholesterolemia, hypertriglyceridemia, and high low-density lipoprotein cholesterol. Furthermore, we identified 9 metabolites (eg, acetyl phosphate, glycerol, and pyruvic acid), predominantly enriched in dyslipidemia-related pathways and associated with both core gut microbial taxa and macronutrient-to-PA ratios.

CONCLUSIONS: This study identified varied associations between macronutrient-to-PA ratios and dyslipidemia and depicted the potential modulatory roles of gut microbiota and fecal metabolites.},
}

@article {pmid40371437,
year = {2025},
author = {Zhao, X and Chen, A and Gong, X and Zhang, P and Cui, K and Li, S and Zhang, W and Zhu, C and Gang, H and Huo, J and Xie, F and Qin, D},
title = {Metabolite-mediated responses of phyllosphere microbiota to powdery mildew infection in resistant and susceptible black currant cultivars.},
journal = {Horticulture research},
volume = {12},
number = {7},
pages = {uhaf092},
pmid = {40371437},
issn = {2662-6810},
abstract = {Plant-metabolite-microbe interactions play essential roles in disease suppression. Most studies focus on the root exudates and rhizosphere microbiota to fight soil-borne pathogens, but it is poorly understood whether the changes in phyllosphere metabolites can actively recruit beneficial microbes to enhance disease resistance. In this study, the differences of phyllosphere microbial communities and key leaf metabolites were systematically explored in resistant and susceptible black currant cultivars related to powdery mildew (PM) by integrating microbiome and metabolomic analyses. The results showed that the diversity and composition of microbiome changed, as highlighted by a reduction in microbial alpha-diversity and beta-diversity of susceptible cultivars. An increasing fungal network complexity and a decreasing bacterial network complexity occurred in resistant cultivar. Bacillus, Burkholderia (bacteria), and Penicillium (fungi) were identified as keystone microorganisms and resistance effectors in resistant cultivar. Metabolites such as salicylic acid, trans-zeatin, and griseofulvin were more abundant in resistant cultivar, which had a positive regulatory effect on the abundance of bacterial and fungal keystones. These findings unravel that resistant cultivar can enrich beneficial microorganisms by adjusting leaf metabolites, thus showing the external disease-resistant response. Moreover, the reduced stomatal number and increased tissue thickness were observed in resistant cultivar, suggesting inherent physical structure also provides a basic defense against PM pathogens. Therefore, resistant black currant cultivar displayed multilevel defense responses of physical structures, metabolites, and microorganisms to PM pathogens. Collectively, our study highlights the potential for utilizing phyllosphere microbiome dynamics and metabolomic adjustments in agricultural practices, plant breeding, and microbiome engineering to develop disease-resistant crops.},
}

@article {pmid40371176,
year = {2025},
author = {Reji, L and Duan, J and Myneni, SCB and Zhang, X},
title = {Distinct microbiomes underlie divergent responses of methane emissions from diverse wetland soils to oxygen shifts.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf063},
pmid = {40371176},
issn = {2730-6151},
abstract = {Hydrological shifts in wetlands, a globally important methane (CH4) source, are critical constraints on CH4 emissions and carbon-climate feedbacks. A limited understanding of how hydrologically driven oxygen (O2) variability affects microbial CH4 cycling in diverse wetlands makes wetland CH4 emissions uncertain. Transient O2 exposure significantly stimulated anoxic CH4 production in incubations of Sphagnum peat from a temperate bog by enriching for polyphenol oxidizers and polysaccharide degraders, enhancing substrate flow toward methanogenesis under subsequent anoxic conditions. To assess whether shifts in soil microbiome structure and function operate similarly across wetland types, here we examined the sensitivity of different wetland soils to transient oxygenation. In slurry incubations of Sphagnum peat from a minerotrophic fen, and sediments from a freshwater marsh and saltmarsh, we examined temporal shifts in microbiomes coupled with geochemical characterization of slurries and incubation headspaces. Oxygenation did not affect microbiome structure and anoxic CH4 production in mineral-rich fen-origin peat and freshwater marsh soils. Key taxa linked to O2-stimulated CH4 production in the bog-origin peat were notably rare in the fen-origin peat, supporting microbiome structure as a primary determinant of wetland response to O2 shifts. In contrast to freshwater wetland experiments, saltmarsh geochemistry-particularly pH-and microbiome structure were persistently and significantly altered postoxygenation, albeit with no significant impact on greenhouse gas emissions. These divergent responses suggest wetlands may be differentially resistant to O2 fluctuations. With climate change driving greater O2 variability in wetlands, our results inform mechanisms of wetland resistance and highlight microbiome structure as a potential resiliency biomarker.},
}

@article {pmid40371158,
year = {2025},
author = {Liu, Y and Ning, H and Li, Y and Li, Y and Ma, J},
title = {The microbiota in breast cancer: dysbiosis, microbial metabolites, and therapeutic implications.},
journal = {American journal of cancer research},
volume = {15},
number = {4},
pages = {1384-1409},
pmid = {40371158},
issn = {2156-6976},
abstract = {The human microbiome plays a pivotal role in host health and disease, with emerging evidence underscoring its significant influence on the development and progression of breast cancer. Studies have revealed that dysbiosis in both the gut and breast tissue microbiota is strongly associated with an elevated risk of breast cancer. Distinct microbial profiles have been identified among healthy individuals, patients with benign breast conditions, and those with malignant tumors, with further variations observed across different ethnic groups and breast cancer subtypes. The complex interplay between breast cancer risk factors and microbial populations, coupled with the direct impact of microbial communities and their metabolites on inflammatory pathways and immune responses, underscores the importance of this field. Additionally, the interaction between gut microbiota and therapeutic modalities such as chemotherapy and radiotherapy is of particular interest, as these interactions can significantly influence treatment outcomes, either enhancing or diminishing efficacy. This review explores the effects of the Mediterranean diet, probiotics, prebiotics, and natural medicinal products on gut microbiota, emphasizing their potential as innovative therapeutic strategies. Notably, the use of engineered probiotics within the tumor microenvironment represents a promising frontier in breast cancer treatment. In conclusion, research on the human microbiome not only deepens our understanding of breast cancer pathogenesis but also lays the groundwork for the development of novel and targeted therapeutic interventions.},
}

@article {pmid40371119,
year = {2025},
author = {Wang, L and Li, N and Zheng, Y and Huang, Q and Cui, G and Cheng, X and He, Y and Niu, Y and Sun, Y and Wang, X and Luo, H and Liu, P and Tan, J and Huang, B and Li, L and Ma, P and Li, D and Li, Y and Li, J and Yu, Z and Ren, Z and Yuan, Y},
title = {The tongue coating microbiome is perturbed in atrial fibrillation and partly normalized after catheter ablation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1508089},
pmid = {40371119},
issn = {1664-302X},
abstract = {BACKGROUND: There is accumulating evidence linking the microbiome and cardiovascular diseases. Nevertheless, no existing studies have been conducted on atrial fibrillation (AF) and the oral microbiome.

