@article {pmid40065594,
year = {2025},
author = {Sun, Y and Yu, YT and Castillo, XO and Anderson, R and Wang, M and Sun, Q and Tallmadge, R and Sams, K and Reboul, G and Zehr, J and Brown, J and Wang, X and Marra, N and Stanhope, B and Grenier, J and Pusterla, N and Divers, T and Mittel, L and Goodman, LB},
title = {Investigation of the Blood Microbiome in Horses With Fever of Unknown Origin.},
journal = {Veterinary medicine and science},
volume = {11},
number = {2},
pages = {e70272},
doi = {10.1002/vms3.70272},
pmid = {40065594},
issn = {2053-1095},
support = {//Harry M. Zweig Memorial Fund for Equine Research/ ; 1U18FD006993//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network/ ; 1U18FD006716//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network/ ; W81XWH-22-1-0891//Department of Defense/ ; },
mesh = {Horses ; Animals ; *Horse Diseases/microbiology/virology/blood/epidemiology ; Case-Control Studies ; *Fever of Unknown Origin/veterinary/microbiology/etiology ; Microbiota ; Male ; Female ; },
abstract = {BACKGROUND: Fever of unknown origin (FUO) without a respiratory component is a frequent clinical presentation in horses. Multiple pathogens, both tick-borne and enteric, can be involved as etiologic agents. An additional potential mechanism is intestinal barrier dysfunction.

OBJECTIVES: This case-control study aimed to detect and associate microbial taxa in blood with disease state.

STUDY DESIGN: Areas known for a high prevalence of tick-borne diseases in humans were chosen to survey horses with FUO, which was defined as fever of 101.5°F or higher with no signs of respiratory illness or other recognisable diseases. Blood samples and clinical parameters were obtained from 52 FUO cases and also from matched controls from the same farms. An additional 23 febrile horses without matched controls were included.

METHODS: Broadly targeted polymerase chain reaction (PCR) amplification directed at conserved sequence regions of bacterial 16S rRNA, parasite 18S rRNA, coronavirus RdRp and parvovirus NS1 was performed, followed by deep sequencing. To control for contamination and identify taxa unique to the cases, metagenomic sequences from the controls were subtracted from those of the cases, and additional targeted molecular testing was performed. Sera were also tested for antibodies to equine coronavirus.

RESULTS: Over 60% of cases had intestinal microbial DNA circulating in the blood. Nineteen percent of cases were attributed to infection with Anaplasma phagocytophilum, of which two were subtyped as human-associated strains. A novel Erythroparvovirus was detected in two cases and two controls. Serum titres for equine coronavirus were elevated in some cases but not statistically different overall between the cases and controls.

MAIN LIMITATIONS: Not all pathogens are expected to circulate in blood, which was the sole focus of this study.

CONCLUSIONS: The presence of commensal gut microbes in blood of equine FUO cases is consistent with a compromised intestinal barrier, which is highlighted as a direction for future study.},
}

Horses
Animals
*Horse Diseases/microbiology/virology/blood/epidemiology
Case-Control Studies
*Fever of Unknown Origin/veterinary/microbiology/etiology
Microbiota
Male
Female

@article {pmid40065353,
year = {2025},
author = {Liu, GS and Song, Y and Yan, JS and Chai, YJ and Zhao, YF and Ma, H},
title = {Identification of enterotype for patients with Alzheimer's disease.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {299},
pmid = {40065353},
issn = {1479-5876},
mesh = {*Alzheimer Disease/microbiology ; Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Aged ; *RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; Case-Control Studies ; Neural Networks, Computer ; Aged, 80 and over ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) is a progressive and chronic neurodegenerative disorder of the central nervous system, characterized by behavioral and dysexecutive deficits. Its pathogenesis is closely associated with the intestinal flora. This study aimed to explore the enterotypes in AD by identifying key bacteria through machine learning and species co-occurrence network analysis.

METHODS: The collection of fecal samples from AD patients was followed by 16 S rRNA analysis using QIIME2. Enterotype clustering was conducted at the genus level, and deep neural network (DNN) classification models were developed for AD and healthy controls within each enterotype.

RESULTS: Analysis of three 16 S rRNA gut microbiome datasets identified three distinct enterotypes: Escherichia_Shigella (ET-E), Faecalibacterium (ET-F), and Bacteroides (ET-B). The ET-E is mainly characterized by the absence of Akkermansia in AD group. The Akkermansia was significantly positively correlated with Eubacterium_coprostanoligenes_group and negatively correlated with biosynthesis and amino acid metabolism. The ET-F highly expressed Agathobacter, un_f__Lachnospiraceae, Lachnoclostridium, and low expressed Dorea in AD group. Among them, Agathobacter was significantly positively correlated with un_f__Lachnospiraceae, and un_f__Lachnospiraceae was significantly positively correlated with Lachnoclostridium. The Dorea was significantly negatively correlated with Lachnoclostridium. The AD from ET-B group had high expression of two beneficial bacteria, Butyricicoccus and Parabacteroides. The findings suggest that the ET-E enterotype may predispose individuals to AD, with Akkermansia identified as a potential risk factor. Conversely, the ET-B enterotype appears to be associated with milder symptoms, with Butyricicoccus and Parabacteroides potentially serving as protective factors. Therefore, a comprehensive understanding of the species characteristics and interactions within different enterotypes is essential for modulating the gut-brain axis and mitigating AD symptoms.},
}

*Alzheimer Disease/microbiology
Humans
*Gastrointestinal Microbiome/genetics
Male
Female
Aged
*RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification
Feces/microbiology
Case-Control Studies
Neural Networks, Computer
Aged, 80 and over

@article {pmid40065181,
year = {2025},
author = {Iliev, ID and Ananthakrishnan, AN and Guo, CJ},
title = {Microbiota in inflammatory bowel disease: mechanisms of disease and therapeutic opportunities.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40065181},
issn = {1740-1534},
abstract = {Perturbations in the intestinal microbiome are strongly linked to the pathogenesis of inflammatory bowel disease (IBD). Bacteria, fungi and viruses all make up part of a complex multi-kingdom community colonizing the gastrointestinal tract, often referred to as the gut microbiome. They can exert various effects on the host that can contribute to an inflammatory state. Advances in screening, multiomics and experimental approaches have revealed insights into host-microbiota interactions in IBD and have identified numerous mechanisms through which the microbiota and its metabolites can exert a major influence on the gastrointestinal tract. Looking into the future, the microbiome and microbiota-associated processes will be likely to provide unparalleled opportunities for novel diagnostic, therapeutic and diet-inspired solutions for the management of IBD through harnessing rationally designed microbial communities, powerful bacterial and fungal metabolites, individually or in combination, to foster intestinal health. In this Review, we examine the current understanding of the cross-kingdom gut microbiome in IBD, focusing on bacterial and fungal components and metabolites. We examine therapeutic and diagnostic opportunities, the microbial metabolism, immunity, neuroimmunology and microbiome-inspired interventions to link mechanisms of disease and identify novel research and therapeutic opportunities for IBD.},
}

@article {pmid40065148,
year = {2025},
author = {Hiratsuka, D and Matsuo, M and Kashiwabara, K and Inoue, M and Ishizawa, C and Iida, R and Fukui, Y and Aikawa, S and Hiraoka, T and Harada, M and Wada-Hiraike, O and Osuga, Y and Hirota, Y},
title = {Comparison of diagnostic tests for chronic endometritis and endometrial dysbiosis in recurrent implantation failure: Impact on pregnancy outcomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {8272},
pmid = {40065148},
issn = {2045-2322},
mesh = {Humans ; Female ; Pregnancy ; *Endometritis/microbiology/diagnosis ; *Dysbiosis/diagnosis/microbiology ; Adult ; *Endometrium/microbiology/pathology ; *Embryo Implantation ; *Pregnancy Outcome ; Chronic Disease ; Microbiota ; Hysteroscopy ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Chronic endometritis (CE) and endometrial dysbiosis (ED) are major causes of recurrent implantation failure (RIF). CE is diagnosed via hysteroscopy or the endometrial CD138 test; ED is examined using endometrial microbiome testing with next-generation sequencing. ED is characterized by a reduction in Lactobacillus species. However, correlations between the results of the three tests and the efficacy of treatment against CE and ED in pregnancy outcomes remain unclear. We analyzed 73 patients with RIF who underwent all three tests (hysteroscopy, endometrial CD138 test, and endometrial microbiome test). Patients with CE received antibiotics, whereas those with ED received antibiotics and vaginal Lactobacillus probiotics. The incidences of CE diagnosed using hysteroscopy and the CD138 test were 56.2 and 49.3%, respectively, and the prevalence of ED was 53.4%. No correlations were observed among the test-positive individuals in these three tests. Among patients with ED, 88.9% had a post-treatment clinical pregnancy, a significantly higher rate than that in patients without ED (p = 0.021). Multivariate analysis demonstrated that ED was associated with clinical pregnancy (odds ratio (OR): 6.29, p = 0.031). In conclusion, the three tests detected different populations of patients with RIF. ED diagnosed using the endometrial microbiome test was associated with favorable pregnancy outcomes after testing.},
}

Humans
Female
Pregnancy
*Endometritis/microbiology/diagnosis
*Dysbiosis/diagnosis/microbiology
Adult
*Endometrium/microbiology/pathology
*Embryo Implantation
*Pregnancy Outcome
Chronic Disease
Microbiota
Hysteroscopy
Anti-Bacterial Agents/therapeutic use

@article {pmid40065134,
year = {2025},
author = {Jalil, A and Perino, A and Dong, Y and Imbach, J and Volet, C and Vico-Oton, E and Demagny, H and Plantade, L and Gallart-Ayala, H and Ivanisevic, J and Bernier-Latmani, R and Hapfelmeier, S and Schoonjans, K},
title = {Bile acid 7α-dehydroxylating bacteria accelerate injury-induced mucosal healing in the colon.},
journal = {EMBO molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {40065134},
issn = {1757-4684},
support = {310030_189178/SNSF_/Swiss National Science Foundation/Switzerland ; CRSII5_180317/1/SNSF_/Swiss National Science Foundation/Switzerland ; CRSII5_180317/1/SNSF_/Swiss National Science Foundation/Switzerland ; CRSII5_180317/1/SNSF_/Swiss National Science Foundation/Switzerland ; },
abstract = {Host-microbiome communication is frequently perturbed in gut pathologies due to microbiome dysbiosis, leading to altered production of bacterial metabolites. Among these, 7α-dehydroxylated bile acids are notably diminished in inflammatory bowel disease patients. Herein, we investigated whether restoration of 7α-dehydroxylated bile acids levels by Clostridium scindens, a human-derived 7α-dehydroxylating bacterium, can reestablish intestinal epithelium homeostasis following colon injury. Gnotobiotic and conventional mice were subjected to chemically-induced experimental colitis following administration of Clostridium scindens. Colonization enhanced the production of 7α-dehydroxylated bile acids and conferred prophylactic and therapeutic protection against colon injury through epithelial regeneration and specification. Computational analysis of human datasets confirmed defects in intestinal cell renewal and differentiation in ulcerative colitis patients while expression of genes involved in those pathways showed a robust positive correlation with 7α-dehydroxylated bile acid levels. Clostridium scindens administration could therefore be a promising biotherapeutic strategy to foster mucosal healing following colon injury by restoring bile acid homeostasis.},
}

@article {pmid40064825,
year = {2025},
author = {Richard, PI and Baltosser, WH and Williams, PH and He, Q},
title = {Phylogenetic analysis of microbial CP-lyase cluster genes for bioremediation of phosphonate.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {42},
pmid = {40064825},
issn = {2191-0855},
support = {80NSSC22M0043//Arkansas Space Grant Consortium/ ; },
abstract = {The ever-increasing use of phosphonates and their derivatives has resulted in the discharge of large quantities of these materials into the ecosystem, causing pollution and harmful shifts in microbiome composition. We conducted an extensive phylogenetic analysis to address this mounting problem and to help determine suitable microbes for bioremediation in specific environments. The 84 microorganisms included in our study span the gamut of species and occupied habitats. They degrade phosphonates by expressing an enzyme complex; CP-Lyase transcribed from 14 cistrons. Of the organisms studied, 12, 39, and 25 are singularly suitable for mostly freshwater, marine, or terrestrial habitats, respectively. Others adapted to multihabitats include Calothrix sp. PCC 7507 (both freshwater and marine habitats), Escherichia coli, Kaistia soli, Limoniibacter endophyticus, Marivita sp. and Virgibacillus dokdonensis (both marine and terrestrial habitats), Acidithiobacillus ferrooxidans (both freshwater and terrestrial habitats), with Paenibacillus contaminans suitable for freshwater, marine, and terrestrial habitats. All organisms were statistically rooted to glutathione peroxidase for phylogenetic perspective with tree topology dependent upon 50% or greater support. Clustered genes have been shown to have co-evolved based on striking nucleotide similarity and clade groupings within the tree topologies generated.},
}

@article {pmid40064239,
year = {2025},
author = {Okunlola, FO and Okunlola, AR and Adetuyi, BO and Soliman, MES and Alexiou, A and Papadakis, M and Fawzy, MN and El-Saber Batiha, G},
title = {Beyond the Gut: Unraveling the Multifaceted Influence of Microbiome on Cardiovascular Health.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2025.03.002},
pmid = {40064239},
issn = {2405-4577},
abstract = {Cardiovascular disease is one of the leading causes of death worldwide. Even while receiving adequate pharmacological treatment for their hypertension, people are nonetheless at greater risk for cardiovascular disease. There is growing evidence that the gut microbiota may have major positive and negative effects on blood pressure and illnesses related with it as more study into this topic is conducted. Trimethylamine n-oxide (TMAO) and short-chain fatty acids (SCFA) are two major by-products of the gut microbiota. TMAO is involved in the formation of other coronary artery diseases, including atherosclerosis and hypertension, while SCFAs play an important role in controlling blood pressure. Numerous investigations have confirmed the established link between dietary salt intake and hypertension. Reducing sodium in the diet is linked to lower rates of cardiovascular disease morbidity and mortality as well as lower rates of blood pressure and hypertension. In both human and animal research, high salt diets increase local and systemic tissue inflammation and compromise gut architecture. Given that the gut microbiota constantly interacts with the immune system and is required for the correct maturation of immune cells, it is scientifically conceivable that it mediates the inflammatory response. This review highlights the therapeutic possibilities for focusing on intestinal microbiomes as well as the potential functions of the gut microbiota and its metabolites in the development of hypertension.},
}

@article {pmid40064231,
year = {2025},
author = {Jia, Y and Huang, D and Lan, X and Sun, X and Lin, W and Sun, W and Wang, Y},
title = {Community structure and metabolic potentials of keystone taxa and their associated bacteriophages within rice root endophytic microbiome in response to metal(loid)s contamination.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126028},
doi = {10.1016/j.envpol.2025.126028},
pmid = {40064231},
issn = {1873-6424},
abstract = {Heavy metal (HM) contamination of agricultural products is of global environmental concern as it directly threatened the food safety. Plant-associated microbiome, particularly endophytic microbiome, hold the potential for mitigating HM stress as well as promoting plant growth. The metabolic potentials of the endophytes, especially those under the HM stresses, have not been well addressed. Rice, a major staple food worldwide, is more vulnerable to HM contamination compared to other crops and therefore requires special attentions. Therefore, this study selected rice as the target plants. Geochemical analysis and amplicon sequencing were combined to characterize the rice root endophytic bacterial communities and identify keystone taxa in two HM-contaminated rice fields. Metagenomic analysis was employed to investigate the metabolic potentials of these keystone taxa. Burkholderiales and Rhizobiales were identified as predominant keystone taxa. The metagenome-assembled genome (MAG)s associated with these keystone populations suggested that they possessed diverse genetic potentials related to metal resistance and transformation (e.g., As resistance and cycling, V reduction, Cr efflux and reduction), and plant growth promotion (nitrogen fixation, phosphate solubilization, oxidative stress resistance, indole-3-acetic acid, and siderophore production). Moreover, bacteriophages encoding auxiliary metabolism genes (AMGs) associated with the HM resistance as well as nitrogen and phosphate acquisition were identified, suggesting that these phages may contribute to these crucial biogeochemical processes within rice roots. The current findings revealed the beneficial roles of rice endophytic keystone taxa and their associated bacteriophages within HM-contaminated rice root endophytic microbiome, which may provide valuable insights on future applications of employing root microbiome for safety management of agriculture productions.},
}

@article {pmid40064155,
year = {2025},
author = {Cryan, JF},
title = {Microbiome and Brain Development: A Tale of Two Systems.},
journal = {Annals of nutrition & metabolism},
volume = {},
number = {},
pages = {1-19},
doi = {10.1159/000544950},
pmid = {40064155},
issn = {1421-9697},
abstract = {BACKGROUND: For the past two decades there has been a growing appreciation of the role that the microbiota (the trillions of microorganisms within and on our bodies) plays as one of the key regulators of gut-brain function and has led to the appreciation of the importance of a distinct microbiota-gut-brain axis across the lifespan but especially during neurodevelopment.

SUMMARY: The gut microbiota and its relevant metabolites interact with the immune and the central nervous systems during critical temporal windows of development. These critical developmental windows perinatally (during the first 1000 days) are susceptible timepoints for insults that can endure long-lasting effects on the microbiota-gut-brain axis. Accumulating evidence shows that a variety of factors can impact the microbiota in early life including mode of birth delivery, antibiotic exposure, mode of nutritional provision, infection, stress as well as host genetics. Additionally, sex differences occur in response to microbial manipulations in early life although the underlying mechanisms underpinning such effects remains elusive. Animal models have been essential in delineating a role of the microbiome in neurodevelopmental disorders ranging from autism spectrum disorder to attention deficit hyperactivity disorder. This mechanistic perspective should be supplemented with more translational studies to evaluate the applicability of findings from animal models to human subjects.