MATERIALS AND METHODS: We collected and sequenced 245 AF tongue-coating samples and 26 AF samples after catheter ablation from Zhengzhou and Guangshan, China. We characterized tongue coating microbiome, constructed microbial classifiers in the discovery cohort, and verified their diagnostic potential in a cross-regional cohort.

RESULTS: Tongue coating microbial richness and diversity were significantly increased in the AF group compared to the control group, indicating increased bacterial colonization. The classifiers based on four optimal tongue coating microbial markers achieved good diagnostic efficiency in AF cohorts, with area under the curve (AUC) of 99.10 and 98.62% in the discovery and validation cohorts, respectively, and 97.97% in the cross-regional cohort. Paroxysmal AF and persistent AF shared similar taxonomic features, but some specific differential bacteria acted in the AF progression. Moreover, the outcomes revealed that catheter ablation contributed to rehabilitating oral bacterial disorders.

CONCLUSION: This was the first cross-sectional and longitudinal research of oral microbiome in AF patients and the alternations after catheter ablation, which offers promising new perspectives for AF clinical diagnosis and management.},
}

@article {pmid40371116,
year = {2025},
author = {Sun, X and Yang, B and Chen, C},
title = {Uncovering the heterogeneity of the gut microbial taxa associated with the contents of different fatty acids in muscle with cecum luminal content and fecal samples from two pig populations.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1575383},
pmid = {40371116},
issn = {1664-302X},
abstract = {Fatty acids in pork are involved in cellular physiological functions and related to meat nutrition, tenderness, and flavor. Increasing evidences have suggested that short-chain fatty acids produced by the gut microbiota may affect host metabolism and energy utilization. However, the association between gut microbiota and long-chain fatty acids (LCFAs) in pork has been largely unknown. In this study, the microbial compositions of 243 cecum content samples from Erhualian pigs and 235 fecal samples from Bamaxiang pigs were determined by high throughput 16S rRNA gene sequencing. The contents of 12 LCFAs in longissimus dorsi (LD) muscle were also determined for all experimental pigs of both pig populations. We systematically evaluated the contribution of gut microbiota to the variations of muscle fatty acid contents from the α-diversity of gut microbiota, co-abundance groups (CAGs) of Amplicon Sequence Variants (ASVs), and fatty acid-associated bacterial taxa. We identified hundred ASVs and > 40 bacterial taxa that were significantly associated with muscle fatty acid contents in two pig populations. Different numbers and bacterial taxa associated with the content of specific LCFAs in muscle were detected between cecum luminal content and fecal samples, suggesting the heterogeneity of the specific LCFA-associated bacterial taxa between two gut locations. We uncovered some interesting associations between bacterial taxa and muscle fatty acid contents. The strongest association was observed between the ASV annotated to Akkermansia and the n-6/n-3 polyunsaturated fatty acid ratio (p = 6.45E-04, Z = -9.65). The gut microbiota could explain 1.47-4.62% variation of muscle contents of twelve fatty acids. The functional prediction analysis identified that the KEGG pathways related to the metabolisms of carbohydrate and lipids, and to fat digestion and absorption were positively associated with the contents of muscle fatty acids. However, adipocytokine signaling pathway and thermogenesis were negatively associated with muscle fatty acid contents. The results from this study provided the basic knowledge for improving the muscle fatty acid contents by regulating the gut microbiome.},
}

@article {pmid40371112,
year = {2025},
author = {Zheng, H and Liu, D and Li, Y and Chen, Z and Li, J and Dong, Y and Yang, C and Miao, Y and Yuan, J and Ding, W},
title = {Wetland restoration suppresses microbial carbon metabolism by altering keystone species interactions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1570703},
pmid = {40371112},
issn = {1664-302X},
abstract = {Soil bacteria play a pivotal role in regulating multifaceted functions of terrestrial ecosystems. Unraveling the succession of bacterial communities and the feedback mechanism on soil organic carbon (SOC) dynamics help embed the ecology of microbiome into C cycling model. However, how wetland restoration drives soil bacterial community assembly and species association to regulate microbial C metabolism remains unclear. Here, we investigated soil bacterial diversity, community structure and co-occurrence network, enzyme activities and SOC decomposition in restored wetlands for one, three, and four years from paddy fields in Northeast China. Wetland restoration for three and four years increased taxonomic (richness) and phylogenetic diversities by 2.39-3.96% and 2.13-3.02%, respectively, and increased the relative contribution of nestedness to community dissimilarity, indicating increased richness changed soil bacterial community structure. However, wetland restoration for three and four years decreased the richness index of aerobic Firmicutes by 5.04-5.74% due to stronger anaerobic condition characterized by increased soil Fe[2+]/Fe[3+] from 0.20 to 0.64. Besides, wetland restoration for four years decreased network complexity (characterized by decreased node number by 2.51%, edge number by 9.62%, positive/negative edge number by 6.37%, average degree by 5.74% and degree centralization by 6.34%). Robustness index decreased with the increase of restoration duration, while vulnerability index increased with the increase of restoration duration, indicating that wetland restoration decreased network stability of soil bacterial communities. These results might be because stronger anaerobic condition induced the decrease of aerobic Bacilli richness index in keystone module, thereby reducing positive association within keystone module. Decreased positive species association within keystone module in turn weakened microbial C metabolism by decreasing hydrolase activities from 7.49 to 5.37 mmol kg SOC[-1] h[-1] and oxidase activities from 627 to 411 mmol kg SOC[-1] h[-1], leading to the decrease of SOC decomposition rate from 1.39 to 1.08 g C kg SOC[-1] during wetland restoration. Overall, our results suggested that although wetland restoration after agricultural abandonment increased soil bacterial diversity, it decreased positive association within Bacilli-dominated keystone module under stronger anaerobic condition, which weakened microbial C metabolism and SOC decomposition.},
}

@article {pmid40371088,
year = {2025},
author = {Yan, L and Wang, X and Liu, X and Cai, J and Zhang, Z and Yang, B},
title = {An analysis of electroacupuncture as adjunctive treatment for insomnia: a new perspective targeting GABA-mediated microbiome-gut-brain axis.},
journal = {Frontiers in neurology},
volume = {16},
number = {},
pages = {1504316},
pmid = {40371088},
issn = {1664-2295},
abstract = {INTRODUCTION: Insomnia is a prevalent psychiatric disorder that significantly impacts mental and physical health. Emerging evidence suggests that gut microbiota, particularly γ-aminobutyric acid (GABA) producing bacteria, plays a critical role in the microbiome-gut-brain axis (MGBA), influencing sleep and mental states. Electroacupuncture (EA) has been shown to have favorable anti-insomnia effects. This research protocol outlines a randomized controlled trial (RCT) designed to investigate the efficacy of EA in modulating GABA levels via the MGBA to alleviate insomnia.

METHODS AND ANALYSIS: The study will use glutamate (Glu) concentrations of p-chlorophenylalanine (PCPA) -induced insomnia rat model to examine whether EA at specific acupoints can increase GABA levels in the brain and plasma by enhancing the abundance of GABA-producing gut bacteria. A second experiment will transplant stool from insomnia rats into germ-free mice to evaluate the causal role of microbiota in insomnia pathology. Primary outcome measures include changes in GABA and Glu levels, data about the open field test, and gut microbiota composition.

DISCUSSION: This study will provide insights into the therapeutic mechanisms of EA targeting the MGBA in the treatment of insomnia and contribute to the development of novel therapeutic strategies.

ETHICS AND DISSEMINATION: This study has been approved by the Laboratory Animal Center of Xiamen University (No. XMULAC20220100). The study findings will be submitted for publication in peer-reviewed academic journals.},
}

@article {pmid40371001,
year = {2025},
author = {Nakao, M and Hosokawa, N and Ziren, W and Yamamoto, T and Ebisu, Y and Watanabe, N and Watari, T and Otsuka, Y and Osawa, R},
title = {Capnocytophaga cynodegmi bacteremia associated with a cat bite in a patient with systemic lupus erythematosus on hemodialysis: A case report.},
journal = {IDCases},
volume = {40},
number = {},
pages = {e02240},
pmid = {40371001},
issn = {2214-2509},
abstract = {The genus Capnocytophaga, which is part of the oral microbiome of both humans and animals, has the potential to cause severe infections in humans following animal bites. A 59-year-old man with systemic lupus erythematosus (SLE) on hemodialysis presented with cellulitis of the left upper limb after being bitten by his cat and was admitted to our hospital. Blood cultures were obtained, and empiric treatment with ampicillin/sulbactam was initiated. The patient developed a non-severe drug eruption on the 3rd hospital day, prompting a switch to ceftriaxone. Thin spindle-shaped Gram-negative bacilli were isolated from the blood cultures 127 h (5 days and 7 h) after obtained blood sample, and the patient completed a 2-weeks course of ceftriaxone with complete recovery. The isolate was identified as Capnocytophaga cynodegmi by MALDI-TOF MS and 16S rRNA gene sequencing. This case highlights the importance of considering C. cynodegmi in cat bite-associated infections. Obtaining blood cultures and extending incubation periods may be crucial for identifying the causative pathogen and guiding appropriate treatment in such cases.},
}

@article {pmid40370569,
year = {2025},
author = {Wei, W and Schnabl, B},
title = {Unlocking the potential of the gut microbiome in liver regeneration: Benefits and mechanistic insights.},
journal = {Acta pharmaceutica Sinica. B},
volume = {15},
number = {3},
pages = {1715-1716},
pmid = {40370569},
issn = {2211-3835},
}

@article {pmid40370529,
year = {2025},
author = {Adamko, DJ and Hildebrand, KJ},
title = {The changing epidemiology of paediatric childhood asthma and allergy in different regions of the world.},
journal = {Frontiers in allergy},
volume = {6},
number = {},
pages = {1584928},
pmid = {40370529},
issn = {2673-6101},
abstract = {Allergic disorders encompass a variety of conditions including asthma, atopic dermatitis, food allergy, allergic rhinitis, and eosinophilic esophagitis. These atopic disorders are connected via an abnormal host immune response to the environment. A series of longitudinal cross-sectional studies conducted over the past 3 decades have reported on the epidemiological trends that contribute towards the development of pediatric asthma and allergic disease. Infant birth cohort studies assessing the microbiome have offered clues as to the underlying biological mechanisms and basis for allergic disease. Why this abnormal immune response is occurring is the basis of decades of research and the reasons for this chapter. Our understanding of the biology of the immune system has increased exponentially with the advances in genomic testing, providing further opportunity for targeted treatments and more importantly, primary prevention of atopic disease.},
}

@article {pmid40370449,
year = {2025},
author = {Xie, X and Chen, X and Wang, X and Wang, S and Qi, P},
title = {Dual regulatory effects of gut microbiota and their metabolites in rheumatoid arthritis: balancing pathogenic and protective mechanisms.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1584023},
pmid = {40370449},
issn = {1664-3224},
mesh = {Humans ; *Arthritis, Rheumatoid/metabolism/microbiology/immunology/etiology ; *Gastrointestinal Microbiome/immunology ; Animals ; Biomarkers ; },
abstract = {Rheumatoid arthritis is a chronic autoimmune disorder characterized by destructive, symmetric joint inflammation and synovitis, resulting in substantial disability that profoundly compromises patients' quality of life. Its pathogenesis encompasses complex interactions between genetic and environmental factors. Recent advances in bacterial DNA sequencing technologies have uncovered a significant correlation between the human gut microbiota composition and rheumatoid arthritis progression. Growing clinical and experimental evidence establishes the gut-joint axis as a crucial mediator in rheumatoid arthritis pathogenesis. Comprehensive investigation of gut microbial communities and their metabolites' influence on rheumatoid arthritis mechanisms, coupled with the elucidation of microbiome's bidirectional regulatory effects in disease development, not only deepens our understanding of pathological processes but also establishes a theoretical framework for developing novel diagnostic biomarkers and personalized therapeutic interventions to enhance patient outcomes.},
}