KEY MESSAGES: Studies examining the translation of these effects from animal models to humans are currently ongoing with evidence for microbial modulation of neurocognitive development and neurodevelopmental risk increasing.},
}

@article {pmid40064088,
year = {2025},
author = {Lehr, PP and Gschwendtner, S and Du, B and Rennenberg, H and Schloter, M and Zörb, C},
title = {Grapevines and trees: A biodiversity study of microbiomes in an established temperate agroforestry system.},
journal = {Journal of environmental management},
volume = {379},
number = {},
pages = {124882},
doi = {10.1016/j.jenvman.2025.124882},
pmid = {40064088},
issn = {1095-8630},
abstract = {Biodiversity is threatened particularly in perennial crop cultivation such as fruit trees or grapevines. If established, agroforestry has the potential to increase biodiversity by providing a higher habitat heterogeneity at the example of grapevine (Vitis vinifera L. cv. Riesling) cultivated together with oak or poplar trees for 12 years. Together with the rhizosphere microbiome, the root metabolome was quantified as an indicator of root exudation. Since the root metabolome does not fully align with the exudate metabolome, we are using the root metabolome as a proxy for the exudate metabolome. The results reveal that co-cultivation of grapevine with trees reduces the nutrient availability in the soil and changes the root metabolome of both, grapevine and trees with a more distinct effect of trees on grapevine than vice versa, particularly for oak. Apparently, root-to-root signalling takes place between trees and grapevine. Co-cultivation of grapevine and oak trees also enhanced the alpha diversity of the microbiome. Correlation analysis revealed strong positive correlations between distinct microbial families and metabolites enriched in the roots of Riesling. Thus, microbiome analyses support the view that root-to-root interaction in mixed cultivation of grapevine with trees is mediated by root exudation.},
}

@article {pmid40063888,
year = {2025},
author = {Saraphol, B and Hinthong, W and Chienwichai, P and Pumipuntu, N and Reamtong, O and Srisook, T and Premsuriya, J},
title = {Analysis of the fecal microbiome and metabolome in dairy cows with different body condition scores.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0319461},
pmid = {40063888},
issn = {1932-6203},
mesh = {Animals ; Cattle ; *Feces/microbiology ; *Metabolome ; Female ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; },
abstract = {Holstein Friesian is the most popular breed of dairy cows worldwide due to its exceptional milk production capabilities. In dairy cow management, the body condition score (BCS) is a useful tool, serving as a reliable indicator of a cow's nutritional status and overall health. It is determined via a subjective visual and tactile assessment of fat cover and muscle mass. A low BCS is associated with decreased milk production and fertility. While genetic and nutritional factors have previously been associated with BCS, their effects are often moderate. In this study, we compared the fecal microbiome and the untargeted fecal metabolome of normal (BCS ≥ 3, n = 16) and thin (BCS < 3, n = 16) Holstein Friesian dairy cows. The 16S rRNA gene-based metagenomic analysis revealed that thin cows had significantly higher levels of Clostridiaceae, Erysipelotrichales, Erysipelotrichaceae, and Turicibacter, while normal cows had higher levels of Clostridiales_vadinBB60_group, UCG-010, Bacteroidaceae, Ruminococcaceae, Paludibacteraceae, Alistipes, and Bacteroides. The fecal metabolomic analysis showed that key signaling pathways, including the mechanistic target of rapamycin (mTOR), phosphatidylinositol 3-kinase (PI3K)-Akt, and AMP-activated protein kinase (AMPK) pathways, were enriched in thin cows. In addition, a significant correlation was observed between differential microbial taxa and metabolites. Notably, Clostridiaceae and Erysipelotrichaceae species are linked to inflammation, infectious diseases, and conditions such as ruminal acidosis. Additionally, the mTOR, PI3K-Akt, and AMPK pathways are known to be activated by both nutrient deficiencies and inflammation. We propose that, in addition to genetic and nutritional factors, gut microbiome dysbiosis may contribute to subclinical health conditions, such as chronic inflammation and acidosis, which indirectly affect the cow's BCS. These findings are guiding our ongoing research on the underlying health conditions in thin cows to better understand the role that the gut microbiome plays in the regulation of the body condition.},
}

Animals
Cattle
*Feces/microbiology
*Metabolome
Female
*RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome

@article {pmid40063791,
year = {2025},
author = {Morrison, ML and Xue, KS and Rosenberg, NA},
title = {Quantifying compositional variability in microbial communities with FAVA.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {11},
pages = {e2413211122},
doi = {10.1073/pnas.2413211122},
pmid = {40063791},
issn = {1091-6490},
support = {R01 HG005855/HG/NHGRI NIH HHS/United States ; R21-AI168860//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Microbiota/genetics ; *Phylogeny ; Bacteria/genetics/classification/isolation & purification ; Humans ; },
abstract = {Microbial communities vary across space, time, and individual hosts, generating a need for statistical methods capable of quantifying variability across multiple microbiome samples at once. To understand heterogeneity across microbiome samples from different host individuals, sampling times, spatial locations, or experimental replicates, we present FAVA (FST-based Assessment of Variability across vectors of relative Abundances), a framework for characterizing compositional variability across two or more microbiome samples. FAVA quantifies variability across many samples of taxonomic or functional relative abundances in a single index ranging between 0 and 1, equaling 0 when all samples are identical and 1 when each sample is entirely composed of a single taxon (and at least two distinct taxa are present across samples). Its definition relies on the population-genetic statistic FST, with samples playing the role of "populations" and taxa playing the role of "alleles." Its mathematical properties allow users to compare datasets with different numbers of samples and taxonomic categories. We introduce extensions that incorporate phylogenetic similarity among taxa and spatial or temporal distances between samples. We demonstrate FAVA in two examples. First, we use FAVA to measure how the taxonomic and functional variability of gastrointestinal microbiomes across individuals from seven ruminant species changes along the gastrointestinal tract. Second, we use FAVA to quantify the increase in temporal variability of gut microbiomes in healthy humans following an antibiotic course and to measure the duration of the antibiotic's influence on temporal microbiome variability. We have implemented this tool in an R package, FAVA, for use in pipelines for the analysis of microbial relative abundances.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Microbiota/genetics
*Phylogeny
Bacteria/genetics/classification/isolation & purification
Humans

@article {pmid40063675,
year = {2025},
author = {Chavarria, X and Park, HS and Oh, S and Kang, D and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY},
title = {Using gut microbiome metagenomic hypervariable features for diabetes screening and typing through supervised machine learning.},
journal = {Microbial genomics},
volume = {11},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001365},
pmid = {40063675},
issn = {2057-5858},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Supervised Machine Learning ; *Diabetes Mellitus, Type 1/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Adult ; Bacteria/genetics/classification/isolation & purification ; Metagenome ; Support Vector Machine ; Aged ; Algorithms ; },
abstract = {Diabetes mellitus is a complex metabolic disorder and one of the fastest-growing global public health concerns. The gut microbiota is implicated in the pathophysiology of various diseases, including diabetes. This study utilized 16S rRNA metagenomic data from a volunteer citizen science initiative to investigate microbial markers associated with diabetes status (positive or negative) and type (type 1 or type 2 diabetes mellitus) using supervised machine learning (ML) models. The diversity of the microbiome varied according to diabetes status and type. Differential microbial signatures between diabetes types and negative group revealed an increased presence of Brucellaceae, Ruminococcaceae, Clostridiaceae, Micrococcaceae, Barnesiellaceae and Fusobacteriaceae in subjects with diabetes type 1, and Veillonellaceae, Streptococcaceae and the order Gammaproteobacteria in subjects with diabetes type 2. The decision tree, elastic net, random forest (RF) and support vector machine with radial kernel ML algorithms were trained to screen and type diabetes based on microbial profiles of 76 subjects with type 1 diabetes, 366 subjects with type 2 diabetes and 250 subjects without diabetes. Using the 1000 most variable features, tree-based models were the highest-performing algorithms. The RF screening models achieved the best performance, with an average area under the receiver operating characteristic curve (AUC) of 0.76, although all models lacked sensitivity. Reducing the dataset to 500 features produced an AUC of 0.77 with sensitivity increasing by 74% from 0.46 to 0.80. Model performance improved for the classification of negative-status and type 2 diabetes. Diabetes type models performed best with 500 features, but the metric performed poorly across all model iterations. ML has the potential to facilitate early diagnosis of diabetes based on microbial profiles of the gut microbiome.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Diabetes Mellitus, Type 2/microbiology
*RNA, Ribosomal, 16S/genetics
*Supervised Machine Learning
*Diabetes Mellitus, Type 1/microbiology
*Metagenomics/methods
Male
Female
Middle Aged
Adult
Bacteria/genetics/classification/isolation & purification
Metagenome
Support Vector Machine
Aged
Algorithms

@article {pmid40063530,
year = {2025},
author = {Serbanescu, M and Lee, S and Li, F and Boppana, SH and Elebasy, M and White, JR and Mintz, CD},
title = {Effects of Perioperative Exposure on the Microbiome and Outcomes From an Immune Challenge in C57Bl/6 Adult Mice.},
journal = {Anesthesia and analgesia},
volume = {},
number = {},
pages = {},
doi = {10.1213/ANE.0000000000007467},
pmid = {40063530},
issn = {1526-7598},
abstract = {BACKGROUND: Previous work suggests that the gut microbiome can be disrupted by antibiotics, anesthetics, opiates, supplemental oxygen, or nutritional deprivation-all of which are common and potentially modifiable perioperative interventions that nearly all patients are exposed to in the setting of surgery. Gut microbial dysbiosis has been postulated to be a risk factor for poor surgical outcomes, but how perioperative care-independent of the surgical intervention-impacts the gut microbiome, and the potential consequences of this impact have not been directly investigated.

METHODS: We developed a perioperative exposure model (PEM) in C57Bl/6 mice to emulate the most common elements of perioperative medicine other than surgery, which included 12 hours of nutritional deprivation, 4 hours of volatile general anesthetic, 7 hours of supplemental oxygen, surgical antibiotics (cefazolin), and opioid pain medication (buprenorphine). Gut microbial dynamics and inferred metabolic changes were longitudinally assessed before-and at 3 time points after-PEM by 16S rRNA amplicon sequencing. We then used fecal microbial transplant in secondary abiotic mice to test if, compared to preexposure microbiota, day 3 post-PEM microbial communities affect the clinical response to immune challenge in an endotoxemia model.

RESULTS: We observed transient changes in microbiota structure and function after the PEM, including reduced biodiversity, loss of diverse commensals associated with health (including Lactobacillus, Roseburia, and Ruminococcus), and changes in microbiota-mediated amino acid metabolic pathways. Mice engrafted with day 3 post-PEM microbial communities demonstrated markedly reduced survival after endotoxemia compared to those bearing preexposure communities (7-day survival of ~20% vs ~70%, P = .0002).

CONCLUSIONS: These findings provide the first clear evidence that the combined effects of common perioperative factors, independent of surgery, cause gut microbial dysbiosis and alter the host response to inflammation in the postoperative period.},
}

@article {pmid40063366,
year = {2025},
author = {Su, F and Su, M and Wei, W and Wu, J and Chen, L and Sun, X and Liu, M and Sun, S and Mao, R and Bourgonje, AR and Hu, S},
title = {Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2476570},
doi = {10.1080/19490976.2025.2476570},
pmid = {40063366},
issn = {1949-0984},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; *Dysbiosis/microbiology ; Animals ; Bacteria/metabolism/genetics/classification ; Genomics ; Metabolomics ; Proteomics ; Multiomics ; },
abstract = {Numerous studies have accelerated the knowledge expansion on the role of gut microbiota in inflammatory bowel disease (IBD). However, the precise mechanisms behind host-microbe cross-talk remain largely undefined, due to the complexity of the human intestinal ecosystem and multiple external factors. In this review, we introduce the interactome concept to systematically summarize how intestinal dysbiosis is involved in IBD pathogenesis in terms of microbial composition, functionality, genomic structure, transcriptional activity, and downstream proteins and metabolites. Meanwhile, this review also aims to present an updated overview of the relevant mechanisms, high-throughput multi-omics methodologies, different types of multi-omics cohort resources, and computational methods used to understand host-microbiota interactions in the context of IBD. Finally, we discuss the challenges pertaining to the integration of multi-omics data in order to reveal host-microbiota cross-talk and offer insights into relevant future research directions.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/metabolism
*Gastrointestinal Microbiome
*Host Microbial Interactions
*Dysbiosis/microbiology
Animals
Bacteria/metabolism/genetics/classification
Genomics
Metabolomics
Proteomics
Multiomics

@article {pmid40063073,
year = {2025},
author = {Yasin, M and Zohoori, FV and Kumah, EA and Subramanian, M and Dean, P and Orr, CH},
title = {Effect of Fluoride on Gut Microbiota: A Systematic Review.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuae202},
pmid = {40063073},
issn = {1753-4887},
support = {//Teesside University/ ; },
abstract = {CONTEXT: Fluoride can prevent dental caries by inhibiting demineralization and promoting remineralization of teeth while affecting the physiology of oral microbiota, thus inhibiting cellular enzymes. However, the effect of systemic fluoride on gut microbiota is unknown.

OBJECTIVE: To explore the impacts of systemic fluoride on gut microbiota composition and abundance and associated functions such as gene and metabolic regulation.

DATA SOURCES: A systematic database search was conducted of MEDLINE, Web of Science, Scopus, PubMed, CINAHL, and Embase to find articles on studies reporting the effects of fluoride on gut microbiota.

DATA EXTRACTION: Forty-nine studies were included (n = 42 in animals, 4 of humans, 3 in vitro studies) after screening for title, abstract, and full text using Covidence to check against eligibility criteria. Data were extracted using Covidence and study quality was assessed using the Mixed Method Appraisal Tool by 2 reviewers independently.

DATA ANALYSIS: Two human studies of dental fluorosis and 1 of patients with breast cancer (intestinal fluorine-18 fluorodeoxyglucose uptake) showed significant differences in gut microbial composition, with increased relative abundance of Acidobacteria and Proteobacteria, and decreased abundance of Firmicutes and Bacteroidetes. An ex vivo study of human feces indicated that ≤ 2 mg L-1 NaF might boost "health-associated" taxa, but concentrations (≥ 10 mg L-1 NaF) could increase the ratio of some unhealthy microbes after 24 hours. The animal studies examined the effects of high fluoride doses in water and diet (50-1200 mg L-1 NaF) for long-term (1-6 months) and short-term (6 hours to 7 days) exposure, with all showing a significant disturbance in the Firmicutes to Bacteroidota ratio.

CONCLUSION: In humans, high doses potentially may be detrimental to the microbiome, whereas ≤ 2 mg L-1 NaF had positive effects. Similarly, in animals, ≥ 50 mg L-1 NaF was unsafe, whereas ≤ 25 mg L-1 NaF had harmless effects.

PROSPERO registration No. CRD42022347357.},
}

@article {pmid40062854,
year = {2025},
author = {Zhang, F and Luan, J and Suo, L and Wang, H and Zhao, Y and Sun, T and Ni, Y and Cao, H and Zou, X and Liu, B},
title = {Altered gut microbiota and metabolite profiles in community-acquired pneumonia: a metagenomic and metabolomic study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0263924},
doi = {10.1128/spectrum.02639-24},
pmid = {40062854},
issn = {2165-0497},
abstract = {UNLABELLED: Emerging evidence suggests that altered gut microbiota is linked to community-acquired pneumonia (CAP), but the potential mechanisms by which gut microbiota and its metabolites contribute to the development of CAP remain unclear. Fecal samples from 32 CAP patients and 36 healthy controls were analyzed through metagenomic sequencing and metabolomic profiling. The gut microbiota composition in CAP patients showed significant differences and lower diversity compared to healthy controls. Genera involved in short-chain fatty acid (SCFA) production, such as Faecalibacterium, Ruminococcus, and Eubacterium, as well as species like Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, Prevotella copri, and Ruminococcus bromii, were significantly depleted in CAP patients. Bacterial co-occurrence network analysis revealed an over-representation of pro-inflammatory bacteria, which contributed to the core gut microbiome in CAP patients. Metabolomic analysis of fecal samples identified a distinct metabolic profile, with a notable increase in arachidonic acid, but a decrease in secondary bile acids, such as deoxycholic acid, lithocholic acid, and ursodeoxycholic acid, compared to healthy controls. Spearman correlation analysis between differential microbiota and bile acids showed that Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, and Prevotella copri were positively correlated with ursocholic acid, lithocholic acid, and ursodeoxycholic acid, respectively. Our results suggest that the reduction in secondary bile acids, insufficient production of SCFAs, and an overabundance of pro-inflammatory bacteria may contribute to metabolic inflammation in the body. These factors could play a key role in the pathogenesis of CAP, driven by gut microbiota alterations.

IMPORTANCE: This study presents a comprehensive metagenomic and metabolomic analysis of fecal samples from community-acquired pneumonia (CAP) patients, identifying key characteristics, such as decreased secondary bile acids, imbalanced short-chain fatty acid production, and increased pro-inflammatory bacteria. These findings provide valuable insights into the mechanisms linking gut microbiota alterations to CAP pathogenesis and suggest that targeting the gut microbiota could be a promising strategy for intervening in CAP.},
}

@article {pmid40062772,
year = {2025},
author = {Connolly, JP and Kelly, L},
title = {The physical biogeography of Fusobacterium nucleatum in health and disease.},
journal = {mBio},
volume = {},
number = {},
pages = {e0298924},
doi = {10.1128/mbio.02989-24},
pmid = {40062772},
issn = {2150-7511},
abstract = {UNLABELLED: Fusobacterium nucleatum (Fn) is an oral commensal inhabiting the human gingival plaque that is rarely found in the gut. However, in colorectal cancer (CRC), Fn can be isolated from stool samples and detected in metagenomes. We hypothesized that ecological characteristics of the gut are altered by disease, enabling Fn to colonize. Multiple genomically distinct populations of Fn exist, but their ecological preferences are unstudied. We identified six well-separated populations in 133 Fn genomes and used simulated metagenomes to demonstrate sensitive detection of populations in human oral and gut metagenomes. In 9,560 samples from 11 studies, Fn population C2 animalis is elevated in gut metagenomes from CRC and Crohn's disease patients and is observed more frequently in CRC stool samples than in the gingiva. Polymorphum, the most prevalent gingival Fn population, is significantly increased in Crohn's stool samples; this effect was significantly stronger in male hosts than in female. We find polymorphum genomes are enriched for biosynthetic gene clusters and fluoride exporters, while C2 animalis are high in iron transporters. Fn populations thus associate with specific clinical and demographic phenotypes and harbor distinct functional features. Ecological differences in closely related groups of bacteria inform microbiome impacts on human health.

IMPORTANCE: Fusobacterium nucleatum is a bacterium normally found in the gingiva. F. nucleatum generally does not colonize the healthy gut, but is observed in approximately a third of colorectal cancer (CRC) patient guts. F. nucleatum's presence in the gut during CRC has been linked to worse prognosis and increased tumor proliferation. Here, we describe the population structure of F. nucleatum in oral and gut microbiomes. We report substantial diversity in gene carriage among six distinct populations of F. nucleatum and identify population disease and body-site preferences. We find the C2 animalis population is more common in the CRC gut than in the gingiva and is enriched for iron transporters, which support gut colonization in known pathogens. We find that C2 animalis is also enriched in Crohn's disease and type 2 diabetes, suggesting ecological commonalities between the three diseases. Our work shows that closely related bacteria can have different associations with human physiology.},
}

@article {pmid40062764,
year = {2025},
author = {Watkins, E and Lin, J and Lingohr-Smith, M and Yong, C and Tangirala, K and Collins, K},
title = {Biological, Clinical, and Sociobehavioral Factors Associated with Disproportionate Burden of Bacterial Vaginosis in the United States: A Comprehensive Literature Review.},
journal = {Journal of women's health (2002)},
volume = {},
number = {},
pages = {},
doi = {10.1089/jwh.2024.0583},
pmid = {40062764},
issn = {1931-843X},
abstract = {Background: Bacterial vaginosis (BV), a common gynecological infection characterized by reduced lactic acid-producing bacteria and increased anerobic bacteria in the vaginal microbiome, is associated with adverse health outcomes. Methods: A PubMed search for English-language articles about BV in the USA and factors contributing to disparities in BV risk, with an emphasis on the role of the vaginal microbiome, published from August 2012 to August 2022, identified 760 articles. Results: Among the 52 articles meeting the prespecified criteria, BV prevalence varied among different populations and disproportionately impacted Black women (49-51%), Hispanic ethnicity (32-43%), and women of reproductive age (30%). Differences in microbial ecology and host genetics were important factors underlying these disparities. Colonization of BV-associated bacteria was more common in women of color than in non-Hispanic White women. Other factors linked with disproportionate burden included multiple/same-sex partners, obesity, immunosuppression, and C-section birth. Conclusions: BV prevalence was multifactorial, with some populations having higher prevalence rates and distinctive microbiome profiles that may predispose them to the condition. BV treatment and recurrence prevention were challenging due to the complex interplay of biological, clinical, and sociobehavioral factors. Understanding these disparate risk factors is critical to reducing BV burden.},
}

@article {pmid40062725,
year = {2025},
author = {Galindo-Moreno, P and Gutierrez-Garrido, L and Duarte, J and Robles-Vera, I and Martin-Morales, N and O'Valle, F and Olaechea, A and Carrillo-Galvez, AB and Padial-Molina, M},
title = {Evolution in the Peri-Implant Oral Microbiome and Their Relationship to Long-Term Marginal Bone Loss: A Randomized Clinical Study.},
journal = {Clinical oral implants research},
volume = {},
number = {},
pages = {},
doi = {10.1111/clr.14426},
pmid = {40062725},
issn = {1600-0501},
support = {//Dentsply Sirona Iberia/ ; CTS-138//Junta de Andalucía/ ; CTS-164//Junta de Andalucía/ ; CTS-1028//Junta de Andalucía/ ; PID2020-116347RB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; //MIS Implants Technologies Ltd./ ; },
abstract = {OBJECTIVES: To analyze the clinical, radiographic, and microbiological changes around implants with a multiphosphonate-treated surface, prosthetically loaded with two different protocols after 5 years of functional loading.

MATERIAL AND METHODS: A randomized clinical trial was designed to initiate prosthetic loading over single dental implants after 8 (control) or 4 weeks (test). Several variables were analyzed, including patients' level variables, intrasulcular biofilm, and marginal bone level at several time points, from 1 to 60 months after loading.

RESULTS: A total of 23 patients attended the 5-year follow-up visit. No clinical variable changed over time, except mucosal thickness from dental impressions to prosthesis delivery. No significant radiographic differences were observed either over time or between groups. Microbiologically, there was a change in the microbiome from the constitution of the biological width to the final follow-up. Seven species changed significantly, with a significant increase in Porphyromonas gingivalis and Tannerella forsythia from 12 to 60 months and a decrease in the other species. However, changes in the relative abundance of species over time, whether increasing or decreasing, did not show a correlation with marginal bone loss.

CONCLUSION: Implants with a multiphosphonate-treated surface showed no differences in clinical and radiographic variables after 5 years of function, regardless of the prosthetic loading protocol used. From a microbiological point of view, although there was an evolution of the microbiome in the peri-implant sulcus towards Socransky's red circle pathogenic bacteria, no microorganism showed a significant correlation with the radiographic changes produced in the peri-implant bone over time.

TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT03059108.},
}

@article {pmid40062472,
year = {2025},
author = {Keane, K and Stephens, M and Roizes, S and Xue, J and Liao, S and von der Weid, PY},
title = {The Spatiotemporal Development of Mesenteric Lymphatic Changes in the TNF[ΔARE/+] Mouse Model of Terminal Ileitis.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00334.2024},
pmid = {40062472},
issn = {1522-1547},
support = {623941//Crohn's and Colitis Canada (Crohn et Colite Canada)/ ; //Lymphedema Research and Education Program, Snyder Institute for Chronic Diseases, University of Calgary/ ; },
abstract = {Crohn's disease (CD) is a chronic inflammatory bowel disease which also encompasses significant alterations of the mesenteric lymphatic system. Whether these changes are a mere consequence of, or directly contribute to the inflammation is unknown. Here we characterized the spatial and temporal development of these events in the TNF[ΔARE/+] mouse, which develops CD-like ileitis and significant mesenteric lymphatic alterations. At 8-, 12-, 20-, and 28 weeks of age, specific pathogen-free (SPF), germ-free (GF) TNF[ΔARE/+] and WT mice were assessed for ileitis via myeloperoxidase activity (MPO) while mesenteric lymphatic alterations were assessed by confocal immunofluorescence imaging. Lymphatic alterations in the SPF TNF[ΔARE/+] occurred in a stepwise manner between 8 and 28 weeks of age beginning with the development of mesenteric lymphadenopathy at 8 weeks despite no significant ileitis. By 12 weeks ileal MPO significantly elevates concomitantly with lymphangiectasia of the mesenteric collecting lymphatic vessels (CLV) and clustering of CD45[+] immune cells around them. At 20 weeks, significant lymphangiogenesis of the initials (ILV) and tertiary lymphoid organs aligned along lymphatic collectors (CA-TLOs) had developed. At 28 weeks, lymphangiectasia, lymphangiogenesis, and CA-TLOs increased. However, 28-week-old GF TNF[ΔARE/+], while displaying no ileitis, presented with mesenteric lymphadenopathy, lymphangiectasia, and lymphangiogenesis but no immune cell clustering nor CA-TLOs. The TNF[ΔARE/+] mice develop terminal ileitis and lymphatic alterations in a stepwise manner beginning with MLN lymphadenopathy and ileal inflammation, followed by CLV dilation and lymphangiogenesis. These lymphatic alterations are exacerbated by the gut microbiome, with immune cell clustering and TLO formation being entirely dependent of its presence.},
}

@article {pmid40062463,
year = {2025},
author = {Roth, BJ and Khooblall, P and Leelani, N and Suryavanshi, M and Shumaker, A and Werneburg, G and Miller, A and Bajic, P},
title = {Antimicrobial resistance and biofilm formation of penile prosthesis isolates: insights from in-vitro analysis.},
journal = {The journal of sexual medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/jsxmed/qdaf001},
pmid = {40062463},
issn = {1743-6109},
support = {//Coloplast Corporation/ ; },
abstract = {BACKGROUND: Inflatable penile prostheses (IPPs) have been shown to harbor biofilms in the presence and absence of infection despite exposure to various antimicrobials. Microbes persisting on IPPs following antibiotic exposure have not been adequately studied to assess biofilm formation capacity and antibiotic resistance.

AIM: In this study, we aimed to assess these properties of microbes obtained from explanted infected and non-infected IPPS using an in vitro model.

METHODS: 35 bacterial isolates were grown and tested against various single-agent or multiple agent antibiotic regimens including: bacitracin, cefaclor, cefazolin, gentamicin, levofloxacin, trimethoprim-sulfamethoxazole, tobramycin, vancomycin, piperacillin/tazobactam, gentamicin + piperacillin/tazobactam, gentamicin + cefazolin, and gentamicin + vancomycin. Zones of inhibition were averaged for each sample site and species. Statistics were analyzed with Holm's corrected, one-sample t-tests against a null hypothesis of 0. Isolates were also allowed to form biofilms in a 96-well polyvinyl plate and absorbance was tested at 570 nm using a microplate reader.

OUTCOMES: Resistance was determined via clinical guidelines or previously established literature, and the mean and standard deviation of biofilm absorbance values were calculated and normalized to the optical density600 of the bacterial inoculum.

RESULTS: Every species tested was able to form robust biofilms with the exception of Staphylococcus warneri. As expected, most bacteria were resistant to common perioperative antimicrobial prophylaxis. Gentamicin dual therapy demonstrated somewhat greater efficacy.

STRENGTHS AND LIMITATIONS: This study examines a broad range of antimicrobials against clinically obtained bacterial isolates. However, not all species and antibiotics tested had standardized breakpoints, requiring the use of surrogate values from the literature. The microbes included in this study and their resistance genes are expectedly biased towards those that survived antibiotic exposure, and thus reflect the types of microbes which might "survive" in vivo exposure following revisional surgery.

CLINICAL TRANSLATION: Despite exposure to antimicrobials, bacteria isolated during penile prosthesis revision for both infected and non-infected cases exhibit biofilm forming capacity and extensive antibiotic resistance patterns in vitro. These microbes merit further investigation to understand when simple colonization vs re-infection might occur.

CONCLUSIONS: Although increasing evidence supports the concept that all IPPs harbor biofilms, even in the absence of infection, a deeper understanding of the characteristics of bacteria that survive revisional surgery is warranted. This study demonstrated extensive biofilm forming capabilities, and resistance patterns among bacteria isolated from both non-infected and infected IPP revision surgeries. Further investigation is warranted to determine why some devices become infected while others remain colonized but non-infected.},
}

@article {pmid40062406,
year = {2025},
author = {Moutsoglou, D and Ramakrishnan, P and Vaughn, BP},
title = {Microbiota transplant therapy in inflammatory bowel disease: advances and mechanistic insights.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2477255},
doi = {10.1080/19490976.2025.2477255},
pmid = {40062406},
issn = {1949-0984},
mesh = {Humans ; *Inflammatory Bowel Diseases/therapy/microbiology/immunology ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Animals ; },
abstract = {Microbiota transplant therapy is an emerging therapy for inflammatory bowel disease, but factors influencing its efficacy and mechanism remain poorly understood. In this narrative review, we outline key elements affecting therapeutic outcomes, including donor factors (such as age and patient relationship), recipient factors, control selection, and elements impacting engraftment and its correlation with clinical response. We also examine potential mechanisms through inflammatory bowel disease trials, focusing on the interplay between the microbiota, host, and immune system. Finally, we briefly explore potential future directions for microbiota transplant therapy and promising emerging treatments.},
}

Humans
*Inflammatory Bowel Diseases/therapy/microbiology/immunology
*Fecal Microbiota Transplantation
*Gastrointestinal Microbiome
Animals

@article {pmid40062050,
year = {2025},
author = {Almuntashiri, SA and Alsubaie, FF and Alotaybi, M},
title = {Plant-Based Diets and Their Role in Preventive Medicine: A Systematic Review of Evidence-Based Insights for Reducing Disease Risk.},
journal = {Cureus},
volume = {17},
number = {2},
pages = {e78629},
pmid = {40062050},
issn = {2168-8184},
abstract = {Plant-based diets have gained increasing attention for their potential role in preventive medicine, particularly in reducing the risk of chronic diseases such as type 2 diabetes, cardiovascular disease, obesity, and metabolic syndrome. This systematic review synthesizes evidence from 32 longitudinal studies to evaluate the impact of plant-based diets on disease prevention and health outcomes. The review identifies consistent patterns, including improved metabolic health, weight management, cardiovascular risk reduction, and positive effects on gut microbiome composition and inflammation. However, inconsistencies arise due to variability in diet definitions, mixed findings on specific outcomes, and heterogeneity in study populations. Critical gaps in the literature include the lack of long-term studies, limited mechanistic insights, underrepresentation of diverse populations, and a need for more rigorous intervention studies and personalized nutrition approaches. Identified research gaps highlight the need for long-term studies, deeper exploration of mechanistic pathways, and greater inclusivity of diverse populations. These insights underscore the significance of plant-based diets as a cornerstone of preventive medicine while emphasizing the necessity for targeted interventions and personalized approaches to maximize their benefits. The findings contribute to a growing body of evidence supporting the integration of plant-based dietary strategies into public health policies and clinical practices.},
}

@article {pmid40061946,
year = {2025},
author = {Guan, Y and Cheng, H and Zhang, N and Cai, Y and Zhang, Q and Jiang, X and Wang, A and Zeng, H and Jia, B},
title = {The role of the esophageal and intestinal microbiome in gastroesophageal reflux disease: past, present, and future.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1558414},
pmid = {40061946},
issn = {1664-3224},
mesh = {Humans ; *Gastroesophageal Reflux/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; *Dysbiosis/immunology ; *Esophagus/microbiology/immunology ; Animals ; },
abstract = {Gastroesophageal reflux disease (GERD) is one of the common diseases of the digestive system, and its incidence is increasing year by year, in addition to its typical symptoms of acid reflux and heartburn affecting the quality of patients' survival. The pathogenesis of GERD has not yet been clarified. With the development of detection technology, microbiome have been studied in depth. Normal microbiome are symbiotic with the host and can assist the host to fulfill the roles of digestion and absorption, and promote the development of the host. Dysbiosis of the microbiome forms a new internal environment, under which it may affect the development of GERD from the perspectives of molecular mechanisms: microbial activation of Toll-like receptors, microbial stimulation of cyclooxygenase-2 expression, microbial stimulation of inducible nitrous oxide synthase, and activation of the NLRP3 inflammatory vesicle; immune mechanisms; and impact on the dynamics of the lower gastrointestinal tract. This review will explore the esophageal microbiome and intestinal microbiome characteristics of GERD and the mechanisms by which dysbiotic microbiome induces GERD.},
}

Humans
*Gastroesophageal Reflux/microbiology/immunology
*Gastrointestinal Microbiome/immunology
*Dysbiosis/immunology
*Esophagus/microbiology/immunology
Animals

@article {pmid40061819,
year = {2024},
author = {Ren, HY and Lv, Y and Ma, BN and Gao, C and Yuan, HM and Meng, HH and Cao, ZQ and Chen, YT and Zhang, YX and Zhang, YT and Liu, W and Fan, YP and Li, MH and Wu, YX and Feng, ZY and Zhang, XX and Luo, ZJ and Tang, QY and Wesselius, A and Chen, J and Luo, HX and , and Qin, QR and Chen, L and Yu, EY},
title = {Cohort Profile: TRacing Etiology of Non-communicable Diseases (TREND): Rationale, Progress and Perspective.},
journal = {Phenomics (Cham, Switzerland)},
volume = {4},
number = {6},
pages = {584-591},
pmid = {40061819},
issn = {2730-5848},
abstract = {UNLABELLED: The TRacing Etiology of Non-communicable Diseases (TREND) cohort is a prospective longitudinal cohort and biobank that is mainly based in Ma'anshan, Anhui Province, China. The primary aim of the study is to decipher comprehensive molecular characterization and deep phenotyping for a broad spectrum of chronic non-communicable diseases (NCDs), which focuses on providing mechanistic insights with diagnostic, prognostic and therapeutic implications. The recruitment was initiated in 2023 and is expected to complete in 2025 with 20,000 participants originated from urban and rural area. In the first phase, 3360 participants were recruited. Follow-up visits are scheduled annually and intervally for a total of 30 years. The cohort includes individuals aged over 18 years. Two participants with first-degree linkage were recruited from a household. The age distribution of recruited participants was stratified into four categories: 18-45, 45-55, 55-65, and ≥65 years, aligning with the population proportions of Ma'anshan. Meanwhile, the gender distribution was controlled by pairing men and women from the same household. Data collected at baseline includes socio-economic information, medical history, lifestyle and nutritional habits, anthropometrics, blood oxygen, electrocardiogram (ECG), heart sound, as well as blood, urine and feces tests results. Molecular profiling includes genome, proteome, metabolome, microbiome and extracellular vesicles -omics. Blood, urine and fecal samples are collected and stored at -80 °C in a storage facility for future research.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00196-4.},
}

@article {pmid40061431,
year = {2025},
author = {Alamri, A and Alhassan, M and Almutairi, AK and Jayaseeli, N and Berg, RP and Stensvold, CR and Andersen, LO and Nielsen, HV and AlKhater, SA},
title = {Airway Microbiota Profiles in Children With and Without Asthma: A Comparative Study.},
journal = {Journal of asthma and allergy},
volume = {18},
number = {},
pages = {349-361},
pmid = {40061431},
issn = {1178-6965},
abstract = {BACKGROUND: Asthma is a common chronic respiratory disease that affects children and adults and can have a serious impact on their quality of life. Factors contributing to the development of asthma and related exacerbations are multifactorial, with microbial communities colonizing the airways possibly playing a key role.

METHODS: The study included asthmatic (79) and healthy children (57) aged 5-16 years. Nasal and throat swabs were collected, and bacterial (16s rRNA) and fungal (18s rRNA) amplicon sequence analysis was performed. Diversity indices and the most abundant microbial genera were estimated accordingly.

RESULTS: At the level of the bacteriome in the nasal samples, the asthma group had significantly lower diversity than the control group (p = 0.02). However, the microbiota of the asthma cohort was more evenly distributed, and staphylococci were enriched in the control group. Throat samples collected from the asthma cohort revealed significantly lower diversity (p < 0.0001), with a significant difference in species composition between the two groups (p = 0.005). Enriched bacterial species were different within the asthma subgroups (controlled vs uncontrolled asthma). The fungal microbiome of the nasal and throat samples showed no difference in species richness between the two groups, however, a significant difference in beta diversity (species composition) was detected. The nasal samples from the control group were enriched with Malassezia species, while the asthma cases were enriched with Mucor species. On the other hand, throat specimens of the asthma group were found to be enriched with Candida and Saccharomyces.

CONCLUSION: Our findings suggest that asthmatic samples were less diverse than the control samples with certain microbial genera enriching some study groups. Addressing the biomarkers that influence the progression of asthma could lead to improved care for children suffering from severe asthmatic episodes, possibly by including targeted therapies and prevention strategies.},
}

@article {pmid40061321,
year = {2025},
author = {Lamichhane, S and Dickens, AM and Buchacher, T and Lou, ET and Charron-Lamoureux, V and Kattelus, R and Karmacharya, P and Pinto da Silva, L and Kråkström, M and Rasool, O and Sen, P and Walker, C and Patan, A and Gentry, EC and Arzoomand, A and Lakshmikanth, T and Mikeš, J and Mebrahtu, A and Vatanen, T and Raffatellu, M and Zengler, K and Hyötyläinen, T and Xavier, RJ and Brodin, P and Lahesmaa, R and Dorrestein, PC and Knip, M and Orešič, M},
title = {Trajectories of microbiome-derived bile acids in early life - insights into the progression to islet autoimmunity.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.18.25322275},
pmid = {40061321},
abstract = {Recent studies reveal that gut microbes produce diverse bile acid conjugates, termed microbially conjugated bile acids (MCBAs). However, their regulation and health effects remain unclear. Here, we analyzed early-life MCBA patterns and their link to islet autoimmunity. We quantified 110 MCBAs in 303 stool samples collected longitudinally (3- 36 months) from children who developed one or more islet autoantibodies and controls who remained autoantibody-negative. Stool MCBAs showed distinct age-dependent trajectories and correlated with gut microbiome composition. Altered levels of ursodeoxycholic and deoxycholic acid conjugates were linked to islet autoimmunity as well as modulated monocyte activation in response to immunostimulatory lipopolysaccharide and Th17/Treg cell balance. These findings suggest MCBAs influence immune development and type 1 diabetes risk.},
}

@article {pmid40061054,
year = {2025},
author = {Dixon, R and Egan, S and Payne, M and Mullally, C and Chapman, B},
title = {Bacterial transfer during sexual intercourse as a tool for forensic detection.},
journal = {iScience},
volume = {28},
number = {2},
pages = {111861},
pmid = {40061054},
issn = {2589-0042},
abstract = {In forensic science, detecting transfers of physical and biological material is critical for establishing evidence of criminal involvement. Unique bacterial signatures from the reproductive system transfer during unprotected penetrative intercourse offer a novel tool for criminal investigation. Here, we demonstrate this transfer using full-length 16S rRNA gene sequencing and discuss the impact of barrier contraceptives. These microbial signatures can potentially aid in sexual assault casework for perpetrator identification when human male DNA is absent.},
}

@article {pmid40060808,
year = {2025},
author = {Gao, B and Shi, X and Zhao, M and Ren, F and Xu, W and Gao, N and Shan, J and Shen, W},
title = {Mixture Effects of Polystyrene Microplastics on the Gut Microbiota in C57BL/6 Mice.},
journal = {ACS omega},
volume = {10},
number = {8},
pages = {7597-7608},
pmid = {40060808},
issn = {2470-1343},
abstract = {Microplastics are plastic particles with sizes of less than 5 mm. The ubiquity of microplastics in the environment has raised serious public health concerns. Microplastics could disturb the composition of the gut microbiota due to both chemical composition and physical interactions, which might further influence the metabolism and immune function of the host. However, most of the exposure studies chose microplastics of specific sizes. In the natural environment, living organisms are exposed to a mixture of microplastics of various sizes. In this study, male C57BL/6 mice were exposed to polystyrene (PS) microplastics with different sizes, including microplastics with diameters of 0.05-0.1 μm (PS0.1 group, 100 ppb), 9-10 μm (PS10 group, 100 ppb), and microplastic mixtures of both 0.05-0.1 and 9-10 μm (PSMix group) at a total concentration of 100 ppb (50 ppb for each size). Mixture effects of microplastics were investigated on the composition of bacteria and fungi as well as functional metagenome and microbial genes encoding antibiotic resistance and virulence factors. We found that some bacteria, fungi, and microbial metabolic pathways were only altered in the PSMix group, not in the PS0.1 or PS10 group, suggesting the toxic effects of the microplastic mixture on the composition of fungi and bacteria, and the functional metagenome is different from the effects of microplastics at specific sizes. Meanwhile, altered genes encoding antibiotic resistance and virulence factors in the PSMix group were shared with the PS0.1 and PS10 groups, possibly due to functional redundancy. Our findings help improve the understanding of the toxic effects of the microplastic mixture on the gut microbiome.},
}

@article {pmid40060755,
year = {2025},
author = {Yi, D and Li, T and Xiao, Y and Zhang, X and Hao, Q and Zhang, F and Qiu, T and Yang, G and Sun, X and Dong, Y and Wang, N},
title = {Fecal microbiota transplantation for the treatment of intestinal and extra-intestinal diseases: Mechanism basis, clinical application, and potential prospect.},
journal = {Bioengineering & translational medicine},
volume = {10},
number = {2},
pages = {e10728},
pmid = {40060755},
issn = {2380-6761},
abstract = {To review the theoretical basis and therapeutic effects of fecal microbiota transplantation (FMT) in various diseases in animal experiments and clinical studies, as well as the limitations and current standards of FMT application. PubMed and Web of Science databases were searched for articles published only in English between 1975 and 2023 on reliable results of animal experiments and clinical treatment of FMT. The properties of the gut microbiota and its interactions with the host metabolism are critical to human health, and microbiome disturbance is closely associated with human intestinal and extra-intestinal diseases. Therefore, therapeutic tools targeting on the modulation of gut microbiota have attracted increasing attention, among which FMT represents the most widely studied intervention strategy. This review gathered and summarized application of FMT in intestinal diseases, metabolic diseases, hypertension, cancer, nervous system diseases and arthritis, and elaborated the beneficial effects that can be achieved by altering the microbiota with FMT and the mechanisms of action. In addition, the potential risks and side effects of FMT approach are discussed, as well as current efforts to standardize the development of FMT. Through a systemic review of the outcome and mechanism of FMT in the treatment of intestinal diseases and extra-intestinal diseases, we aimed to provide a theoretical basis for the construction of an optimized FMT framework, so as to better exert its application prospects.},
}

@article {pmid40060716,
year = {2025},
author = {Zhao, Y and Yuan, X and Ran, W and Zhao, Z and Su, D and Song, Y},
title = {The Ecological Restoration Strategies in Terrestrial Ecosystems Were Reviewed: A New Trend Based on Soil Microbiomics.},
journal = {Ecology and evolution},
volume = {15},
number = {3},
pages = {e70994},
pmid = {40060716},
issn = {2045-7758},
abstract = {Soil microorganisms play a pivotal role in the biogeochemical cycle and serve as crucial indicators of ecological restoration in terrestrial ecosystems. The soil microbial community is regarded as a pivotal participant in environmental processes, offering both positive and negative feedback to diverse media within the ecosystem. This community can serve as a potential indicator in ecological monitoring and restoration processes. Consequently, an increasing number of scholars are directing their research towards the field of soil microbial ecology in diverse ecosystems and fragile areas, with the aim of elucidating the intricate interactions between microbes and vegetation. However, the implementation of soil microbiome in ecological restoration remains in the experimental stage due to the interference of extreme events and the complexity of governance measures. Consequently, a comprehensive evaluation of existing research is imperative. This review aims to address the ecological crises currently experienced by diverse terrestrial ecosystems and to provide a comprehensive overview of the specific practices of soil microorganisms in the context of ecological restoration. We also incorporate them into fragile habitats and identify urgent issues that need to be addressed in the ecological restoration process of fragile areas.},
}

@article {pmid40060518,
year = {2025},
author = {Day, AW and Perez-Lozada, J and DiLeo, A and Blandino, K and Maguire, J and Kumamoto, CA},
title = {Candida albicans Colonization Modulates Murine Ethanol Consumption and Behavioral Responses Through Elevation of Serum Prostaglandin E 2 and Impact on the Striatal Dopamine System.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.25.640044},
pmid = {40060518},
issn = {2692-8205},
abstract = {UNLABELLED: Candida albicans is a commensal yeast that is a common component of the gastrointestinal (GI) microbiome of humans. C. albicans has been shown to bloom in the GI tract of individuals with alcohol use disorder (AUD) and can promote and increase the severity of alcoholic liver disease (ALD). However, the effects of C. albicans blooms on the host in the context of AUD or AUD-related phenotypes, such as ethanol preference, have been unstudied. In this work, we report a reduction in ethanol consumption and preference in mice colonized with C. albicans . C. albicans- colonized mice exhibited elevated levels of serum PGE 2 and reduced ethanol preference was reversed by injection with antagonists of PGE 2 receptors. Further, injection of mice with a PGE 2 derivative decreased their ethanol preference. These results show that PGE 2 acting on its receptors EP1 and EP2 drives reduced ethanol preference in C. albicans- colonized mice. We also showed altered transcription of dopamine receptors in the dorsal striatum of C. albicans- colonized mice and more rapid acquisition of ethanol conditioned taste aversion, suggesting alterations to reinforcement or aversion learning. Finally, C. albicans -colonized mice were more susceptible to ethanol-induced motor coordination impairment showing significant alterations to the behavioral effects of ethanol. This study identifies a member of the fungal microbiome that alters ethanol preference and demonstrates a role for PGE 2 signaling in these phenotypes.