Humans
*Arthritis, Rheumatoid/metabolism/microbiology/immunology/etiology
*Gastrointestinal Microbiome/immunology
Animals
Biomarkers

@article {pmid40370404,
year = {2025},
author = {Li, Y and He, X and Luo, G and Zhao, J and Bai, G and Xu, D},
title = {Innovative strategies targeting oral microbial dysbiosis: unraveling mechanisms and advancing therapies for periodontitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1556688},
pmid = {40370404},
issn = {2235-2988},
mesh = {Humans ; *Dysbiosis/therapy/microbiology ; *Periodontitis/microbiology/therapy ; Probiotics/therapeutic use ; *Microbiota ; *Mouth/microbiology ; Porphyromonas gingivalis/pathogenicity ; Phage Therapy ; Tannerella forsythia/pathogenicity ; },
abstract = {Periodontitis, a prevalent inflammatory oral disease, is intricately linked to disruptions in the oral microbiome, a state known as microbial dysbiosis. This review explores the pivotal roles of key pathogens, including Porphyromonas gingivalis and Tannerella forsythia, in driving periodontitis and examines the underlying molecular mechanisms that disrupt microbial homeostasis. We discuss how interactions among bacterial species affect the oral ecosystem's balance and how microbial metabolites influence the host immune responses, contributing to disease progression. Leveraging these insights, we propose cutting-edge therapeutic approaches aimed at restoring microbial equilibrium. These include personalized pharmacological interventions tailored to individual microbiome profiles and innovative microbiome-targeted strategies such as probiotic formulations and bacteriophage therapy. By precisely modulating microbial communities, these strategies hold promise for enhancing treatment efficacy, preventing disease recurrence, and mitigating issues like antimicrobial resistance. Overall, this review paves the way for novel prevention and management techniques in periodontitis, offering significant improvements in oral health outcomes for patients.},
}

Humans
*Dysbiosis/therapy/microbiology
*Periodontitis/microbiology/therapy
Probiotics/therapeutic use
*Microbiota
*Mouth/microbiology
Porphyromonas gingivalis/pathogenicity
Phage Therapy
Tannerella forsythia/pathogenicity

@article {pmid40370343,
year = {2025},
author = {Hernandes Villani, G and Grullón-Penkova, IF and Bartz, P and Masanga, J and Lasky, JR and Cavaleri, MA and Wood, TE and Bachelot, B},
title = {Tropical Forest Soil Microbiome Modulates Leaf Heat Tolerance More Strongly Under Warming Than Ambient Conditions.},
journal = {Ecology and evolution},
volume = {15},
number = {5},
pages = {e71425},
pmid = {40370343},
issn = {2045-7758},
abstract = {It is unclear how plants respond to increasing temperatures. Leaf heat tolerance (LHT) is often at its upper limit in tropical forests, suggesting that climate change might negatively impact these forests. We hypothesized that intraspecific variation in LHT might be associated with changes in the soil microbiome, which might also respond to climate. We hypothesized that warming would increase LHT through changes in the soil microbiome: we combined an in situ tropical warming experiment with a shade house experiment in Puerto Rico. The shade house experiment consisted of growing seedlings of Guarea guidonia, a dominant forest species, under different soil microbiome treatments (reduced arbuscular mycorrhizal fungi, reduced plant pathogens, reduced microbes, and unaltered) and soil inoculum from the field experiment. Heat tolerance was determined using chlorophyll fluorescence (F V /F m) on individual seedlings in the field and on groups of seedlings (per pot) in the shade house. We sequenced soil fungal DNA to analyze the impacts of the treatments on the soil microbiome. In the field, seedlings from ambient temperature plots showed higher F V /F m values under high temperatures (0.648 at 46°C and 0.067 at 52°C) than seedlings from the warming plots (0.535 at 46°C and 0.031 at 52°C). In the shade house, the soil microbiome treatments significantly influenced the fungal community composition and LHT (T crit and F V /F m). Reduction in fungal pathogen abundance and diversity altered F V /F m before T 50 for seedlings grown with soil inoculum from the warming plots but after T 50 for seedlings grown with soil inoculum from the ambient plots. Our findings emphasize that the soil microbiome plays an important role in modulating the impacts of climate change on plants. Understanding and harnessing this relationship might be vital for mitigating the effects of warming on forests, emphasizing the need for further research on microbial responses to climate change.},
}

@article {pmid40370113,
year = {2025},
author = {Jiang, H and Zhou, C and Liang, Z and Wu, W and Ahmed, T and Gao, Q and Liao, M and Cao, H},
title = {Serratia marcescens Sm85 produces dimethyl disulfide defense against rice sheath blight and effects on phyllosphere bacterial community.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.8853},
pmid = {40370113},
issn = {1526-4998},
support = {//Anhui Agricultural University Postdoctoral Stability Fund/ ; 03087003//Anhui Agricultural University Postdoctoral Stability/ ; },
abstract = {BACKGROUND: Rice sheath blight (RSB), caused by Rhizoctonia solani Kuhn, significantly impacts rice yield and quality. The extensive use of chemical pesticides, while often effective, requires high application rates, causes environmental damage, is expensive, and contributes to the development of pesticide resistance. The lack of reliability and robustness of these conventional techniques necessitates the development of sustainable and environmentally friendly agricultural practices. Identifying novel biological control agents is crucial for developing effective and eco-friendly strategies to manage RSB.