IMPORTANCE: Candida albicans is a commensal yeast that is found in the gut of most individuals. C. albicans has been shown to contribute to alcoholic liver disease. Outside of this, the impact of intestinal fungi on alcohol-use disorder (AUD) had been unstudied. As AUD is a complex disorder characterized by high relapse rates, and there are only 3 FDA-approved therapies for the maintenance of abstinence, it is important to study novel AUD contributors to find new therapeutic targets. Here we show that an intestinal fungus, C. albicans , can alter mammalian ethanol consumption through an immune modulator, prostaglandin E 2 . The results highlight novel contributors to AUD-related phenotypes and further implicate the gut-brain axis in AUD. Future studies could lead to new therapeutic avenues for the treatment of AUD.},
}

@article {pmid40060402,
year = {2025},
author = {McDermott, CR and Gao, Z and Mirmajlesi, AS and Ntim, C and Kimbark, K and Thomas, D and Mughal, Z and Zhang, XS and Zhou, X and Popov, D and Halchenko, A and Xing, J and Thakker-Varia, S and Alder, J and Millonig, JH and Samuels, BA and Blaser, MJ and DiCicco-Bloom, E},
title = {The 16p11.2 microdeletion influences how early-life microbiota perturbations affect hippocampal development and behavior throughout the lifespan.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.25.639888},
pmid = {40060402},
issn = {2692-8205},
abstract = {Neurodevelopmental disorders result from interactions between genetic predisposition and environmental risk factors, with infancy being the most vulnerable period. We designed a longitudinal study to determine how short-term antibiotic exposure during early postnatal life impacts the gut microbiome, neurodevelopment, and behavior, and whether these alterations were exacerbated by the neurodevelopmental disorder-associated 16p11.2 microdeletion (16pDel) mutation. The cephalosporin antibiotic, cefdinir, broadly altered the gut microbiome acutely, with persistent reductions in several Lachnospiraceae genera despite overall recovery. These alterations preceded long-term behavioral changes, including reduced juvenile sociability, compromised risk assessment, and deficits in associative learning. Remarkably, only cefdinir-exposed 16pDel mice had changes in hippocampal stem cell proliferation, subsequent adolescent cell numbers, and gene expression compared to other groups, demonstrating that genetic predisposition can modulate the effects of early-life antibiotic exposure on neurodevelopment. These alterations may be mediated by gastrointestinal disturbances, as cefdinir-exposed 16pDel males had increased intestinal permeability and shifted metabolite profiles including arginine biosynthesis and glycerophospholipid metabolism. Taken together, this study highlights how early-life microbial alterations affect behavior and reveals that genetic predisposition influences antibiotic-induced changes in hippocampal development. Further, these insights identify metabolic mechanisms as potential targets for intervention and may raise concerns regarding antibiotic use during infancy.},
}

@article {pmid40060387,
year = {2025},
author = {Kim, M and Wang, J and Pilley, SE and Lu, RJ and Xu, A and Kim, Y and Liu, M and Fu, X and Booth, SL and Mullen, PJ and Benayoun, BA},
title = {Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.03.592475},
pmid = {40060387},
issn = {2692-8205},
abstract = {Decline in ovarian function with age not only affects fertility but is also linked to a higher risk of age-related diseases in women (e.g . osteoporosis, dementia). Intriguingly, earlier menopause is linked to shorter lifespan; however, the underlying molecular mechanisms of ovarian aging are not well understood. Recent evidence suggests the gut microbiota may influence ovarian health. In this study, we characterized ovarian aging associated microbial profiles in mice and investigated the effect of the gut microbiome from young and estropausal female mice on ovarian health through fecal microbiota transplantation. We demonstrate that the ovarian transcriptome can be broadly remodeled after heterochronic microbiota transplantation, with a reduction in inflammation-related gene expression and trends consistent with transcriptional rejuvenation. Consistently, these mice exhibited enhanced ovarian health and increased fertility. Using metagenomics-based causal mediation analyses and serum untargeted metabolomics, we identified candidate microbial species and metabolites that may contribute to the observed effects of fecal microbiota transplantation. Our findings reveal a direct link between the gut microbiota and ovarian health.},
}

@article {pmid40060342,
year = {2024},
author = {Koyyala, VPB and Kantharia, C and Darooka, N and Kumar, M and Ranjan, P and Anikhindi, S and Bansal, NK and Sharma, P and Bhalla, DVP and Kumar, M and Sharma, M and Abrol, D and Sahni, P and Ardhanari, R and Pradeep, R and Yadav, A and John, S and Rawat, S and Parikh, P and Selvasekar, C and Aggarwal, S},
title = {Inflammatory Bowel Disease and Colorectal Cancer: An Eternal Fire in a Beautiful Garden.},
journal = {South Asian journal of cancer},
volume = {13},
number = {4},
pages = {300-304},
pmid = {40060342},
issn = {2278-330X},
abstract = {Inflammatory bowel disease (IBD), encompassing Crohn's disease and ulcerative colitis, significantly increases the risk of colitis-associated cancer (CAC). Chronic inflammation, a key contributor to carcinogenesis, disrupts immune surveillance, induces deoxyribonucleic acid (DNA) damage, and alters genetic and epigenetic pathways. Molecular pathways such as STAT3, mTOR, and NF-κB drive CAC progression, while unique microbiome alterations-loss of Faecalibacterium prausnitzii and increases in Escherichia coli and Fusobacterium species-exacerbate the inflammatory milieu. CAC accounts for 2% of all colon cancers and up to 15% of IBD-related deaths. Risk correlates with IBD duration, increasing approximately 1% annually after the first decade. Surveillance via colonoscopy is crucial, with chromoendoscopy recommended for high-risk cases. Preventive drugs, including aminosalicylates, thiopurines, and biologics, offer modest benefits but lack conclusive evidence. Post-CAC diagnosis, immunosuppressants are discontinued in favor of corticosteroids, with 5-aminosalicylates continued as needed. The use of immune checkpoint inhibitors remains controversial due to exacerbation of colitis. Emerging insights into the gut microbiota's role in IBD and CAC may revolutionize prevention and management strategies. Advances in screening, surveillance, and therapeutic approaches have reduced CAC mortality, underscoring the importance of personalized medicine and ongoing research to address these complex conditions.},
}

@article {pmid40060340,
year = {2024},
author = {Agrawal, M and Surendran, AK and Venkatesh, KK and Velammal, PNKP and Zope, S and Goel, A and Pathak, A and Mittal, M and K K, V and Vinakar, AS and Agrawal, D and Parikh, PM},
title = {Screening for Colorectal Carcinoma in India: Real-World Scenario, Pitfalls, and Solutions.},
journal = {South Asian journal of cancer},
volume = {13},
number = {4},
pages = {229-235},
pmid = {40060340},
issn = {2278-330X},
abstract = {INTRODUCTION: Noninvasive colorectal cancer (CRC) screening has introduced innovative blood- and stool-based biomarkers, improving early detection and enabling personalized solutions. Global and Indian adoption of CRC screening remains a public health challenge. This study evaluates the real-world utility of screening colonoscopy, as recommended by global guidelines.

METHODOLOGY: A survey based on the American Medical Association (AMA) guidelines was designed, setting 45+ years as the cutoff age for colonoscopy screening. A Google form was shared via social media application with health care professionals. Participation was voluntary, responses were collected over 30 days, and data were analyzed.

RESULTS: A total of 2,199 individuals' data were analyzed. Among these, 1,374 were eligible for screening colonoscopy, out of which only 7.14% (98/1,374) actually underwent the procedure.

CONCLUSION: Among various cancer programs, screening sigmoidoscopy has proved to improve both CRC-specific mortality and all-cause mortality. Unfortunately, its utilization is suboptimal, at best. Even among the highly educated medical community, the real-world utility was only in 7.14% of the eligible population. Barriers include invasive nature of intervention, need for appropriate bowel preparation, operator dependence, and small but significant risk of serious toxicity. An important method of increasing utility of screening colonoscopy is use of a test that can identify high-risk population, who can then be persuaded to undergo screening colonoscopy. This is the value of recently developed noninvasive blood- and stool-based tests, like Guardant Health's Shield. Being U.S. Food and Drug Administration (FDA) approved with specificity of 90% and sensitivity of 84%, it should be offered to all eligible persons who can afford it, thereby increasing colonoscopy use and potentially saving lives.},
}

@article {pmid40060328,
year = {2025},
author = {Pietruska, A and Macklin, KS and Wang, X and Krehling, JT and Dormitorio, T and Hauck, R},
title = {Investigation of Intestinal Health in Broiler Chickens Following Salmonella Typhimurium and Coccidiosis Vaccination and Challenge with Salmonella Typhimurium.},
journal = {The journal of poultry science},
volume = {62},
number = {},
pages = {2025009},
pmid = {40060328},
issn = {1349-0486},
abstract = {Salmonella enterica and coccidia (Eimeria spp.) are important intestinal pathogens in broiler production. Salmonella has high zoonotic potential, and coccidia are responsible for large economic losses. Live vaccines reduce shedding of Salmonella and minimize the impact of coccidial infections on broiler performance. This study investigated the interaction between both vaccines on the intestinal health of broilers. The 2 × 2 experimental design included vaccination against Salmonella Typhimurium (ST) (no vaccination or vaccination on day 14) and vaccination against coccidiosis (no vaccination or vaccination on day 1). On day 28, all groups were challenged with a ST marker strain resistant to nalidixic acid. Re-isolation of ST from the liver and ceca on day 42 indicated higher susceptibility to systemic infection with ST in birds vaccinated against coccidiosis than that in unvaccinated birds. On day 42, cecal immunoglobulin A (IgA) levels against ST decreased in the group vaccinated against ST and coccidia compared to those in all other groups. IgG antibodies in the cecal contents significantly decreased in the group vaccinated against coccidiosis compared to that of the group vaccinated against ST. There was no difference in systemic IgG levels among groups. Analysis of the cecal microbiota revealed a significant difference in beta diversity on days 28 and 42 between the groups vaccinated against coccidiosis and unvaccinated groups. Functional pathway profiling showed increased activity of pathways associated with carbohydrate and arachidonic acid metabolism in the group vaccinated against ST compared to that in other groups. Gene expression of claudin 1, claudin 4, E-cadherin, β-catenin, and zonula occludens 2 in the cecal wall differed between the groups on days 28 and 42. These findings indicated the significant influence of ST and coccidiosis vaccines on the intestinal health of broilers; however, further studies are required to clarify the implications for health and performance.},
}

@article {pmid40060187,
year = {2025},
author = {Cao, J and Ma, Y and Fu, J and Wang, Z and Zhao, Y and Zhong, N and Zhao, P},
title = {Bacillus atrophaeus DX-9 biocontrol against potato common scab involves significant changes in the soil microbiome and metabolome.},
journal = {aBIOTECH},
volume = {6},
number = {1},
pages = {33-49},
pmid = {40060187},
issn = {2662-1738},
abstract = {UNLABELLED: Potato common scab (CS) is a worldwide disease, caused by Streptomyces spp., and its presence reduces the market value of potatoes. A nontoxic and potentially effective approach in many control strategies is the use of antagonistic microbes as biocontrol agents. In this study, Bacillus atrophaeus DX-9 was isolated and assessed for its ability to protect against CS. Through integrated metagenomic and metabolomic analyses, changes in the soil microbial community structure and soil properties were analyzed to understand the effects of Bacillus atrophaeus DX-9 on CS. These studies revealed that DX-9 inoculation could significantly decrease CS disease rate, disease index, and the number of CS pathogens, along with an increase in soil N and P content. Our metagenomic assays identified 102 phyla and 1154 genera, and DX-9 inoculation increased the relative abundances of the phyla Pseudomonadota, Chloroflexota and Gemmatimonadota. Additionally, an increase in the relative abundance of genera, such as Bradyrhizobium, Agrobacterium, and Nitrobacter, were significantly and positively correlated with soil N and P. Metabolomic analysis revealed that DX-9 inoculation significantly increased the soil levels of phytolaccoside A, 7,8-dihydropteroic acid, novobiocin, and azafrin. These compounds were enriched in microbe pathway metabolites, including xenobiotic biodegradation and metabolism, biosynthesis of other secondary metabolites, and metabolism of cofactors and vitamins. In summary, the use of Bacillus atrophaeus DX-9 against potato CS offers an alternative biocontrol method that can improve both soil microbial community and properties. This study provides insight into the potential mechanisms by which microbial inoculants can control CS disease.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42994-025-00199-3.},
}

@article {pmid40060035,
year = {2025},
author = {Seyedmoalemi, MA and Saied-Moallemi, Z},
title = {Association between periodontitis and Alzheimer's disease: A narrative review.},
journal = {IBRO neuroscience reports},
volume = {18},
number = {},
pages = {360-365},
pmid = {40060035},
issn = {2667-2421},
abstract = {Periodontitis is a chronic inflammatory disease that progressively damages the supporting structures of teeth, resulting in gum bleeding, inflammation, gum recession, and eventual tooth loss. Key factors, including poor oral hygiene, plaque accumulation, smoking, inadequate nutrition, and genetic predisposition, drive its development. Recent evidence underscores the potential role of periodontitis as a contributing factor to systemic diseases, including Alzheimer's disease (AD). AD is a neurodegenerative disorder marked by memory loss, cognitive decline, and brain inflammation. Emerging clinical and experimental studies indicate that these two conditions share overlapping risk factors and may be interconnected. One notable finding is the detection of specific periodontal pathogens, such as Porphyromonas gingivalis (P. gingivalis), in the brains of individuals with AD. This suggests a possible link between chronic oral infections and neurodegeneration. These pathogens are believed to exacerbate neuroinflammatory processes by activating microglia and promoting systemic inflammation, which is central to AD pathogenesis. Further research is needed to clarify the biological mechanisms underlying this association. Targeted interventions that address periodontitis, such as anti-inflammatory therapies or treatments targeting specific pathogens like P. gingivalis, could potentially mitigate its impact on the onset and progression of AD, offering a novel avenue for prevention and management strategies.},
}

@article {pmid40060029,
year = {2025},
author = {Yan, C and Si, T and Zheng, W and Huang, L and Wen, L and Shen, H and Qu, M},
title = {Characteristics of Gut Microbiota and Plasma Metabolites in Patients with Post-Stroke Depression.},
journal = {Neuropsychiatric disease and treatment},
volume = {21},
number = {},
pages = {477-489},
pmid = {40060029},
issn = {1176-6328},
abstract = {PURPOSE: The changes in gut microbiota and plasma metabolites have been proposed to play a key role in post stroke depression (PSD), but clinical study based on combined omics is still in lack. This study aimed to investigate the characteristics of gut microbiota and plasma metabolites in patients 3 months after the onset of acute ischemic stroke (AIS), compare PSD and non-PSD groups, and explore possible diagnostic biomarkers.

PATIENTS AND METHODS: Seventy patients with stroke were included at 3 months after AIS onset. Plasma and fecal samples were collected. Gut microbiome was examined using 16S rRNA sequencing, and plasma metabolites were assessed via targeted liquid chromatography-mass spectrometry.

RESULTS: Of the 70 patients with ischemic stroke, 25 (35.71%) were diagnosed with PSD. At the genus level, patients with PSD had increased abundance of Parabacteroides, Pyramidobacter, Anaeroglobus, Haliangium, Staphylococcus, CAG-56, Shuttleworthia, and Epulopiscium, and decreased levels of the Eubacterium eligens group and Prevotella. In patients with PSD, 12 plasma metabolites were altered, with cortisol and pyroglutamic acid levels increased, while 2-phosphoglyceric acid, 3-phosphoglycerate, phosphorylcholine, tryptophan, caffeine, N-methylalanine, ornithine, serotonin, theophylline, and vanillic acid were decreased. Enriched metabolic pathways included glutathione, tryptophan, and caffeine metabolism. Furthermore, significant correlations were observed between gut microbial dysregulation and major plasma metabolite alterations. The areas under the curve values of gut microbiota, plasma metabolites, and the combined dataset for PSD diagnosis were 0.704, 0.875, and 0.940, respectively.

CONCLUSION: This study identified the characteristics of gut microbiota and plasma metabolites as well as a panel of combined biomarkers in 3-month PSD, possibly providing a new theoretical framework for diagnosis and treatment.},
}

@article {pmid40059472,
year = {2025},
author = {Elahi, Z and Mokhtaryan, M and Mahmoodi, S and Shahroodian, S and Darbandi, T and Ghasemi, F and Ghanavati, R and Darbandi, A},
title = {All Properties of Infertility Microbiome in a Review Article.},
journal = {Journal of clinical laboratory analysis},
volume = {},
number = {},
pages = {e25158},
doi = {10.1002/jcla.25158},
pmid = {40059472},
issn = {1098-2825},
support = {4150//Behbahan Faculty of Medical Sciences/ ; },
abstract = {BACKGROUND: The microbiome is crucial for many physiological processes, including immunity, metabolism, and reproduction.

AIMS: This review aims to contribute to a detailed understanding of the microbiome of the genital tract, which can lead to better management of dysbiosis and reproductive disorders.

METHODS: Data from the four international information databases Medline, Scopus, Embase, and Google Scholar. The search strategy was based on the combination of the following terms: "microbiota," "microbiome," "microfilm," "microflora," "fertility," or "infertility."

RESULT: The advent of next-generation sequencing-based technologies during the last decade has revealed the presence of microbial communities in nearly every part of the human body, including the reproductive system. Several studies have shown significant differences between the microbiota of the vagina and endometrium, as well as other parts of the upper genital tract.

DISCUSSION: The human microbiome plays a critical role in determining a person's health state, and the microbiome of the genital tract may impact fertility potential before and after assisted reproductive treatments (ARTs).

CONCLUSION: To completely understand the role of the microbiome, future research should focus not only on the description of microbiota but also on the interaction between bacteria, the production of biofilms, and the interaction of microorganisms with human cells.},
}

@article {pmid40059439,
year = {2025},
author = {Szaraz, D and Bohm, J and Cerulova, S and Bodokyova, L and Danek, Z and Machacek, C and Borilova Linhartova, P},
title = {Bacterial genera in the fluids from apical periodontitis-related radicular cysts: An observational study.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.14220},
pmid = {40059439},
issn = {1365-2591},
support = {NU20-08- 00205//Ministerstvo Zdravotnictví Ceské Republiky/ ; //Horizon 2020 Framework Programme/ ; 65269705//University Hospital Brno, Ministry of Health, Czech Republic - RVO/ ; },
abstract = {AIM: This study aimed to evaluate bacteriome profiles (diversity, composition and relative abundances of bacterial genera) of the fluids from apical periodontitis (AP)-related radicular cysts (RCs).

METHODOLOGY: This observational study included 29 patients with AP and RC with complete sample triplets (supragingival plaque, cryopulverized tooth and cystic fluid). The bacteriome profiles of each matrix as well as of negative controls (NCs) were examined using 16S rRNA amplicon sequencing.

RESULTS: Bacteriome profiles of cystic fluids differed from NCs in 79% of cases. The number of distinct amplicon sequence variants and Shannon index detected in cystic fluids and cryopulverized teeth were significantly lower than in paired supragingival plaque samples. Gram-negative genera and anaerobic genera were more abundant in cystic fluids than in paired cryopulverized teeth or their supragingival plaques. The relative abundances of the genera Prevotella_7/Prevotella, Fusobacterium and Porphyromonas were higher in cystic fluids than in paired cryopulverized teeth and NCs; their relative abundances dominated (>20%) in individual cystic fluids. Also, DNA from the genus Fretibacterium was significantly more commonly found in cryopulverized teeth and cystic fluids than in supragingival plaque samples. The relative abundances of this gram-negative bacterial genera in cryopulverized teeth differed from NCs; the difference from cystic fluids was borderline insignificant.

CONCLUSIONS: Although the alpha-diversity in the cystic fluids is much lower compared to supragingival plaques, most cystic fluids are not sterile. DNA from specific anaerobic gram-negative bacterial genera dominated the fluids from AP-related RCs.},
}

@article {pmid40059228,
year = {2025},
author = {Thapa, A and Hasan, MR and Kabir, AH},
title = {Transcriptional reprogramming and microbiome dynamics in garden pea exposed to high pH stress during vegetative stage.},
journal = {Planta},
volume = {261},
number = {4},
pages = {83},
pmid = {40059228},
issn = {1432-2048},
support = {5SFAES-293007//College of Arts, Education, and Sciences, University of Louisiana Monroe/ ; },
mesh = {*Pisum sativum/microbiology/genetics/physiology ; Hydrogen-Ion Concentration ; *Microbiota/genetics ; *Symbiosis ; Stress, Physiological/genetics ; Soil/chemistry ; Gene Expression Regulation, Plant ; Soil Microbiology ; Plant Roots/microbiology/genetics ; },
abstract = {High soil pH induces the upregulation of genes involved in oxidative stress and nutrient transport, while the enrichment of beneficial microbes (Variovorax, Chaetomium, and Pseudomonas) highlights their potential role in promoting stress adaptation. High soil pH severely impacts plant growth and productivity, yet the transcriptomic changes and microbial dynamics underlying stress adaptation in garden pea (Pisum sativum ssp. hortense) remain unclear. This study demonstrates that high soil pH leads to stunted growth, reduced biomass, impaired photosynthesis, and nutrient status in garden pea. Further, disruption in key nitrogen-fixing bacteria (Rhizobium indicum, R. leguminosarum, and R. redzepovicii), along with the downregulation of NifA and NifD genes and upregulation of NifH in nodules highlights the critical role of micronutrient balance in legume-microbe symbiosis and a compensatory response to maintain nitrogen status. RNA seq analysis revealed extensive transcriptional reprogramming in roots, characterized by the upregulation of oxidative stress response genes (e.g., oxidoreductase and glutathione transferase activities, metal ion transporters) and the downregulation of genes related to ammonia-lyase activity and ion binding, reflecting broader disruptions in nutrient homeostasis. KEGG pathway analysis identified enrichment of MAPK signaling pathway, likely interacting with other pathways associated with stress tolerance, metabolic adjustment, and structural reorganization as part of adaptive responses to high pH. Root microbiome analysis showed significant enrichment of Variovorax, Shinella, and Chaetomium, suggesting host-driven recruitment under high pH stress. Stable genera, such as Pseudomonas, Novosphingobium, Mycobacterium, Herbaspirillum, and Paecilomyces, displayed resilience to stress conditions, potentially forming core microbiome components for adaptation to high pH. In a targeted study, inoculation of plants with an enriched microbiome, particularly C. globosum, under high pH conditions improved growth parameters and increased the abundance of Stenotrophomonas and Pseudomonas in the roots. It suggests that these bacterial genera may act as helper microbes to C. globosum, collectively promoting stress resilience in pea plants suffering from high pH. These findings provide a foundation for microbiome-aided breeding programs and the development of microbial consortia to enhance the adaptation of pea plants to high pH conditions.},
}

*Pisum sativum/microbiology/genetics/physiology
Hydrogen-Ion Concentration
*Microbiota/genetics
*Symbiosis
Stress, Physiological/genetics
Soil/chemistry
Gene Expression Regulation, Plant
Soil Microbiology
Plant Roots/microbiology/genetics

@article {pmid40059174,
year = {2025},
author = {Jin, X and Cheng, AG and Chanin, RB and Yu, FB and Dimas, A and Jasper, M and Weakley, A and Yan, J and Bhatt, AS and Pollard, KS},
title = {Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {71},
pmid = {40059174},
issn = {2049-2618},
support = {1563159//National Science Foundation/ ; HL160862/HL/NHLBI NIH HHS/United States ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/genetics/classification/isolation & purification ; *Bacterial Adhesion/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Animals ; Metagenome ; Mice ; Promoter Regions, Genetic ; Intestines/microbiology ; },
abstract = {BACKGROUND: Bacteria use invertible genetic elements known as invertons to generate heterogeneity among a population and adapt to new and changing environments. In human gut bacteria, invertons are often found near genes associated with cell surface modifications, suggesting key roles in modulating dynamic processes such as surface adhesion and intestinal colonization. However, comprehensive testing of this hypothesis across complex bacterial communities like the human gut microbiome remains challenging. Metagenomic sequencing holds promise for detecting inversions without isolation and culturing, but ambiguity in read alignment limits the accuracy of the resulting inverton predictions.

RESULTS: Here, we developed a customized bioinformatic workflow-PhaseFinderDC-to identify and track invertons in metagenomic data. Applying this method to a defined yet complex gut community (hCom2) across different growth environments over time using both in vitro and in vivo metagenomic samples, we detected invertons in most hCom2 strains. These include invertons whose orientation probabilities change over time and are statistically associated with environmental conditions. We used motif enrichment to identify putative inverton promoters and predict genes regulated by inverton flipping during intestinal colonization and surface adhesion. Analysis of inverton-proximal genes also revealed candidate invertases that may regulate flipping of specific invertons.

CONCLUSIONS: Collectively, these findings suggest that surface adhesion and intestinal colonization in complex gut communities directly modulate inverton dynamics, offering new insights into the genetic mechanisms underlying these processes. Video Abstract.},
}

*Gastrointestinal Microbiome/genetics
Humans
*Bacteria/genetics/classification/isolation & purification
*Bacterial Adhesion/genetics
*Metagenomics/methods
Computational Biology/methods
Animals
Metagenome
Mice
Promoter Regions, Genetic
Intestines/microbiology

@article {pmid40059170,
year = {2025},
author = {Duan, Y and Xu, C and Wang, W and Wang, X and Xu, N and Zhong, J and Gong, W and Zheng, W and Wu, YH and Myers, A and Chu, L and Lu, Y and Delzell, E and Hsing, AW and Yu, M and He, W and Zhu, S},
title = {Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {146},
pmid = {40059170},
issn = {1741-7015},
support = {Grant No. 2022YFC2705303//the National Key R&D Program of China/ ; Grant No. 2022YFC2705300//the National Key R&D Program of China/ ; Grant No. 2024C03180//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Obesity/microbiology ; Middle Aged ; *Siblings ; Adult ; *Smoking/adverse effects ; China/epidemiology ; Cohort Studies ; Body Mass Index ; RNA, Ribosomal, 16S/genetics ; Aged ; Female ; },
abstract = {BACKGROUND: Individuals who smoke tend to have a lower body mass index (BMI) but face an increased risk of obesity-related diseases. This study investigates this paradox from the perspective of gut microbiota.

METHODS: We conducted microbiome analyses to identify smoking-related microbial genera and created a smoking-related microbiota index (SMI) using 16S rRNA sequencing data from 4000 male participants in WELL-China cohort and Lanxi cohort. We employed logistic regression to explore the association between SMI and obesity indices derived from dual-energy X-ray absorptiometry. Cox regression analyses were conducted to explore the association of SMI with incident of obesity-related diseases. To further control for unmeasured familial confounders, sibling comparison analyses were conducted using between-within (BW) model.

RESULTS: The smoking-related microbiota index (SMI) showed a positive association with BMI and other obesity indices. Further analyses revealed that SMI is linked to obesity-related diseases, with hazard ratios (95% confidence intervals) of 1.97 (1.41-2.75) for incident diabetes, 1.31 (1.01-1.71) for major adverse cardiovascular events, and 1.70 (1.05-2.75) for obesity-related cancers. Results from sibling comparison analyses reinforced these findings.

CONCLUSIONS: While smoking may reduce weight through various mechanisms, alterations in gut microbiota related to smoking are associated with weight gain. Further research is required to determine if changes in the smoking-related microbiome contribute to weight gain following smoking cessation.},
}

Humans
Male
*Gastrointestinal Microbiome
*Obesity/microbiology
Middle Aged
*Siblings
Adult
*Smoking/adverse effects
China/epidemiology
Cohort Studies
Body Mass Index
RNA, Ribosomal, 16S/genetics
Aged
Female

@article {pmid40059138,
year = {2025},
author = {Zhang, C and Zhong, B and Jiang, Q and Lu, W and Wu, H and Xing, Y and Wu, X and Zhang, Z and Zheng, Y and Li, P and Li, Z and Lin, Z and Chen, Y and Hong, C and Zhao, Z and Zhang, T and Liang, W and Zhang, Y and Zhang, C and Yuan, JX and Liu, C and Wang, J and Yang, K},
title = {Distinct airway mycobiome signature in patients with pulmonary hypertension and subgroups.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {148},
pmid = {40059138},
issn = {1741-7015},
support = {82241012, 82270052, 82120108001, 82170065, 82170069, 82370063//National Natural Science Foundation of China/ ; 82241012, 82270052, 82120108001, 82170065, 82170069, 82370063//National Natural Science Foundation of China/ ; 82241012, 82270052, 82120108001, 82170065, 82170069, 82370063//National Natural Science Foundation of China/ ; 82241012, 82270052, 82120108001, 82170065, 82170069, 82370063//National Natural Science Foundation of China/ ; 2024ZD0528700//National Science and Technology Innovation 2030, Major Project- Research on Cancer, Cardiovascular, Respiratory and Metabolic Diseases/ ; },
mesh = {Humans ; Male ; Female ; Middle Aged ; *Mycobiome ; *Hypertension, Pulmonary/microbiology ; Adult ; Aged ; Fungi/classification/isolation & purification ; Lung/microbiology ; },
abstract = {BACKGROUND: The association between lung microbiome and pulmonary hypertension (PH) remain unknown. This study aims to define the airway mycobiome signature and its potential correlation with clinical parameters of PH.

METHODS: Overall, 244 patients with PH and 120 healthy controls (CON) were recruited from three independent centers. The PH group was divided into subgroups not using antibiotics or corticosteroids (non-ANT/CORT), and those using ANT, CORT, or ANT + CORT within 1 month, and clinical classification (Groups 1, 3, and 4), World Health Organization functional class (I-IV), and disease severity based on mean pulmonary artery pressure or pulmonary vascular resistance levels for in-depth comparison.

RESULTS: Distinct airway mycobiome profiles were observed in PH, CON, and PH subgroups. Linear discriminant analysis effect size analysis showed increased Purpureocillium, Issatchenkia, and Cyberlindnera and decreased Peroneutypa, Simplicillium, and Metarhizium in patients with PH (non-ANT/CORT, ANT, CORT, and ANT + CORT) than in CON. Receiver operating characteristic analysis indicated a strong prediction of the two fungal genera sets in distinguishing PH and its subgroups from CON. The two major fungal phyla, Ascomycota and Basidiomycota, correlated differently with major clinical factors. Increased connections among the top fungal phyla or genera were observed in the PH than in the CON group. Dominant enrichment (Purpureocillium, Issatchenkia, and Cyberlindnera) and diminishment (Peroneutypa, Simplicillium, and Metarhizium) of fungal genera consistently and strongly predicted PH without being influenced by different PH subgroups.

CONCLUSIONS: This study provides the first description of the unique airway mycobiome signature in PH and among different PH subgroups.},
}

Humans
Male
Female
Middle Aged
*Mycobiome
*Hypertension, Pulmonary/microbiology
Adult
Aged
Fungi/classification/isolation & purification
Lung/microbiology

@article {pmid40058902,
year = {2025},
author = {Revelo-Romo, DM and Hurtado Gutiérrez, NH and Hidalgo Troya, A and Amaya-Gómez, CV and Flórez-Martínez, DH and Overmann, J and Villegas Torres, MF and González Barrios, AF},
title = {Omics approaches to explore the coffee fermentation microecosystem and its effects on cup quality.},
journal = {Food research international (Ottawa, Ont.)},
volume = {206},
number = {},
pages = {116035},
doi = {10.1016/j.foodres.2025.116035},
pmid = {40058902},
issn = {1873-7145},
mesh = {*Fermentation ; *Coffee/microbiology ; *Coffea/microbiology/chemistry/metabolism ; Microbiota ; Metagenomics/methods ; Seeds/microbiology/metabolism ; Food Handling/methods ; },
abstract = {The cultivation and postharvest processing of coffee constitute the basis of the subsistence and traditional culture for rural family-owned farms, as well as for the economic success of commercial enterprises in many coffee-producing countries worldwide. The quality of the final beverage is determined by a multitude of variables. A key post-harvest factor is the spontaneous fermentation of the coffee beans, conducted directly on the farm, to remove the mucilage that firmly adheres to the beans. The effect of this fermentation step on the aromatic profile of the coffee is not yet sufficiently understood. All of the above have drawn the attention of researchers on the application of various omics approaches to elucidate fermentation processes in more detail. These approaches have been used to study the fermentation of Arabica (Coffea arabica) beans, as this species is economically most important worldwide. It is known that Arabica mild coffee is obtained through the wet method, which involves fermenting depulped coffee beans using various strategies and then washing the fermented coffee with clean water. In contrast, the fermentation of Canephora coffee beans has been much less studied using omics technologies. This review highlights the trends and future research in coffee fermentation based on a scientometric analysis, supplemented by a traditional systematic literature review. It highlights the composition of the coffee fermentation microbiome, as elucidated by metagenomics applications, in light of several factors that can influence its structure. Additionally, it considers the metabolites associated with microbial metabolism that can influence the chemical composition of coffee beans and, consequently, the cup quality. In this way, this review evidences the promising path in understanding microbial functions in coffee fermentation and in particular in the development of microbial inocula and in the refinement of fermentation processes to improve coffee quality.},
}

*Fermentation
*Coffee/microbiology
*Coffea/microbiology/chemistry/metabolism
Microbiota
Metagenomics/methods
Seeds/microbiology/metabolism
Food Handling/methods

@article {pmid40058892,
year = {2025},
author = {Esmail, GA and Uriot, O and Mottawea, W and Denis, S and Sultan, S and Njoku, EN and Chiba, M and Tosh, S and Blanquet-Diot, S and Hammami, R},
title = {Western diet-based NutriCol medium: A high-pectin, low-inulin culture medium promoted gut microbiota stability and diversity in PolyFermS and M-ARCOL continuous in vitro models.},
journal = {Food research international (Ottawa, Ont.)},
volume = {206},
number = {},
pages = {115993},
doi = {10.1016/j.foodres.2025.115993},
pmid = {40058892},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Inulin/metabolism ; *Fermentation ; *Diet, Western ; *Pectins ; *Colon/microbiology/metabolism ; Dietary Fiber/analysis ; Culture Media ; Feces/microbiology/chemistry ; Mannans ; Galactans/metabolism ; Models, Biological ; Fatty Acids, Volatile/metabolism/analysis ; },
abstract = {Optimizing fermentation media to accurately reflect the colonic environment remains a challenge in developing in vitro models that simulate the human colon. This study aimed to develop a fermentation medium, Nutritive Colonic (NutriCol), which mimics colonic chyme with fiber content reflective of a typical Western diet and compared to the widely used MacFarlane medium. MacFarlane/NutriCol media contained the following fiber (g/L): potato starch (5/0.1), pectin (2/5.6), xylan (2/4.4), arabinogalactan (2/1.8), guar gum (1/0.4), glucomannan (0/0.8), and inulin (1/0.2). The performance of NutriCol was evaluated using two in vitro models: PolyFermS, which simulates the human proximal colon, and M-ARCOL, which mimics both the lumen and mucosa of the human colon. In the PolyFermS model, findings revealed that NutriCol maintained microbiota α-diversity closer to the donor fecal samples and significantly higher than MacFarlane (Shannon's p ≤ 0.01; Simpson's p ≤ 0.001). In contrast, no significant differences in α-diversity were observed between NutriCol and MacFarlane in the M-ARCOL model, likely due to differences in model design and donor microbiome composition. Microbial community structure, assessed by Bray-Curtis distance and A Permutational multivariate analysis of variance (PERMANOVA), revealed significant variations between the two media in both models (PolyFermS: p = 0.02; M-ARCOL: p = 0.01). Additionally, NutriCol demonstrated a higher capacity to cultivate gut microbes, with increased ASV numbers compared to MacFarlane across PolyFermS and M-ARCOL. SCFAs production was influenced by media composition, individual microbiome structure, and the colonic model used. In the M-ARCOL, NutriCol significantly increased acetate (p = 0.0006) and butyrate (p = 0.02) levels compared to MacFarlane. While a similar trend was observed with the PolyFermS, the differences were not statistically significant (p > 0.05). This increase is attributed to the enrichment of SCFA-producing bacteria, such as Butyricicoccus, Lachnospira, Oscillospiraceae UCG-003, Clostridium butyricum, and Lachnospiraceae NK4A136-group. Additionally, NutriCol generated lower levels of intestinal gases (H2, O2, CO2, and CH4) than MacFarlane in the M-ARCOL model. In conclusion, our study demonstrates that NutriCol, a growth medium specifically designed to replicate the typical fiber content of a Western diet, supports gut microbiota diversity and structure better than the established MacFarlane medium. NutriCol's impact was model- and donor-dependent, enhancing microbiota diversity in PolyFermS, while promoting SCFA production and reducing gas levels in M-ARCOL.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Inulin/metabolism
*Fermentation
*Diet, Western
*Pectins
*Colon/microbiology/metabolism
Dietary Fiber/analysis
Culture Media
Feces/microbiology/chemistry
Mannans
Galactans/metabolism
Models, Biological
Fatty Acids, Volatile/metabolism/analysis

@article {pmid40058710,
year = {2025},
author = {Bai, J and Gong, C and Hu, YJ and Bruner, DW and Torres, MA and Buchwald, ZS and Lin, JY},
title = {Skin Microbiome, Inflammation, and Skin Toxicities in Women with Breast Cancer Receiving Moderately Hypofractionated Radiation Therapy.},
journal = {International journal of radiation oncology, biology, physics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijrobp.2025.02.044},
pmid = {40058710},
issn = {1879-355X},
abstract = {PURPOSE: Up to 95% of women during and after radiation therapy (RT) for breast cancer have reported cutaneous toxicity. However, the biologic link between skin microbiome and skin toxicities from RT remains largely unknown. This study aimed to assess the associations of skin microbiome with clinician- and patient-reported skin toxicities and inflammatory markers in women with breast cancer receiving RT.

MATERIALS AND METHODS: A prospective, longitudinal study was conducted at a single institution. Thirty-two women with breast cancer undergoing moderately hypofractionated RT for 3-4 weeks after breast conserving surgery were enrolled and 30 of them were analyzed. 240 swabs for skin microbiome and 120 plasma samples collected pre-RT baseline (T1), week-1 of RT (T2), week-3 of RT (T3), and 3-months post-RT (T4), from the cancer-affected and contralateral healthy breasts. Skin microbiome specimens were processed using 16S V1-V3 sequencing.