RESULTS: This study identifies S. marcescens 85 (Sm85), isolated from rice stems, as a potential biocontrol agent against RSB. Sm85 produces the volatile chemical dimethyl disulfide (DMDS), which has antagonistic activity both in vivo (67.4% effective) and in vitro (97.7% effective). DMDS disrupts pathogen cell membrane integrity by increasing reactive oxygen species (ROS) production and reducing ergosterol content. The pot experiments demonstrated that DMDS treatment significantly reduces RSB lesion length, with a control effect comparable to commercial fungicides. The high-throughput data revealed that DMDS application alters the phyllosphere microbial community structure, increasing its richness and diversity. Notably, DMDS treatment enriches potentially beneficial bacteria such as Stenotrophomonas and Burkholderia, known for their roles in plant stress tolerance and pesticide degradation. Functional gene analysis reveals an upregulation of sulfur metabolism-related genes in the phyllosphere microbiome, suggesting adaptive responses to DMDS.

CONCLUSION: This study highlights the potential of Sm85 and its volatile metabolite DMDS as eco-friendly alternatives for RSB management, while also emphasizing the importance of considering microbial community dynamics in biocontrol strategies. © 2025 Society of Chemical Industry.},
}

@article {pmid40370098,
year = {2025},
author = {Wang, N and Wu, M and Gu, W and Dai, C and Shao, Z and Subbalakshmi, KP},
title = {MSFT-transformer: a multistage fusion tabular transformer for disease prediction using metagenomic data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {3},
pages = {},
doi = {10.1093/bib/bbaf217},
pmid = {40370098},
issn = {1477-4054},
support = {JUSRP123035//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Computational Biology/methods ; Algorithms ; },
abstract = {More and more recent studies highlight the crucial role of the human microbiome in maintaining health, while modern advancements in metagenomic sequencing technologies have been accumulating data that are associated with human diseases. Although metagenomic data offer rich, multifaceted information, including taxonomic and functional abundance profiles, their full potential remains underutilized, as most approaches rely only on one type of information to discover and understand their related correlations with respect to disease occurrences. To address this limitation, we propose a multistage fusion tabular transformer architecture (MSFT-Transformer), aiming to effectively integrate various types of high-dimensional tabular information extracted from metagenomic data. Its multistage fusion strategy consists of three modules: a fusion-aware feature extraction module in the early stage to improve the extracted information from inputs, an alignment-enhanced fusion module in the mid stage to enforce the retainment of desired information in cross-modal learning, and an integrated feature decision layer in the late stage to incorporate desired cross-modal information. We conduct extensive experiments to evaluate the performance of MSFT-Transformer over state-of-the-art models on five standard datasets. Our results indicate that MSFT-Transformer provides stable performance gains with reduced computational costs. An ablation study illustrates the contributions of all three models compared with a reference multistage fusion transformer without these novel strategies. The result analysis implies the significant potential of the proposed model in future disease prediction with metagenomic data.},
}

*Metagenomics/methods
Humans
*Metagenome
*Computational Biology/methods
Algorithms

@article {pmid40369689,
year = {2025},
author = {Zuffa, S and Lay, C and Wimborne, EA and Rodriguez, AH and Wu, Y and Nobrega, FL and Bartke, N and Hokken-Koelega, ACS and Knol, J and Roeselers, G and Swann, JR},
title = {Milk phospholipid-coated lipid droplets modulate the infant gut microbiota and metabolome influencing weight gain.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {120},
pmid = {40369689},
issn = {2049-2618},
support = {MR/W003597/1/MRC_/Medical Research Council/United Kingdom ; BB/W00139X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Phospholipids/chemistry ; *Milk, Human/chemistry ; *Lipid Droplets/chemistry/metabolism ; *Infant Formula/chemistry ; *Weight Gain ; Female ; *Metabolome ; Male ; Feces/microbiology/chemistry ; Bacteria/classification/isolation & purification/genetics ; Infant, Newborn ; Breast Feeding ; },
abstract = {BACKGROUND: The supramolecular structure and composition of milk fat globules in breast milk is complex. Lipid droplets in formula milk are typically smaller compared to human milk and differ in their lipid and protein composition. These droplets play an important role in gut and immune maturation, and their components possess antimicrobial and antiviral properties. Here, the influence of a concept infant formula (IF) containing large milk phospholipid-coated lipid droplets on the maturation of the infant microbiota, metabolome, and weight gain in the first year of life was investigated.

RESULTS: Formula-fed infants were randomized to receive either a standard IF (Control) or a Test formula containing large milk phospholipid-coated lipid droplets (Test) until 17 weeks of age. A breast-fed Reference group was also investigated. At 3 months of age, several taxa identified as opportunistic pathogens (e.g., Enterobacter, Klebsiella, Enterococcus, Streptococcus) were less abundant in the Test stools compared to Control, while an enrichment of the butyrate-producing Ruminococcaceae and Lachnospiraceae was observed. These findings indicate that the Test formula resulted in gut microbiota maturation trajectories more comparable to healthy breast-fed infants. This was accompanied by variation in several fecal and plasma metabolites at 3 months of age related to gut microbial metabolism including bile acids, hippurate, phenylacetylglycine, trimethylamine, and various lipids and fatty acids. At 12 months, measures of subcutaneous fat and body mass index (BMI) were significantly higher in infants receiving standard IF compared to those receiving breast milk. However, this weight gain and adiposity was attenuated in the Test group infants.

CONCLUSIONS: The presence of large phospholipid-coated lipid droplets in formula milk positively influenced the development of the infants' gut microbiota, their metabolomic profiles, and their body composition to more closely resemble breast-fed infants compared to standard IF. These droplets may further enhance the restriction of pathogenic bacteria seen with standard infant formula and suggest a potential impact on infant metabolic programming that may contribute to physiological development. Video Abstract.},
}

Humans
*Gastrointestinal Microbiome
Infant
*Phospholipids/chemistry
*Milk, Human/chemistry
*Lipid Droplets/chemistry/metabolism
*Infant Formula/chemistry
*Weight Gain
Female
*Metabolome
Male
Feces/microbiology/chemistry
Bacteria/classification/isolation & purification/genetics
Infant, Newborn
Breast Feeding