RESULTS: Differences in skin microbiome of the treated breasts during RT (T2 and T3) were observed compared to the skin microbiome of pre-RT baseline breasts (T1) and contralateral, healthy breasts, with the affected breasts having an increased abundance of pathogenetic Finegoldia (p=0.001), Dermacoccus (p=0.01), and Variovorax (p=0.003) during RT. Longitudinal analysis showed that decreased Variovorax but increased Staphylococcus were associated with increased clinician-reported grade 2 pruritus (p=0.002) and dermatitis (p=0.012), and increased patient-reported moderate or severe darkened skin (p=0.002) and itchy skin (p=0.012). Additionally, the plasma IFN-γ was associated with changes in skin microbiome in women with breast cancer undergoing RT.

CONCLUSIONS: This study shows changes in the skin microbiome during well-tolerated moderately hypofractionated breast RT. The skin microbiome return towards baseline appears to associate with improvement of clinician- and patient-reported skin toxicities post-treatment. While there were few high-grade toxicities observed among frequently prescribed courses of hypofractionated whole breast RT, changes in skin microibome may be of interest as further targets of symptomatic relief or intervention as ultrahypofractionated courses become more common.},
}

@article {pmid40058701,
year = {2025},
author = {Wang, Y and Li, T and Dong, Z and Zhang, Q and Mi, J and Wang, Q and Lin, G and Ma, Q and Jia, R and Huang, S},
title = {Extracellular vesicles from Lactobacillus fermentum enhance intestinal barrier integrity and restore gut microbial homeostasis in experimental murine colitis.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.03.001},
pmid = {40058701},
issn = {1541-6100},
abstract = {BACKGROUND: Lactobacillus fermentum (L. fermentum) has been shown to improve intestinal health and treat colitis; however, its precise efficacy and mechanisms in inflammatory bowel disease (IBD) remain unclear.

OBJECTIVES: This study aimed to evaluate whether L. fermentum and its metabolites, extracellular vesicles, and other components could modulate intestinal barrier function and gut microbiota to alleviate dextran sulfate sodium (DSS)-induced colitis in mice.

METHODS: Forty-eight mice were randomly assigned to six groups: Control (CON), DSS, L. fermentum + DSS group (LF + DSS), heat-inactivated L. fermentum + DSS group (LHF + DSS), L. fermentum supernatant solution + DSS group (LSF + DSS), and L. fermentum extracellular vesicles + DSS group (LEV + DSS). After a one-week acclimation, mice were gavaged daily for three weeks. Fresh cultures, including live (LF + DSS), heat-inactivated (LHF + DSS), supernatant (LSF + DSS), and extracellular vesicles (LEV + DSS), were prepared daily. During the final seven days, the control group received normal water, while the other groups received 3% DSS. Data were collected daily, followed by sample collection from the mice.

RESULTS: Herein, significant reductions (P < 0.05) in body weight changes, disease activity index (DAI), intestinal damage, and histology scores were observed in the treatment groups, especially LEV + DSS and LF + DSS. Additionally, compared with the DSS group, colonic mucus secretion, as well as claudin-1 and occludin expression, increased significantly (P < 0.05) in the LEV + DSS and LF + DSS groups, while proinflammatory cytokines interleukin (IL) -1β and tumor necrosis factor-α (TNF-α) decreased (P < 0.05) and IL-10 increased (P < 0.05) in the LEV + DSS group. L. fermentum and its components significantly regulated gut microbiota α-diversity and β-diversity, affecting overall composition. LEfSe analysis revealed an enrichment of beneficial bacteria including Prevotellaceae_UCG-001, Romboutsia, and Ruminococcus in the LF + DSS group, and Akkermansia, Odoribacter, and Marvinbryantia in the LEV + DSS group. Both L. fermentum and its extracellular vesicles significantly downregulated the gene expression of TNF-α and IL-1β, while upregulating the expression of IL-10, thereby contributing to the alleviation of colitis symptoms.

CONCLUSIONS: This study reveals that L. fermentum alleviates colitis through modulation of the gut microbiota and reinforcement of the intestinal mucosal barrier, with its extracellular vesicles potentially playing a key role in this regulatory process.},
}

@article {pmid40058670,
year = {2025},
author = {Langgartner, D and Weimer, K and Brunner-Weisser, J and Winkler, R and Mannes, M and Huber-Lang, M and Sterrett, JD and Lowry, CA and Rohleder, N and Bajrami, B and Luippold, AH and Groß, A and Kestler, HA and Tost, H and Meyer-Lindenberg, A and Gündel, H and Jarczok, MN and Reber, SO},
title = {Pawsitive impact: How pet contact ameliorates adult inflammatory stress responses in individuals raised in an urban environment.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.03.013},
pmid = {40058670},
issn = {1090-2139},
abstract = {BACKGROUND: Individuals raised in an urban environment (URBANs) show an exaggerated inflammatory response to the Trier Social Stress Test (TSST) compared with individuals raised in a rural environment. The underlying mechanisms are unclear but may relate to childhood animal contact. As an exaggerated immune (re)activity plays a causal role in the pathogenesis of stress-associated disorders, these findings might explain the higher prevalence of stress-associated disorders in urban vs. rural areas.

METHODS: We recruited physically and emotionally healthy male URBANs, raised in a city with more than 40,000 residents either in the absence (noPETs) or presence (PETs) of household pets. Participants were individually exposed to the TSST, and before and after the TSST, blood and saliva were collected for assessment of different stress-related parameters. An additional saliva sample before the TSST was collected for salivary microbiome analysis. Heart rate (HR) and HR variability (HRV) were recorded continuously. Mental and physical health status, early-life and perceived life stress, current animal contact, and subjective strain induced by TSST exposure were assessed using validated questionnaires.

RESULTS: Here we show that adult healthy male URBANs raised in the absence (noPETs) vs. presence (PETs) of household pets still reported less animal contact during adulthood and were characterized by deficits in their immunoregulatory and intestinal barrier function, which under basal conditions did not translate into a chronic low-grade inflammatory state. This was different under acute psychosocial stress conditions. Exposure to the TSST resulted in a facilitated mobilization of particularly neutrophil granulocytes in noPETs vs. PETs, accompanied by an enhanced pro- and compromised anti-inflammatory systemic stress response.

CONCLUSION: Together, the presence of pets seems to reduce the risk for URBANs to develop stress-associated disorders later in life (i.e., primary prevention) by facilitating immunoregulatory and barrier functions, in turn preventing an overshooting immune activation in response to acute stressors and chronic low-grade inflammation in response to repeated/chronic stressors.},
}

@article {pmid40058669,
year = {2025},
author = {Sánchez, IM and Spielbauer, J and Heijtz, RD},
title = {Maternal peptidoglycan overexposure during late pregnancy alters neurodevelopment and behavior in juvenile offspring.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.03.014},
pmid = {40058669},
issn = {1090-2139},
abstract = {Emerging evidence suggests that maternal gut microbiota-derived metabolites and components influence fetal brain development and subsequent neurodevelopment. This study investigates the effects of maternal overexposure to muramyl dipeptide (MDP)-a bacterial peptidoglycan (PGN) motif recognized by Nod2 receptors-on offspring neurodevelopment and behavior. Time-mated C57BL/6J female mice received MDP via drinking water from gestational days 16-19. Nod2 activation in amniotic fluid was assessed using a Nod2 cell-based reporter assay, showing a significant increase in males 24 h after MDP exposure. Gene expression analysis revealed upregulation of PGN transporters in fetal brains, with males showing higher levels of Slc15a1/PepT1, Slc15a2/PepT2, and Slc46a2. No changes in inflammatory or microglia-related markers were found. Behavioral assessments during the juvenile period revealed sex-specific effects: prenatally exposed males showed reduced social interaction, while females exhibited reduced novelty-induced locomotion and impaired social recognition. These behavioral changes were linked to altered expression of synaptic (Dlg4, Ppp1r9b, Darpp-32) and microglial (Trem-2, Cx3cr1) genes in the prefrontal cortex. Our findings underscore the sex-specific effects of maternal PGN overexposure on offspring neurodevelopment, highlighting the potential role of the maternal microbiome in the neurobiology of neurodevelopmental disorders, even in the absence of infection or robust inflammation.},
}

@article {pmid40058511,
year = {2025},
author = {Zhou, G and Yang, Y and Leng, J and Chen, J and Zhou, H and Ming, R and Jiang, H},
title = {Gut Microbiota-Derived Deoxycholic Acid in Colorectal Cancer Therapy: Critical Considerations and An Extended Clinical Investigation Panorama Analysis.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107683},
doi = {10.1016/j.phrs.2025.107683},
pmid = {40058511},
issn = {1096-1186},
}

@article {pmid40058438,
year = {2025},
author = {Cai, Z and Zhang, M and Zhou, L and Xiong, Y and Wang, H and Chen, Y and Yuan, JB},
title = {Kai-Xin-San polysaccharides exert therapeutic effects on D-gal and Aβ25-35-induced AD rats by regulating gut microbiota and metabolic profile.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {141850},
doi = {10.1016/j.ijbiomac.2025.141850},
pmid = {40058438},
issn = {1879-0003},
abstract = {Metabolic abnormalities and gut microbiota imbalance are intricately linked to the onset and progression of Alzheimer's disease (AD). Kai-Xin-San (KXS) is a traditional herbal formula known for its therapeutic effects on AD. Our previous research indicated that Kai-Xin-San polysaccharide (KXS-P) exhibits a significant therapeutic impact on AD, but the precise mechanisms remain incompletely understood. In this study, untargeted fecal metabolomics and 16S rRNA gene sequencing were used to investigate the potential mechanisms by which KXS-P acts against AD. Key metabolites and gut microbial species were identified using multivariate analysis and a comprehensive examination of intestinal microecology. Our findings revealed that KXS-P improves lipid metabolism in AD rats by modulating a series of lipid molecules and bile acid levels. Additionally, KXS-P regulated gut microbiota composition and restored the symbiotic relationships within the gut microbiome. Notably, the anti-inflammatory effect of KXS-P may be related to its regulation of specific lipotypes levels and the abundance of Romboutsia, Bifidobacterium and Alloprevotella. KXS-P demonstrates the ability to alleviate symptoms of AD rats through multiple mechanisms: ① Improving lipid metabolism and maintaining lipid homeostasis; ② Reducing neuronal and inflammatory damage; ③ Regulating the composition and symbiotic relationships of gut microbiota to preserve intestinal microecological balance.},
}

@article {pmid40058281,
year = {2025},
author = {Balaji, SK and Khuwaja, WM and Hossain, ML and Fernando, LGB and Dong, X},
title = {Neuroimmune interactions between itch neurons and skin microbes.},
journal = {Seminars in immunology},
volume = {78},
number = {},
pages = {101933},
doi = {10.1016/j.smim.2025.101933},
pmid = {40058281},
issn = {1096-3618},
abstract = {Itch is an unpleasant sensation that is encoded by specific sensory neurons called pruriceptors. Itch is associated with almost all skin diseases. Recent studies revealed that many itchy skin diseases are associated with microbiome dysbiosis. Pathogenic microbes secrete proteases and toxins to invade skin cells. Some microbial products can directly activate sensory neurons, while others activate the mammalian immune system and indirectly cause itch. In this review, we summarize the current knowledge on microbe-immune-neuron crosstalks and discuss their relevance in itchy skin diseases.},
}

@article {pmid40058066,
year = {2025},
author = {Mu, X and Feng, L and Wang, Q and Li, H and Zhou, H and Yi, W and Sun, Y},
title = {Decreased gut microbiome-derived indole-3-propionic acid mediates the exacerbation of myocardial ischemia/reperfusion injury following depression via the brain-gut-heart axis.},
journal = {Redox biology},
volume = {81},
number = {},
pages = {103580},
doi = {10.1016/j.redox.2025.103580},
pmid = {40058066},
issn = {2213-2317},
abstract = {Despite the increasing recognition of the interplay between depression and cardiovascular disease (CVD), the precise mechanisms by which depression contributes to the pathogenesis of cardiovascular disease remain inadequately understood. The involvement of gut microbiota and their metabolites to health and disease susceptibility has been gaining increasing attention. In this study, it was found that depression exacerbated cardiac injury, impaired cardiac function (EF%: P < 0.01; FS%: P < 0.05), hindered long-term survival (P < 0.01), and intensified adverse cardiac remodeling (WGA: P < 0.01; MASSON: P < 0.0001) after myocardial ischemia/reperfusion (MI/R) in mice. Then we found that mice receiving microbiota transplants from chronic social defeat stress (CSDS) mice exhibited worse cardiac function (EF%: P < 0.01; FS%: P < 0.01) than those receiving microbiota transplants from non-CSDS mice after MI/R injury. Moreover, impaired tryptophan metabolism due to alterations in gut microbiota composition and structure was observed in the CSDS mice. Mechanistically, we analyzed the metabolomics of fecal and serum samples from CSDS mice and identified indole-3-propionic acid (IPA) as a protective agent for cardiomyocytes against ferroptosis after MI/R via NRF2/System xc-/GPX4 axis, played a role in mediating the detrimental influence of depression on MI/R. Our findings provide new insights into the role of the gut microbiota and IPA in depression and CVD, forming the basis of intervention strategies aimed at mitigating the deterioration of cardiac function following MI/R in patients experiencing depression.},
}

@article {pmid40057978,
year = {2025},
author = {Jeevannavar, A and Florenza, J and Divne, AM and Tamminen, M and Bertilsson, S},
title = {Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf046},
pmid = {40057978},
issn = {1751-7370},
abstract = {Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with two distinct growth phases: a fast-growing phase and a slow-growing phase. Besides the two expected expression clusters, each corresponding to either growth phase, a third transcriptional state was identified across both growth phases. Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth stage, as well as down-regulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism characteristic of the third transcriptional state. In addition, carry-over rRNA reads recapitulated the taxonomic identity of the target while revealing distinct bacterial communities, in co-culture with the eukaryote, each associated with distinct transcriptional states. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability to describe the ecological roles of environmental microeukaryotes, culture-free and reference-free, surpassing alternative methods like metagenomics or metatranscriptomics.},
}

@article {pmid40057969,
year = {2025},
author = {Herrington, RTB and Ellenberger, DT and Rosenfeld, CS},
title = {Maternal probiotic supplementation and effects on the Fetal placenta.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioaf041},
pmid = {40057969},
issn = {1529-7268},
abstract = {Increasing number of pregnant women are consuming probiotics to promote their own health and that of their unborn fetus. Such supplements are presumed to be safe for pregnant mothers and their unborn offspring. For pregnant mothers, such bioactive compounds might lower the risk of constipation, diarrhea, other gastrointestinal conditions, pre-term birth, and prevent adverse pregnancy outcomes, including gestational diabetes mellitus (GDM) and depression/anxiety. More research is needed to examine potential safety of probiotic consumption during pregnancy and long-term health consequences to offspring. The conceptus can also be indirectly affected by maternal probiotic supplementation through microorganism production of bioactive compounds. The placenta is in direct communication with the underlying uterine tissue. Thus, compounds in the maternal blood can easily transfer across the placenta and impact this hormonally sensitive organ. Select studies suggest that disruptions to the maternal microbiome dramatically affects the placenta. In the current review, we will therefore consider the evidence to date of how maternal probiotic supplementation affects the placenta. Three potential mechanisms we will explore include the possibility that maternal probiotic supplementation might impact the putative placenta microbiome. The second potential mechanism we will consider is that maternal probiotic consumption alters bacterial-derived metabolites, including short-chained fatty acids, polyamines, Vitamin B9, and Vitamin B12. The third potential mechanism to be discussed is that such supplements affect maternal and placental immune responses. Before probiotics are promoted for healthy pregnant women and those with gestational disorders, more studies, including those examining the effects on the placenta, are essential.},
}

@article {pmid40057860,
year = {2025},
author = {Lebtig, M and Peschel, A and Kretschmer, D},
title = {Role of Formyl Peptide Receptor 2 and Toll-Like Receptor 2 in Skin Barrier Function and Atopic Dermatitis.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.02.002},
pmid = {40057860},
issn = {1523-1747},
abstract = {The skin acts as a barrier against external threats and plays an important role in tissue repair. Skin cells, including keratinocytes, sense microbe-associated molecular pattern molecules released by members of the bacterial microbiome, and the cellular responses control central processes of skin homeostasis or inflammation. How the combination and amount of different microbe-associated molecular patterns modulate skin cell functions is not yet fully understood. Here, we review the current knowledge of the responses of skin cells to microbe-associated molecular patterns, focusing on Toll-like receptor 2 and formyl peptide receptor 2, two of the most important receptors for sensing the skin microbiome.},
}

@article {pmid40057813,
year = {2025},
author = {Kong, F and Wang, S and Zhang, Y and Li, C and Dai, D and Guo, C and Wang, Y and Cao, Z and Yang, H and Bi, Y and Wang, W and Li, S},
title = {Rumen microbiome associates with postpartum ketosis development in dairy cows: a prospective nested case-control study.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {69},
pmid = {40057813},
issn = {2049-2618},
support = {32130100//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Cattle ; *Ketosis/veterinary ; Female ; *Rumen/microbiology ; *Postpartum Period ; Case-Control Studies ; *Gastrointestinal Microbiome ; *Cattle Diseases/microbiology ; *3-Hydroxybutyric Acid/blood ; Prospective Studies ; Bacteria/classification/isolation & purification/genetics ; Propionates/metabolism/blood ; Energy Metabolism ; Microbiota ; },
abstract = {BACKGROUND: Approximately, one-third of dairy cows suffer from postpartum diseases. Ketosis is considered an important inducer of other postpartum diseases by disrupting energy metabolism. Although the rumen microbiome may be involved in the etiology of ketosis by supplying volatile fatty acids, the rumen environmental dynamics of ketosis cows are unclear. Using multi-omics, this study aimed to elucidate changes in the rumen microbiome during parturition of ketosis cows and the association between the rumen microbiome and host energy metabolism. The study included 810 rumen content samples and 789 serum samples from day - 21 and 21 relative to calving day from 61 ketosis cows and 84 healthy cows.

RESULTS: In ketosis cows, the rumen bacterial composition after parturition changed dramatically and needed a longer time to restore. The molar proportions of propionate were lower in ketosis cows than those in healthy cows on days 3 and 7 and negatively correlated with the serum β-hydroxybutyrate (BHBA) levels. The fermentation sub-pathway of propionate metabolism and partial glucogenic amino acid pathways were downregulated on day 3. Prevotella, UBA1066, and microbiota diversity indices regulate serum BHBA and glucose (GLU) levels via arginine, alanine, glycine, or propionate. Propionate administration to ketosis cows potentially decreased the serum BHBA concentration.

CONCLUSIONS: Collectively, we found rumen disruption happened after calving among ketosis cows, and insufficient glycogenic substrates, such as propionate, may be related to ketosis development. The study findings have implications for the relationship between rumen microbiome dynamics and host energy metabolism, which lays the foundation for the future rumen microbiome investigation for improving postpartum management in cows. Video Abstract.},
}

Animals
Cattle
*Ketosis/veterinary
Female
*Rumen/microbiology
*Postpartum Period
Case-Control Studies
*Gastrointestinal Microbiome
*Cattle Diseases/microbiology
*3-Hydroxybutyric Acid/blood
Prospective Studies
Bacteria/classification/isolation & purification/genetics
Propionates/metabolism/blood
Energy Metabolism
Microbiota

@article {pmid40057571,
year = {2025},
author = {Adams, SE and Cawley, AK and Arnold, D and Hoptroff, MJ and Slomka, V and Matheson, JR and Marriott, RE and Gemmell, MR and Marsh, PD},
title = {A randomised, double-blind clinical study into the effect of zinc citrate trihydrate toothpaste on oral plaque microbiome ecology and function.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {8136},
pmid = {40057571},
issn = {2045-2322},
mesh = {Humans ; *Toothpastes/pharmacology/therapeutic use ; *Dental Plaque/microbiology ; Male ; Female ; Adult ; *Microbiota/drug effects ; Double-Blind Method ; Middle Aged ; Zinc Compounds/pharmacology/therapeutic use/administration & dosage ; Young Adult ; Bacteria/classification/drug effects/genetics/isolation & purification ; },
abstract = {The oral microbiome is a diverse community of microbes residing on all oral surfaces. A balanced oral microbiome is associated with good oral health, and disruption can result in imbalance associated with diseases including gingivitis and dental caries. It is important, therefore, to understand how daily use of oral hygiene products impacts the microbiome. Composition and activity of dental plaque microbiome from 115 participants was analysed after brushing with one of two toothpastes, one containing zinc citrate trihydrate and the other a control toothpaste, in a parallel design. Each participant brushed twice daily for 6-weeks, with samples collected at baseline, 2 and 6-weeks. Metataxonomic analysis demonstrated changes in bacterial communities with use of the zinc toothpaste compared to the control product at community and species level. Increases at the species level were observed for taxa from the genus Veillonella with decrease in a taxon from the genus Fusobacterium for the zinc toothpaste. Analysis of microbiome function based on predicted metagenomic and metatranscriptomic analysis show that use of the zinc toothpaste is associated with an in-vivo reduction in glycolysis, consistent with the mode of action of zinc and, increases in processes linked to gum-health (lysine biosynthesis), and to whole-body health (nitrate reduction). Our findings provide the first understanding of the beneficial modulation of microbiome composition and function by zinc-containing toothpaste in-vivo for oral care benefits.},
}

Humans
*Toothpastes/pharmacology/therapeutic use
*Dental Plaque/microbiology
Male
Female
Adult
*Microbiota/drug effects
Double-Blind Method
Middle Aged
Zinc Compounds/pharmacology/therapeutic use/administration & dosage
Young Adult
Bacteria/classification/drug effects/genetics/isolation & purification

@article {pmid40057258,
year = {2025},
author = {Ragone, P and Parodi, C and Tomasini, N and Ramos, F and Uncos, A and Brandán, CP},
title = {The interplay between Trypanosoma cruzi and the microbiome of Triatoma infestans: Implications for the host's immune response.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107577},
doi = {10.1016/j.actatropica.2025.107577},
pmid = {40057258},
issn = {1873-6254},
abstract = {The infection dynamics of Trypanosoma cruzi is shaped by the parasite's genetics and interactions with host and vector factors. While most studies in the area use axenic parasite cultures devoid of insect fecal components, this study is focused on the immune response and the parasite loads generated after the interaction of T. cruzi with feces from Triatoma infestans in a murine model. First, using metagenomics, we analyzed the microbiota of infected and uninfected feces. Illumina sequencing of the 16S rRNA gene (V3-V4 region) revealed a predominance of the genus Arsenophonus in infected feces and of Enterococcus in uninfected ones. C57BL/6J mice inoculated with T. cruzi infected feces, displayed distinct immune responses compared to those inoculated with culture-derived metacyclic trypomastigotes alone, with lower levels of pro-inflammatory cytokines (IFN-ɣ, TNF-α) and higher amounts of IL-10, suggesting a regulatory response. Besides, total anti-T. cruzi IgG levels remained similar among groups, but IgG1 and IgG2c were reduced in the T. cruzi infected feces group, indicating a balanced Th1/Th2 response. Notably, mice inoculated with T. cruzi infected feces demonstrated significantly reduced blood and muscle parasite loads, potentially limiting inflammation and parasite dissemination. These findings highlight the possible role of vector fecal microbiota in shaping immune responses and influencing disease outcomes during natural T. cruzi infections.},
}

@article {pmid40056901,
year = {2025},
author = {Kuziel, GA and Lozano, GL and Simian, C and Li, L and Manion, J and Stephen-Victor, E and Chatila, T and Dong, M and Weng, JK and Rakoff-Nahoum, S},
title = {Functional diversification of dietary plant small molecules by the gut microbiome.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.01.045},
pmid = {40056901},
issn = {1097-4172},
abstract = {Plants are composed of diverse secondary metabolites (PSMs), which are widely associated with human health. Whether and how the gut microbiome mediates such impacts of PSMs is poorly understood. Here, we show that discrete dietary and medicinal phenolic glycosides, abundant health-associated PSMs, are utilized by distinct members of the human gut microbiome. Within the Bacteroides, the predominant gram-negative bacteria of the Western human gut, we reveal a specialized multi-enzyme system dedicated to the processing of distinct glycosides based on structural differences in phenolic moieties. This Bacteroides metabolic system liberates chemically distinct aglycones with diverse biological functions, such as colonization resistance against the gut pathogen Clostridioides difficile via anti-microbial activation of polydatin to the stilbene resveratrol and intestinal homeostasis via activation of salicin to the immunoregulatory aglycone saligenin. Together, our results demonstrate generation of biological diversity of phenolic aglycone "effector" functions by a distinct gut-microbiome-encoded PSM-processing system.},
}

@article {pmid39961369,
year = {2025},
author = {Tomatsu, S and Abbott, SM and Attarian, H},
title = {Clinical Chronobiology: Circadian Rhythms in Health and Disease.},
journal = {Seminars in neurology},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2538-3259},
pmid = {39961369},
issn = {1098-9021},
abstract = {Circadian rhythms (CRs) are entrainable endogenous rhythms that respond to external stimuli and regulate physiological functions. The suprachiasmatic nucleus (SCN) in the hypothalamus is the mammalian master clock that synchronizes all other tissue-specific peripheral clocks, primarily through gamma-aminobutyric acid (GABA) and vasoactive intestinal polypeptide (VIP). The SCN follows Earth's 24-hour cycle by light entrainment through the retinohypothalamic tract. At the cellular level, the core clock genes CLOCK, BMAL1, PER1-PER3, CRY1, and CRY2 regulate CRs in a negative feedback loop. The circadian disruption of the sleep-wake cycle manifests in at least six distinct clinical conditions. These are the circadian rhythm sleep-wake disorders (CRSWDs). Their diagnosis is made by history, sleep diaries, and actigraphy. Treatment involves a combination of timed light exposure, melatonin/melatonin agonists, and behavioral interventions. In addition, CR disturbances and subsequent misalignment can increase the risk of a variety of illnesses. These include infertility and menstrual irregularities as well as diabetes, obesity, fatty liver disease, and other metabolic syndromes. In addition, a disruption in the gut microbiome creates a proinflammatory environment. CR disturbances increase the risk for mood disorders, hence the utility of light-based therapies in depression. People with neurodegenerative disorders demonstrate significant disturbances in their CRs, and in their sleep-wake cycles. Circadian realignment therapies can also help decrease the symptomatic burden of these disorders. Certain epilepsy syndromes, such as juvenile myoclonic epilepsy (JME), have a circadian pattern of seizures. Circadian disturbances in epilepsy can be both the consequence and cause for breakthrough seizures. The immune system has its own CR. Disturbances in these due to shift work, for instance, can increase the risk of infections. CR disturbances can also increase the risk of cancer by impacting DNA repair, apoptosis, immune surveillance, and cell cycle regulation. Moreover, the timing of chemotherapeutic agents has been shown to increase their therapeutic impact in certain cancers.},
}

@article {pmid40056347,
year = {2025},
author = {Petit, P and Vuillerme, N},
title = {Global research trends on the human exposome: a bibliometric analysis (2005-2024).},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40056347},
issn = {1614-7499},
support = {ANR-19-P3IA-0003//MIAI@Grenoble Alpes/ ; ANR-10-AIRT-05//Agence Nationale de la Recherche/ ; ANR-15-IDEX-02//Agence Nationale de la Recherche/ ; },
abstract = {Exposome represents one of the most pressing issues in the environmental science research field. However, a comprehensive summary of worldwide human exposome research is lacking. We aimed to explore the bibliometric characteristics of scientific publications on the human exposome. A bibliometric analysis of human exposome publications from 2005 to December 2024 was conducted using the Web of Science in accordance with PRISMA guidelines. Trends/hotspots were investigated with keyword frequency, co-occurrence, and thematic map. Sex disparities in terms of publications and citations were examined. From 2005 to 2024, 931 publications were published in 363 journals and written by 4529 authors from 72 countries. The number of publications tripled during the last 5 years. Publications written by females (51% as first authors and 34% as last authors) were cited fewer times (13,674) than publications written by males (22,361). Human exposome studies mainly focused on air pollution, metabolomics, chemicals (e.g., per- and polyfluoroalkyl substances (PFAS), endocrine-disrupting chemicals, pesticides), early-life exposure, biomarkers, microbiome, omics, cancer, and reproductive disorders. Social and built environment factors, occupational exposure, multi-exposure, digital exposure (e.g., screen use), climate change, and late-life exposure received less attention. Our results uncovered high-impact countries, institutions, journals, references, authors, and key human exposome research trends/hotspots. The use of digital exposome technologies (e.g., sensors, and wearables) and data science (e.g., artificial intelligence) has blossomed to overcome challenges and could provide valuable knowledge toward precision prevention. Exposome risk scores represent a promising research avenue.},
}

@article {pmid40056222,
year = {2025},
author = {Addissouky, TA},
title = {Advancing frontiers in skin offensive odor management: from innovative diagnostics to cutting-edge treatments and emerging technologies.},
journal = {Archives of dermatological research},
volume = {317},
number = {1},
pages = {539},
pmid = {40056222},
issn = {1432-069X},
mesh = {Humans ; *Odorants ; *Volatile Organic Compounds ; *Microbiota ; *Sweat/chemistry ; Skin ; Gas Chromatography-Mass Spectrometry ; Electronic Nose ; High-Throughput Nucleotide Sequencing ; Quality of Life ; Probiotics/administration & dosage ; Deodorants ; },
abstract = {Skin bromhidrosis, commonly referred to as body odor, is caused by the microbial breakdown of sweat, leading to the formation of volatile organic compounds (VOCs) that result in unpleasant odors. While body odor is a natural consequence of sweat production, excessive or persistent odor can significantly affect quality of life, causing social stigma and psychological distress. Traditional approaches to managing body odor, such as antiperspirants and deodorants, have limitations, necessitating the development of more advanced diagnostic tools and treatments. This review aims to explore recent advancements in the diagnosis and treatment of skin offensive odor, focusing on cutting-edge technologies and novel approaches. It highlights the interplay of the skin microbiome, sweat gland activity, and external factors in odor formation and investigates innovative solutions for long-term odor management. Emerging diagnostic techniques, such as electronic nose (E-nose) technology, gas chromatography-mass spectrometry (GC-MS), and next-generation sequencing (NGS), enable precise detection and analysis of odor-causing VOCs and microbial profiles. These tools facilitate a deeper understanding of the pathophysiology of odor production. Treatment innovations include nanotechnology-based antimicrobials (e.g., silver and zinc oxide nanoparticles), probiotic formulations for microbiome modulation, and odor-neutralizing compounds such as cyclodextrins and enzymatic neutralizers. Advanced delivery systems, including microneedle patches and nanoencapsulation, enable targeted, sustained release of active ingredients. Additionally, systemic approaches like oral probiotics and dietary interventions offer complementary strategies for managing body odor. The integration of novel diagnostics with innovative topical and systemic treatments offers promising avenues for more effective and personalized management of skin offensive odor. These advancements pave the way for improved quality of life for individuals affected by bromhidrosis, with potential for widespread application in personal care and medical contexts. Clinical trial number: Not applicable.},
}

Humans
*Odorants
*Volatile Organic Compounds
*Microbiota
*Sweat/chemistry
Skin
Gas Chromatography-Mass Spectrometry
Electronic Nose
High-Throughput Nucleotide Sequencing
Quality of Life
Probiotics/administration & dosage
Deodorants

@article {pmid40056186,
year = {2025},
author = {Chen, XX and Ju, Q and Qiu, D and Zhou, Y and Wang, Y and Zhang, XX and Li, JG and Wang, M and Chang, N and Xu, XR and Zhang, YB and Zhao, T and Wang, K and Zhang, Y and Zhang, J},
title = {Microbial dysbiosis with tryptophan metabolites alteration in lower respiratory tract is associated with clinical responses to anti-PD-1 immunotherapy in advanced non-small cell lung cancer.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {74},
number = {4},
pages = {140},
pmid = {40056186},
issn = {1432-0851},
support = {82103446//National Natural Science Foundation of China/ ; 82273226//National Natural Science Foundation of China/ ; 82473215//National Natural Science Foundation of China/ ; 2020QNRC001//China Association for Science and Technology/ ; 2021LC2115//Fourth Military Medical University/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/immunology/drug therapy/metabolism/therapy ; *Tryptophan/metabolism ; *Lung Neoplasms/immunology/drug therapy/therapy/metabolism ; *Dysbiosis/immunology ; Female ; Male ; Middle Aged ; Aged ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; Microbiota/drug effects/immunology ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/metabolism ; Respiratory System/immunology/metabolism/microbiology ; Adult ; },
abstract = {Lower respiratory tract microbiome constitutes a unique immune microenvironment for advanced non-small cell lung cancer as one of dominant localized microbial components. However, there exists little knowledge on the associations between this regional microbiome and clinical responses to anti-PD-1 immunotherapy from clinical perspectives. Here, we equivalently collected bronchoalveolar lavage fluids from 56 advanced NSCLC participants treated with none (untreated, n = 28) or anti-PD-1 immunotherapy (treated, n = 28), which was further divided into responder (n = 17) and non-responder (n = 11) subgroups according to clinical responses, aiming to compare their microbial discrepancy by performing metagenomic sequencing and targeted metabolic alterations by tryptophan sequencing. Correspondingly, microbial diversities transformed significantly after receiving immunotherapeutic agents, where Gammaproteobacteria and Campylobacter enriched, but Escherichia, Streptococcus, Chlamydia, and Staphylococcus reduced at the genus level, differences of which failed to be achieved among subgroups with various clinical responses (responder or non-responder; LDA > 2, P < 0.05[*]). And the relative abundance of Staphylococcus and Streptomyces was escalated in response subgroup to anti-PD-1 immunotherapy by microbial compositional analysis (as relative abundance ≥ 3%, P < 0.05[*]), no significance of which was achieved among treated and untreated groups. In addition, relative abundances of bacterial tryptophan metabolites and its derivatives were also higher in the responder subgroup, distinctively being associated with divergent genera (VIP > 1, P < 0.05[*]). Our study revealed predictive performance of lower respiratory tract microbiome to antitumoral immunotherapy and further suggested that anti-PD-1 immunotherapy may alter lower respiratory tract microbiome composition and interact with its tryptophan metabolites to regulate therapeutic efficacy in advanced NSCLC, performing as potential biomarkers to prognosis and interventional strategies.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/immunology/drug therapy/metabolism/therapy
*Tryptophan/metabolism
*Lung Neoplasms/immunology/drug therapy/therapy/metabolism
*Dysbiosis/immunology
Female
Male
Middle Aged
Aged
*Immunotherapy/methods
*Immune Checkpoint Inhibitors/therapeutic use
Microbiota/drug effects/immunology
Programmed Cell Death 1 Receptor/antagonists & inhibitors/metabolism
Respiratory System/immunology/metabolism/microbiology
Adult

@article {pmid40056175,
year = {2025},
author = {de Fernandes, MG and Nascimento-Silva, G and Rozas, EE and Hardoim, CCP and Custódio, MR},
title = {From Sea to Freshwater: Shared and Unique Microbial Traits in Sponge Associated Prokaryotic Communities.},
journal = {Current microbiology},
volume = {82},
number = {4},
pages = {178},
pmid = {40056175},
issn = {1432-0991},
support = {88887465142/2019-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 2016/17189-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/10157-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
mesh = {*Porifera/microbiology ; Animals ; *Microbiota ; *Fresh Water/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; *Phylogeny ; Symbiosis ; Ecosystem ; Archaea/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; },
abstract = {Despite their ecological significance and biotechnological potential, freshwater sponges remain relatively understudied compared to their marine counterparts. In special, the prokaryotic communities of species from isolated yet highly diverse ecosystems, such as the Amazon Rainforest, remain unknown, leaving an important part of the Porifera microbiome underexplored. Using high-throughput sequencing of the 16S rRNA gene, we unraveled the structure of the microbiota associated to the freshwater sponges Heteromeyenia cristalina and Metania reticulata for the first time. Their microbiome was compared with that of the haplosclerid marine sponges Amphimedon viridis and Haliclona melana; and the tetractinellid Cinachyrella alloclada. Our findings reveal not only a shared core microbiome between the freshwater and marine environments but also indicate functional redundancy in their communities, suggesting that certain microbial metabolic functions are conserved across diverse habitats. Comparisons between ecosystems also revealed that microbiomes of freshwater sponges can be richer and more diverse than those of marine species. Moreover, we compared the microbiome of adults and asexual reproduction structures (buds and gemmules) of sponges from both habitats, revealing a remarkable similarity between adults and their respective offsprings, indicating an important role of vertical transmission in this mode of reproduction. Our observations emphasize the dynamic interactions and the adaptability of the sponge-associated microbiota, providing insights into how these symbiotic associations were affected during the colonization of freshwater environments and shedding light into how symbiotic relationships are maintained throughout generations.},
}

*Porifera/microbiology
Animals
*Microbiota
*Fresh Water/microbiology
*Bacteria/classification/genetics/isolation & purification
*RNA, Ribosomal, 16S/genetics
*Seawater/microbiology
*Phylogeny
Symbiosis
Ecosystem
Archaea/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing

@article {pmid40055814,
year = {2025},
author = {Gao, W and Wang, G and Yuan, H and Chen, Y and Che, J and Cheng, Z and Chen, L and Zhang, L and Zhu, Y and Liu, X and Liu, A and Yang, Q and Cao, P and Qian, W and Huang, W and Schnabl, B and Yang, L and Chu, H},
title = {Gram-positive probiotics improves acetaminophen-induced hepatotoxicity by inhibiting leucine and Hippo-YAP pathway.},
journal = {Cell & bioscience},
volume = {15},
number = {1},
pages = {32},
pmid = {40055814},
issn = {2045-3701},
support = {82470584//National Natural Science Foundation of China/ ; 82000561//National Natural Science Foundation of China/ ; 82270614//National Natural Science Foundation of China/ ; 81974078//National Natural Science Foundation of China/ ; 81570530//National Natural Science Foundation of China/ ; 2022YFA1305600//National Key R&D Program of China/ ; 2023YFC2413804//National Key R&D Program of China/ ; P30 DK120515/DK/NIDDK NIH HHS/United States ; },
abstract = {OBJECTIVES: Drug-induced liver injury (DILI) can be improved by modulating gut microbiota. We aimed to investigate a probiotic mixture comprising Bifidobacterium Longum, Streptococcus thermophilus, and Lactobacillus delbrueckii subspecies bulgaricus (BSL) in mitigating acetaminophen induced liver injury (AILI), and to elucidate the underlying mechanisms.

METHODS: Gut bacterial communities were analyzed in fecal samples from patients with DILI and healthy controls. Mice were pretreated with BSL or PBS for 10 days, then subjected to a single dose of acetaminophen (300 mg/kg) gavage and euthanized 24 h later. Transcriptome sequencing, microbiome, and metabolome sequencing were performed on mouse samples, respectively.

RESULTS: Gut bacterial dysbiosis existed in DILI patients, with a decrease in Gram-positive bacteria and an increase in Gram-negative bacteria. A similar situation occurred in AILI mice. Pretreatment of BSL significantly improved APAP-induced disorders of gut bacteria and alleviated hepatic inflammation and necrosis. Transcriptome sequencing showed that BSL inhibited the hepatic damage pathways, such as Hippo and TGF-β signaling pathway. Metabolomic profiling revealed an obvious increase in oligopeptides containing branched-chain amino acids (BCAAs) in AILI mice, whereas these metabolites were significantly negatively correlated with the abundance of BSL, but positively with key genes of Hippo pathway. In vitro experiments showed that leucine exerted a dose-related exacerbation pattern on APAP-mediated hepatocellular injury. Mice supplemented with leucine resulted in the further overexpression of Yes-associated protein, an increase in oxidative stress, and a worsening of AILI.},
}

@article {pmid40055808,
year = {2025},
author = {Avershina, E and Qureshi, AI and Winther-Larsen, HC and Rounge, TB},
title = {Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {66},
pmid = {40055808},
issn = {2049-2618},
support = {2022067//Helse Sør-Øst RHF/ ; },
mesh = {*Software ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Humans ; *Mycobiome ; *Fungi/genetics/classification/isolation & purification ; *Metagenomics/methods ; Computational Biology/methods ; Ascomycota/genetics/classification/isolation & purification ; Basidiomycota/genetics/isolation & purification/classification ; Databases, Genetic ; },
abstract = {BACKGROUND: The mycobiome, representing the fungal component of microbial communities, is increasingly acknowledged as an integral part of the gut microbiome. However, research in this area remains relatively limited. The characterization of mycobiome taxa from metagenomic data is heavily reliant on the quality of the software and databases. In this study, we evaluated the feasibility of mycobiome profiling using existing bioinformatics tools on simulated fungal metagenomic data.