@article {pmid40369688,
year = {2025},
author = {Reinoso-Peláez, EL and Puente-Sánchez, F and Serrano, M and Calvo, JH and Ramón, M and Saura, M},
title = {Characterization of bacterial communities of ewe's vaginal tract and its potential impact on reproductive efficiency.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {48},
pmid = {40369688},
issn = {2524-4671},
support = {PRE2019-090087//Ministerio de Ciencia, Innovación y Universidades/ ; 2022-04801//Swedish Research Council, Sweden/ ; },
abstract = {The success rate of artificial insemination in sheep remains suboptimal, which has led to an emerging interest in the impact of the reproductive tract microbiome on this process. This research aims to identify the ewes' vaginal core bacterial community, examine the factors influencing bacterial composition, and to determine the association between vaginal bacteria and pregnancy success. By using a robust dataset comprising 331 multiparous ewes from three Spanish breeds (Latxa, Manchega, Rasa Aragonesa) across four herds, this study performed the sequencing of the hypervariable regions V3-V4 of the 16S ribosomal RNA gene and the identification of Amplicon Sequence Variants (ASV) to analyze the bacterial community. Our analysis revealed a core bacterial primarily consisting of the genera Streptobacillus, Histophilus, Fusobacterium, Oceanivirga, and Parvimonas. Alpha and beta diversity, as well as Random Forest analysis, identified that herd and breed were the main drivers of bacterial variability. PERMANOVA analysis also showed significant differences in bacterial composition and abundance associated with pregnancy outcomes. Notably, specific ASVs associated with Fusobacterium, Leptotrichia, Histophilus, Escherichia, and Bacteroides were predominantly found in non-pregnant ewes, while genera such as Pseudomonas, Acinetobacter, and Brevundimonas were more abundant in pregnant ewes. This study contributes to the knowledge about the critical roles of specific bacteria in determining reproductive success in sheep and provides novel insights about the importance of different factors involved in the composition of ewes' vaginal bacterial communities.},
}

@article {pmid40369669,
year = {2025},
author = {Purse, C and Parker, A and James, SA and Baker, DJ and Moss, CJ and Evans, R and Durham, J and Funnell, SGP and Carding, SR},
title = {Intestinal microbiota profiles of captive-bred cynomolgus macaques reveal influence of biogeography and age.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {47},
pmid = {40369669},
issn = {2524-4671},
support = {BB/T008717/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1//BBSRC/ ; },
abstract = {BACKGROUND: Age-associated changes to the intestinal microbiome may be linked to inflammageing and the development of age-related chronic diseases. Cynomolgus macaques, a common animal model in biomedical research, have strong genetic physiological similarities to humans and may serve as beneficial models for the effect of age on the human microbiome. However, age-associated changes to their intestinal microbiome have previously only been investigated in faecal samples. Here, we have characterised and investigated the effects of age in the cynomolgus macaque intestinal tract in luminal samples from both the small and large intestine.

RESULTS: Whole metagenomic shotgun sequencing was used to analyse the microbial communities in intestinal content obtained from six different intestinal regions, covering the duodenum to distal colon, of 24 healthy, captive-bred cynomolgus macaques, ranging in age from 4 to 20 years. Both reference-based and assembly-based computational profiling approaches were used to analyse changes to intestinal microbiota composition and metabolic potential associated with intestinal biogeography and age. Reference-based computational profiling revealed a significant and progressive increase in both species richness and evenness along the intestinal tract. The microbial community composition also significantly differed between the small intestine, caecum, and colon. Notably, no significant changes in the taxonomic abundance of individual taxa with age were found except when sex was included as a covariate. Additionally, using an assembly-based computational profiling approach, 156 putative novel bacterial and archaeal species were identified.

CONCLUSIONS: We observed limited effects of age on the composition of the luminal microbiota in the profiled regions of the intestinal tract except when sex was included as a covariate. The enteric microbial communities of the small and the large intestine were, however, distinct, highlighting the limitations of frequently used faecal microbial profiling as a proxy for the intestinal microbiota. The identification of a number of putative novel microbial taxa contributes to knowledge of the full diversity of the cynomolgus macaque intestinal microbiome.},
}

@article {pmid40369640,
year = {2025},
author = {Ana, DP and O, SJ and Flavia, T and Zhang, Y and Jorge, FL},
title = {Longitudinal host-microbiome dynamics of metatranscription identify hallmarks of progression in periodontitis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {119},
pmid = {40369640},
issn = {2049-2618},
support = {DE021553//National Institute of Dental and Craniofacial Research of the National Institutes of Health (NIDCR/NIH)/ ; DE021553//National Institute of Dental and Craniofacial Research of the National Institutes of Health (NIDCR/NIH)/ ; DE021127//National Institute of Dental and Craniofacial Research of the National Institutes of Health (NIDCR/NIH)/ ; DE021553//National Institute of Dental and Craniofacial Research of the National Institutes of Health (NIDCR/NIH)/ ; },
mesh = {Humans ; Disease Progression ; *Periodontitis/microbiology/pathology ; *Microbiota/genetics ; Longitudinal Studies ; Male ; Female ; *Transcriptome ; Middle Aged ; Adult ; *Bacteria/classification/genetics/isolation & purification ; *Host Microbial Interactions/genetics ; Gene Expression Profiling ; },
abstract = {BACKGROUND: In periodontitis, the interplay between the host and microbiome generates a self-perpetuating cycle of inflammation of tooth-supporting tissues, potentially leading to tooth loss. Despite increasing knowledge of the phylogenetic compositional changes of the periodontal microbiome, the current understanding of in situ activities of the oral microbiome and the interactions among community members and with the host is still limited. Prior studies on the subgingival plaque metatranscriptome have been cross-sectional, allowing for only a snapshot of a highly variable microbiome, and do not include the transcriptome profiles from the host, a critical element in the progression of the disease.

RESULTS: To identify the host-microbiome interactions in the subgingival milieu that lead to periodontitis progression, we conducted a longitudinal analysis of the host-microbiome metatranscriptome from clinically stable and progressing sites in 15 participants over 1 year. Our research uncovered a distinct timeline of activities of microbial and host responses linked to disease progression, revealing a significant clinical and metabolic change point (the moment in time when the statistical properties of a time series change) at the 6-month mark of the study, with 1722 genes differentially expressed (DE) in the host and 111,705 in the subgingival microbiome. Genes associated with immune response, especially antigen presentation genes, were highly up-regulated in stable sites before the 6-month change point but not in the progressing sites. Activation of cobalamin, porphyrin, and motility in the microbiome contribute to the progression of the disease. Conversely, inhibition of lipopolysaccharide and glycosphingolipid biosynthesis in stable sites coincided with increased immune response. Correlation delay analysis revealed that the positive feedback loop of activities leading to progression consists of immune regulation and response activation in the host that leads to an increase in potassium ion transport and cobalamin biosynthesis in the microbiome, which in turn induces the immune response. Causality analysis identified two clusters of microbiome genes whose progression can accurately predict the outcomes at specific sites with high confidence (AUC = 0.98095 and 0.97619).

CONCLUSIONS: A specific timeline of host-microbiome activities characterizes the progression of the disease. The metabolic activities of the dysbiotic microbiome and the host are responsible for the positive feedback loop of reciprocally reinforced interactions leading to progression and tissue destruction. Video Abstract.},
}

Humans
Disease Progression
*Periodontitis/microbiology/pathology
*Microbiota/genetics
Longitudinal Studies
Male
Female
*Transcriptome
Middle Aged
Adult
*Bacteria/classification/genetics/isolation & purification
*Host Microbial Interactions/genetics
Gene Expression Profiling

@article {pmid40369126,
year = {2025},
author = {Piteková, B and Hric, I and Zieg, J and Baranovičová, E and Konopásek, P and Gécz, J and Planet, PJ and Bielik, V},
title = {The gut microbiome and metabolome in children with a first febrile urinary tract infection: a pilot study.},
journal = {Pediatric nephrology (Berlin, Germany)},
volume = {},
number = {},
pages = {},
pmid = {40369126},
issn = {1432-198X},
abstract = {BACKGROUND: Urinary tract infection (UTI) is a common bacterial infection in the pediatric population. Febrile urinary tract infection (fUTI) can lead to severe complications such as urosepsis as well as kidney scarring, chronic kidney disease, and systemic hypertension. Recent research supports the hypothesis that dysbiosis of the microbiome may play a role in the pathogenesis and development of fUTI in infants. Our main aim was to compare the shift in gut microbiota composition between children with the first fUTI and controls.

METHODS: We conducted an observational study with 17 children with the first fUTI compared to 18 healthy controls. We performed analysis of the gastrointestinal microbiome and measurements of metabolites in stool and urine.

RESULTS: In the gut microbiome, we found significant differences with lower α-diversity the Shannon index) and significantly lower relative abundance of probiogenic bacteria (short-chain fatty acids (SCFA)) in children with the first episode of fUTI before the start of antibiotic therapy. Furthermore, our findings confirm that the length of breastfeeding has significant influence on gut microbiota composition, reducing pathogenic bacteria and enhancing beneficial taxa. Shannon diversity, duration of breastfeeding, and specific taxa, particularly Faecalibacterium and Escherichia, emerged as strong predictors linked to the development of fUTI.

CONCLUSIONS: This study demonstrates that gut microbiome changes are associated with the onset of fUTI in children. Machine learning models identified Shannon index, specific bacterial taxa, and breastfeeding as strong predictors of fUTI. The study highlighted the potential role of the gut microbiome in preventing fUTI.},
}

@article {pmid40368925,
year = {2025},
author = {Kabonick, SG and Verma, K and Modesto, JL and Pearce, VH and Winokur, KM and Groisman, EA and Townsend, GE},
title = {Hierarchical glycolytic pathways control the carbohydrate utilization regulator in human gut Bacteroides.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4488},
pmid = {40368925},
issn = {2041-1723},
support = {GM147178//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; GM123798//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; DK132711//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; },
mesh = {Humans ; *Glycolysis ; *Bacteroides/metabolism/genetics ; *Gastrointestinal Microbiome/physiology ; *Bacterial Proteins/metabolism/genetics ; Glucose/metabolism ; Fructose/metabolism ; Animals ; Mice ; Gene Expression Regulation, Bacterial ; Adenosine Triphosphate/metabolism ; Diphosphates/metabolism ; Carbohydrate Metabolism ; },
abstract = {Human dietary choices control the gut microbiome. Industrialized populations consume abundant amounts of glucose and fructose, resulting in microbe-dependent intestinal disorders. Simple sugars inhibit the carbohydrate utilization regulator (Cur), a transcription factor in members of the prominent gut bacterial phylum, Bacteroidetes. Cur controls products necessary for carbohydrate utilization, host immunomodulation, and intestinal colonization. Here, we demonstrate how simple sugars decrease Cur activity in the mammalian gut. Our findings in two Bacteroides species show that ATP-dependent fructose-1,6-bisphosphate (FBP) synthesis is necessary for glucose or fructose to inhibit Cur, but dispensable for growth because of an essential pyrophosphate (PPi)-dependent enzyme. Furthermore, we show that ATP-dependent FBP synthesis is required to regulate Cur in the gut but does not contribute to fitness when cur is absent, indicating PPi is sufficient to drive glycolysis in these bacteria. Our findings reveal how sugar-rich diets inhibit Cur, thereby disrupting Bacteroides fitness and diminishing products that are beneficial to the host.},
}

Humans
*Glycolysis
*Bacteroides/metabolism/genetics
*Gastrointestinal Microbiome/physiology
*Bacterial Proteins/metabolism/genetics
Glucose/metabolism
Fructose/metabolism
Animals
Mice
Gene Expression Regulation, Bacterial
Adenosine Triphosphate/metabolism
Diphosphates/metabolism
Carbohydrate Metabolism

@article {pmid40368677,
year = {2025},
author = {Luan, M and Mao, B and Zhao, Y and Chen, J and Yang, P and Li, W and Lei, H and Yang, Y and Chang, W and Mou, K and Li, P},
title = {Landscapes of gut microbiome and metabolic signatures in vitiligo patients with co-morbid emotional distress.},
journal = {Journal of dermatological science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jdermsci.2025.04.011},
pmid = {40368677},
issn = {1873-569X},
abstract = {BACKGROUND: Vitiligo is a depigmentation disorder frequently associated with emotional distress; however, the precise mechanisms underlying this co-morbidity remain unclear.

OBJECTIVE: This study aims to investigate whether gut dysbiosis and gut metabolites contributes to emotional distress in patients with vitiligo.

METHODS: Depression and anxiety were assessed using the Patient Health Questionnaire-9 and Generalized Anxiety Disorder-7, respectively. Totally enrolled 28 vitiligo patients were diagnosed with depression or anxiety (VWD), 44 without such conditions (VTD), and 37 healthy controls (HC). Stool samples were analyzed using 16S rRNA gene sequencing and liquid chromatography triple quadrupole tandem mass spectrometry.

RESULTS: The intestinal flora of VWD group changed significantly with reduced α-diversity. The β-diversity varied among groups. Megasphaera and Anaerostipes increased in the VWD group, whereas Bilophila etc. decreased. Linear Discriminant Analysis Effect Size revealed Lachnoclostridium as a representative flora in the VWD and Faecalibacterium as a representative flora in the VTD. Metabolites such as L-glutamic acid and indole were lower in the VWD group than in the HC, while oleamide, cuminaldehyde, and taurine were higher in the VWD with VTD group. Lachnoclostridium negatively correlated with indole and L-glutamic acid. This study identified notable variations in pathways involved in the biosynthesis of phenylalanine, tyrosine, and tryptophan bile secretion, GABAergic synapses, and taurine and hypotaurine metabolism between the VWD and HC groups.

CONCLUSION: Specific fecal microbes and metabolites may contribute to the pathogenesis of VWD. These findings provide a novel perspective for addressing emotional distress in patients with vitiligo by targeting the gut-brain-skin axis.},
}

@article {pmid40368267,
year = {2025},
author = {Kay, CD and Tejera, N and Jennings, A and Haldar, S and Bevan, D and Crossman, LC and Li, S and Cassidy, A and Minihane, AM},
title = {Effect of age and sex on the urinary elimination of a single dose of mixed flavonoids: results from a single-arm intervention in healthy UK adults.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2025.05.006},
pmid = {40368267},
issn = {1938-3207},
abstract = {BACKGROUND: Nutrition intervention trials demonstrate that increased flavonoid intake can have clinically meaningful impacts on disease outcomes/biomarkers; however, high variability in absorption and metabolism and large heterogeneity in biochemical and physiological responses are observed. The etiology of this variability is poorly understood.

OBJECTIVE: To explore the relationships between sex, age, and microbiota speciation on mixed flavonoid elimination over 24 hour (h).

METHODS: Healthy males and females (n=163) prospectively recruited on the basis of age (18-30y or 65-77 y) and sex, consumed a standardized flavonoid-rich test meal providing 640mg of cocoa/chocolate flavan-3-ols, 340mg of citrus flavanones, and 390mg of blackberry anthocyanins. Urinary samples collected at baseline (-24 h to 0 h), 0-3.5 h, >3.5h-7 h and >7-24 h were analysed for flavonoids and their metabolites by Ultra high-performance liquid chromatography-mass spectrometry (UPLC-MS/MS). Stool microbiome speciation was determined via Illumina sequencing. Linear mixed-effect models were used to assess differences in cumulative excretion across age and sex with time-by-group interaction taken as the principal analysis of effect.

RESULTS: There were no group (older females, older males, younger females, younger males) differences in total 24 h urinary metabolite recovery, but there was a trend towards a higher rate of cumulative recovery in older males at 24h (β (95% CI) -61.4 (-107, -16.0 younger males compare to older males; P-group at 24hr=0.06). Of 76 metabolites, 20 had significantly different Tmax by age and 9 by sex, with a later mean Tmax observed for older participants (92% of instances). Associations with age were not mediated by BMI or microbiome speciation. Significant differences in Cmax by sex were observed for only 6 metabolites and differences by age for 5 metabolites.

CONCLUSION: Total elimination recovery of (poly)phenols was relatively consistent across age and sex groups, while elimination kinetics differed substantially; possibly resulting from differences in intestinal transit time or kidney clearance. Assuming (poly)phenol metabolites have varying biological activities, establishing dose response relationships, and defining metabolite profiles in population subgroups is required to inform the future development of dietary flavonoid/(poly)phenol recommendations.

CLINICAL TRIAL REGISTRY: NCT01922869.},
}

@article {pmid40368260,
year = {2025},
author = {Peduzzi, G and Archibugi, L and Farinella, R and de Leon Pisani, RP and Vodickova, L and Vodicka, P and Kraja, B and Sainz, J and Bars-Cortina, D and Daniel, N and Silvestri, R and Uysal-Onganer, P and Landi, S and Dulińska-Litewka, J and Comandatore, A and Campa, D and Hughes, DJ and Rizzato, C},
title = {The exposome and pancreatic cancer, lifestyle and environmental risk factors for PDAC.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2025.05.004},
pmid = {40368260},
issn = {1096-3650},
abstract = {Pancreatic cancer (PC), particularly pancreatic ductal adenocarcinoma (PDAC), is a significant global health issue with high mortality rates. PDAC, though only 3% of cancer diagnoses, causes 7% of cancer deaths due to its severity and asymptomatic early stages. Risk factors include lifestyle choices, environmental exposures, and genetic predispositions. Conditions like new-onset type 2 diabetes and chronic pancreatitis also contribute significantly. Modifiable risk factors include smoking, alcohol consumption, non-alcoholic fatty pancreatic disease (NAFPD), and obesity. Smoking and heavy alcohol consumption increase PC risk, while NAFPD and obesity, particularly central adiposity, contribute through chronic inflammation and insulin resistance. Refined sugar and sugar-sweetened beverages (SSBs) are also linked to increased PC risk, especially among younger individuals. Hormonal treatments and medications like statins, aspirin, and metformin have mixed results on PC risk, with some showing protective effects. The gut microbiome influences PC through the gut-pancreas axis, with disruptions leading to inflammation and carcinogenesis. Exposure to toxic substances, including heavy metals and chemicals, is associated with increased PC risk. Glycome changes, such as abnormal glycosylation patterns, are significant in PDAC development and offer potential for early diagnosis. Interactions between environmental and genetic factors are crucial in PDAC susceptibility. Genome-wide association studies (GWAS) have identified several single nucleotide polymorphisms (SNPs) linked to PDAC, but gene-environment interactions remain largely unexplored. Future research should focus on polygenic risk scores (PRS) and large-scale studies to better understand these interactions and their impact on PDAC risk.},
}

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

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

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

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

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

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

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

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

CLINICALTRIALS: gov ID: NCT06250309.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

TRIAL REGISTRATION: NCT05698745.},
}