RESULTS: We identified seven tools claiming to perform taxonomic assignment of fungal shotgun metagenomic sequences. One of these was outdated and required substantial modifications of the code to be functional and was thus excluded. To evaluate the accuracy of identification and relative abundance of the remaining tools (Kraken2, MetaPhlAn4, EukDetect, FunOMIC, MiCoP, and HumanMycobiomeScan), we constructed 18 mock communities of varying species richness and abundance levels. The mock communities comprised up to 165 fungal species belonging to the phyla Ascomycota and Basidiomycota, commonly found in gut microbiomes. Of the tools, FunOMIC and HumanMycobiomeScan needed source code modifications to run. Notably, only one species, Candida orthopsilosis, was consistently identified by all tools across all communities where it was included. Increasing community richness improved precision of Kraken2 and the relative abundance accuracy of all tools on species, genus, and family levels. MetaPhlAn4 accurately identified all genera present in the communities and FunOMIC identified most species. The top three tools for overall accuracy in both identification and relative abundance estimation were EukDetect, MiCoP, and FunOMIC, respectively. Adding 90% and 99% bacterial background did not significantly impact these tools' performance. Among the whole genome reference tools (Kraken2, HMS, and MiCoP), MiCoP exhibited the highest accuracy when the same reference database was used.

CONCLUSION: Our survey of mycobiome-specific software revealed a very limited selection of such tools and their poor robustness due to error-prone software, along with a significant lack of comprehensive databases enabling characterization of the mycobiome. None of the implemented tools fully agreed on the mock community profiles. FunOMIC recognized most of the species, but EukDetect and MiCoP provided predictions that were closest to the correct compositions. The bacterial background did not impact these tools' performance. Video Abstract.},
}

*Software
*Gastrointestinal Microbiome/genetics
*Metagenome
Humans
*Mycobiome
*Fungi/genetics/classification/isolation & purification
*Metagenomics/methods
Computational Biology/methods
Ascomycota/genetics/classification/isolation & purification
Basidiomycota/genetics/isolation & purification/classification
Databases, Genetic

@article {pmid40055708,
year = {2025},
author = {Hall, LM and Ellis, JT and Stark, DJ},
title = {Diagnostic dilemma: application of real-time PCR assays for the detection of Dientamoeba fragilis in medical and veterinary specimens.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {94},
pmid = {40055708},
issn = {1756-3305},
mesh = {Animals ; *Real-Time Polymerase Chain Reaction/methods/veterinary ; *Dientamoeba/genetics/isolation & purification ; Cattle ; Cats ; *Dientamoebiasis/diagnosis/parasitology ; Dogs ; Humans ; Dog Diseases/diagnosis/parasitology ; DNA, Protozoan/genetics ; Cattle Diseases/diagnosis/parasitology ; Reproducibility of Results ; Cat Diseases/diagnosis/parasitology ; Cross Reactions ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: Real-time PCR (qPCR) diagnostics developed for use in human clinical settings have been implemented to identify new animal hosts of the gastrointestinal protozoan Dientamoeba fragilis. The gut microbiome varies between species; unrecognised cross-reactivity could occur when applying these assays to new animal hosts. The use of qPCR diagnostics was assessed for the identification of new animal hosts of the gastrointestinal protozoan Dientamoeba fragilis.

METHODS: Forty-nine cattle, 84 dogs, 39 cats and 254 humans were screened for D. fragilis using two qPCR assays: EasyScreen (Genetic Signatures) and a laboratory-based assay commonly used in Europe. The reliability of the identifications made by these assays were assessed using melt curve analysis of qPCR products, conventional PCR targeting the SSU rDNA sequencing and NGS amplicon sequencing of qPCR product.

RESULTS: PCR products from the D. fragilis identified in cattle had a 9 °C cooler melt curve than when detected in humans. This melt curve discrepancy, indicative of cross-reactivity with an unknown organism, was investigated further. DNA sequencing determined that Simplicimonas sp. was the genera responsible for this cross-reactivity in cattle specimens. Dientamoeba fragilis was not detected in either dogs or cats. There was a discrepancy in the number of positive samples detected using the two qPCR assays when applied to human samples. The EasyScreen assay detected 24 positive samples; the laboratory-based assay detected an additional 34 positive samples. Of the discrepant samples, 5 returned sequence data for D. fragilis, and 29 were unsupported (false) positive samples.

CONCLUSIONS: Analysis of the melt curve after the qPCR reaction is a valuable technique to help differentiate samples containing D. fragilis compared to cross-reactions with non-target organisms. The identification of new animal hosts requires further evidence from either microscopy or DNA sequencing to confirm the presence of D. fragilis. Additionally, to reduce the risk of false-positive results due to non-specific amplification, we recommend reducing the number of PCR cycles to less than 40. Based on these results, we consider the ramifications of this identified cross-reactivity to the known host species distribution of D. fragilis.},
}

Animals
*Real-Time Polymerase Chain Reaction/methods/veterinary
*Dientamoeba/genetics/isolation & purification
Cattle
Cats
*Dientamoebiasis/diagnosis/parasitology
Dogs
Humans
Dog Diseases/diagnosis/parasitology
DNA, Protozoan/genetics
Cattle Diseases/diagnosis/parasitology
Reproducibility of Results
Cat Diseases/diagnosis/parasitology
Cross Reactions
Sensitivity and Specificity

@article {pmid40054656,
year = {2025},
author = {Wu, HH and Leng, S and Eisenstat, DD and Sergi, C and Leng, R},
title = {Targeting p53 for Immune Modulation: Exploring Its Functions in Tumor Immunity and Inflammation.},
journal = {Cancer letters},
volume = {},
number = {},
pages = {217614},
doi = {10.1016/j.canlet.2025.217614},
pmid = {40054656},
issn = {1872-7980},
abstract = {p53, often referred to as the "guardian of the genome," is a critical regulator of cellular responses to stress. p53 plays a dual role in tumor suppression and immune regulation. In addition to its well-known functions of maintaining genomic stability and inducing apoptosis, p53 orchestrates a complex interaction between innate and adaptive immune responses. This involvement contributes to pathogen clearance, immune surveillance, and immunogenic cell death (ICD). This review explores the influence of p53 on immune dynamics, detailing its effects on macrophages, dendritic cells, natural killer cells (NK), T cells, and B cells. This review explains how mutations in p53 disrupt immune responses, promoting tumor immune evasion, and highlights its regulation of inflammatory cytokines and pattern recognition receptors. Furthermore, p53's role in ICD marks it as a key player in antitumor immunity, which has significant implications for cancer immunotherapy. The review also discusses the role of p53 in inflammation, autoimmune diseases, and chronic infections, revealing its dual function in promoting and suppressing inflammation through interactions with NF-κB signaling. Therapeutically, approaches that target p53, including wild-type p53 reactivation and combination therapies with immune checkpoint inhibitors, show considerable promise. Advances in high-throughput technologies, such as single-cell RNA sequencing and CRISPR screens, provide new insights into the immunological functions of p53, including its role in microbiome-immune interactions and immune senescence. This comprehensive review highlights the importance of incorporating immunological insights from p53 into innovative therapeutic strategies, addressing existing knowledge gaps, and paving the way for personalized medicine.},
}

@article {pmid40054557,
year = {2025},
author = {Zhao, C and Peng, Y and Raza, MF and Wang, W and Zhang, Y and Chen, Y and Han, R and Guo, J and Huang, S and Li, W},
title = {A gut bacterial supplement for Asian honey bee (Apis cerana) enhances host tolerance to nitenpyram: Insight from microbiota-gut-brain axis.},
journal = {Environmental research},
volume = {274},
number = {},
pages = {121306},
doi = {10.1016/j.envres.2025.121306},
pmid = {40054557},
issn = {1096-0953},
abstract = {The widespread use of neonicotinoid pesticides has severely impacted honey bees, driving population declines. Gut microbiota are increasingly recognized for their role in mitigating pesticide toxicity. This study evaluated the ability of Gilliamella sp. G0441, a core microbiome member of the Asian honey bee (Apis cerana), to confer resistance to the toxicity of a neonicotinoid nitenpyram. Newly emerged Asian honey bees were first colonized with gut microbiota in the source colony, then divided into four treatments: SS (fed sucrose solution throughout), SN (fed sucrose solution, then exposed to nitenpyram), GS (fed Gilliamella, then sucrose solution), and GN (fed Gilliamella, then exposed to nitenpyram), and their responses-mortality, food consumption, body weight, and sucrose sensitivity-were assessed. The protective effects of Gilliamella administration on the host were further validated using a microbiota-free bee model. Gilliamella supplementation significantly mitigated nitenpyram-induced appetite suppression, weight loss, impaired learning, and gut microbiota disruption. Mechanistic analyses revealed that nitenpyram disrupted brain metabolism via the intestinal MAPK pathway, reducing ascorbate and aldarate metabolism. Prophylactic Gilliamella treatment reversed these effects, restored metabolic balance, and modulated esterase E4 expression, enhancing pesticide resistance. This study underscores Gilliamella's vital role in honey bee resilience to neonicotinoids, offering insights into the microbiota-gut-brain axis (MGBA) as a pathway for enhancing pesticide tolerance and ecological health.},
}

@article {pmid40054499,
year = {2025},
author = {Luan, WW and Gu, HW and Qiu, D and Ding, X and Liu, PM and Hashimoto, K and Yang, JJ and Wang, XM},
title = {Repeated administration of esketamine ameliorates mechanical allodynia in mice with chemotherapy-induced peripheral neuropathy: A role of gut microbiota and metabolites.},
journal = {Neurochemistry international},
volume = {},
number = {},
pages = {105961},
doi = {10.1016/j.neuint.2025.105961},
pmid = {40054499},
issn = {1872-9754},
abstract = {Chemotherapy-induced peripheral neuropathy (CIPN) severely diminishes the quality of life for cancer survivors, yet effective treatments remain scarce. Esketamine, a commonly used anesthetic, has demonstrated neuroprotective effects by restoring gut microbiome dysbiosis. In this study, we investigated the impact of esketamine on nociceptive sensitivity in a mouse model of CIPN and explored the potential involvement of the gut microbiome. In mice treated with oxaliplatin, repeated esketamine doses (in contrast to a single dose) significantly improved the paw withdrawal threshold (PWT). Western blot and qPCR analyses further revealed that repeated esketamine administration markedly reduced microglial activation and neuroinflammation in the dorsal root ganglion (DRG), underscoring its potent anti-inflammatory properties. Moreover, fecal 16S rRNA analysis indicated that esketamine partially restored the abnormal gut microbiota composition (β-diversity). Plasma metabolome analysis showed that repeated esketamine treatment significantly lowered the elevated levels of 6H-indolo[2,3-b]quinoline and restored the reduced levels of (3-exo)-3-[3-methyl-5-(1-methylethyl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]octane observed in oxaliplatin-treated mice. In addition, fecal microbiota transplantation from esketamine-treated CIPN mice notably improved both the diminished PWT and DRG neuroinflammation in oxaliplatin-treated mice. Collectively, these findings suggest that repeated esketamine administration may alleviate mechanical allodynia in CIPN mice by modulating neuroinflammation, gut microbiota, and associated metabolites.},
}

@article {pmid40054447,
year = {2025},
author = {Xiao, X and Zhao, W and Song, Z and Qi, Q and Wang, B and Zhu, J and Lin, J and Wang, J and Hu, A and Huang, S and Wang, Y and Chen, J and Fang, C and Ji, Q and Zhang, N and Meng, L and Wei, X and Chen, C and Cai, S and Chen, S and Ding, K and Li, D and Liu, S and Song, T and Tian, L and Zhang, H and Zhang, Y and Xu, S and Chen, J and Chen, H and Cen, Q and Jiang, F and Hu, G and Tang, C and Guo, W and Wang, X and Zhan, L and Fan, J and Wang, J and Zhou, C and Li, L and Lv, Z and Hu, Y and Lin, X and Mai, G and Luo, L and Yang, T and Wang, W and Kristiansen, K and Chen, L and Yang, H and Ni, M and Gu, Y and Mu, F and Yang, Y and Zhou, J and Wang, J and Zhang, WJ and Han, M and Xu, X and Liu, S},
title = {Microbial ecosystems and ecological driving forces in the deepest ocean sediments.},
journal = {Cell},
volume = {188},
number = {5},
pages = {1363-1377.e9},
doi = {10.1016/j.cell.2024.12.036},
pmid = {40054447},
issn = {1097-4172},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Oceans and Seas ; *RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Phylogeny ; Bacteria/genetics/classification/metabolism ; Microbiota/genetics ; Metagenome ; Metagenomics ; },
abstract = {Systematic exploration of the hadal zone, Earth's deepest oceanic realm, has historically faced technical limitations. Here, we collected 1,648 sediment samples at 6-11 km in the Mariana Trench, Yap Trench, and Philippine Basin for the Mariana Trench Environment and Ecology Research (MEER) project. Metagenomic and 16S rRNA gene amplicon sequencing generated the 92-Tbp MEER dataset, comprising 7,564 species (89.4% unreported), indicating high taxonomic novelty. Unlike in reported environments, neutral drift played a minimal role, while homogeneous selection (HoS, 50.5%) and dispersal limitation (DL, 43.8%) emerged as dominant ecological drivers. HoS favored streamlined genomes with key functions for hadal adaptation, e.g., aromatic compound utilization (oligotrophic adaptation) and antioxidation (high-pressure adaptation). Conversely, DL promoted versatile metabolism with larger genomes. These findings indicated that environmental factors drive the high taxonomic novelty in the hadal zone, advancing our understanding of the ecological mechanisms governing microbial ecosystems in such an extreme oceanic environment.},
}

*Geologic Sediments/microbiology/chemistry
*Oceans and Seas
*RNA, Ribosomal, 16S/genetics
*Ecosystem
Phylogeny
Bacteria/genetics/classification/metabolism
Microbiota/genetics
Metagenome
Metagenomics

@article {pmid40054445,
year = {2025},
author = {Turjeman, S and Rozera, T and Elinav, E and Ianiro, G and Koren, O},
title = {From big data and experimental models to clinical trials: Iterative strategies in microbiome research.},
journal = {Cell},
volume = {188},
number = {5},
pages = {1178-1197},
doi = {10.1016/j.cell.2025.01.038},
pmid = {40054445},
issn = {1097-4172},
mesh = {*Microbiota ; Humans ; *Big Data ; Animals ; Clinical Trials as Topic ; Metagenomics/methods ; Metabolomics/methods ; },
abstract = {Microbiome research has expanded significantly in the last two decades, yet translating findings into clinical applications remains challenging. This perspective discusses the persistent issue of correlational studies in microbiome research and proposes an iterative method leveraging in silico, in vitro, ex vivo, and in vivo studies toward successful preclinical and clinical trials. The evolution of research methodologies, including the shift from small cohort studies to large-scale, multi-cohort, and even "meta-cohort" analyses, has been facilitated by advancements in sequencing technologies, providing researchers with tools to examine multiple health phenotypes within a single study. The integration of multi-omics approaches-such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics-provides a comprehensive understanding of host-microbe interactions and serves as a robust hypothesis generator for downstream in vitro and in vivo research. These hypotheses must then be rigorously tested, first with proof-of-concept experiments to clarify the causative effects of the microbiota, and then with the goal of deep mechanistic understanding. Only following these two phases can preclinical studies be conducted with the goal of translation into the clinic. We highlight the importance of combining traditional microbiological techniques with big-data approaches, underscoring the necessity of iterative experiments in diverse model systems to enhance the translational potential of microbiome research.},
}

*Microbiota
Humans
*Big Data
Animals
Clinical Trials as Topic
Metagenomics/methods
Metabolomics/methods

@article {pmid40054249,
year = {2025},
author = {Walling, LK and Gamache, MH and González-Pech, RA and Harwood, VJ and Ibrahim-Hashim, A and Jung, JH and Lewis, DB and Margres, MJ and McMinds, R and Rasheed, K and Reis, F and van Riemsdijk, I and Santiago-Alarcon, D and Sarmiento, C and Whelan, CJ and Zalamea, PC and Parkinson, JE and Richards, CL},
title = {Incorporating microbiome analyses can enhance conservation of threatened species and ecosystem functions.},
journal = {The Science of the total environment},
volume = {970},
number = {},
pages = {178826},
doi = {10.1016/j.scitotenv.2025.178826},
pmid = {40054249},
issn = {1879-1026},
abstract = {Conservation genomics is a rapidly growing subdiscipline of conservation biology that uses genome-wide information to inform management of biodiversity at all levels. Such efforts typically focus on species or systems of conservation interest, but rarely consider associated microbes. At least three major approaches have been used to study how microorganisms broadly contribute to conservation areas: (1) diversity surveys map out microbial species distribution patterns in a variety of hosts, natural environments or regions; (2) functional surveys associate microbial communities with factors of interest, such as host health, symbiotic interactions, environmental characteristics, ecosystem processes, and biological invasions; and (3) manipulative experiments examine the response of changes to microbial communities or determine the functional roles of specific microbes within hosts or communities by adding, removing, or genetically modifying microbes. In practice, multiple approaches are often applied simultaneously. The results from all three conservation genomics approaches can be used to help design practical interventions and improve management actions, some of which we highlight below. However, experimental manipulations allow for more robust causal inferences and should be the ultimate goal of future work. Here we discuss how further integration of microbial research of a host's microbiome and of free living microbes into conservation biology will be an essential advancement for conservation of charismatic organisms and ecosystem functions in light of ongoing global environmental change.},
}

@article {pmid40056781,
year = {2025},
author = {Chen, H and Li, J and Wu, Y and Li, Y and Zheng, S and Wu, Y and Xuan, R and Wu, L and Miao, J and Wang, Y and Tan, H and Zhou, J and Huang, J and Yan, X},
title = {Structural characteristics of intestinal microbiota of domestic ducks with different body sizes.},
journal = {Poultry science},
volume = {104},
number = {4},
pages = {104930},
doi = {10.1016/j.psj.2025.104930},
pmid = {40056781},
issn = {1525-3171},
abstract = {Domestic ducks are economically important agricultural animals, and their body size is a crucial economic trait. The intestinal flora plays a pivotal role in influencing body metabolism, growth, and development. Currently, no literature is available on the potential effect of the intestinal flora of domestic ducks on body size. This study used 16S rRNA sequencing technology to investigate the fecal microbiota of 229 individuals reared under identical feeding conditions. The findings revealed that partridge ducks with large body sizes (LBS) exhibited a higher level of intestinal microbial diversity than ducks with small body sizes (SBS). Notably, the gut microbiota composition of SBS displayed significantly elevated proportions of Streptococcus, Rothia, and Psychrobacter compared to their counterparts with LBS. Conversely, Lactobacillus was significantly more abundant in LBS. Jeotgalibaca and Psychrobacter were identified as key biomarkers of SBS, whereas Lactobacillus and Bacteroides were predominant biomarkers of LBS. Functional predictions based on intestinal microbiota indicated discernible differences among different body types, particularly evident in non- partridge ducks. The present study investigated the correlation between the intestinal microbiota and body size of domestic ducks, aiming to provide practical insights for the production management of domestic duck farming.},
}

@article {pmid40055466,
year = {2025},
author = {Vaaben, TH and Lützhøft, DO and Koulouktsis, A and Dawoodi, IM and Stavnsbjerg, C and Kvich, L and Gögenur, I and Vazquez-Uribe, R and Sommer, MOA},
title = {Modulating tumor immunity using advanced microbiome therapeutics producing an indole metabolite.},
journal = {EMBO reports},
volume = {},
number = {},
pages = {},
pmid = {40055466},
issn = {1469-3178},
support = {NNF20CC0035580//Novo Nordisk Fonden (NNF)/ ; NNF17CO0028232//Novo Nordisk Fonden (NNF)/ ; NNF21OC0072832//Novo Nordisk Fonden (NNF)/ ; },
abstract = {The gut microbiome has emerged as a key player in modulating immune responses against cancer, suggesting that microbial interventions can enhance treatment outcomes. Indole metabolites produced by probiotic bacteria activate the aryl hydrocarbon receptor (AhR), a transcription factor important for immune cell regulation. Cancer patients with high plasma concentrations of these metabolites have shown improved survival. Building on these findings, we have engineered Escherichia coli Nissle 1917 to produce the AhR agonist indole-3-acetic acid. Delivery of indole-3-acetic acid by tumor-colonizing bacteria changes the tumor microenvironment in a murine model, significantly increasing levels of CXCL9 and IFN-γ and elevating tumor-infiltrating T-cell abundance and activation. Treatment with our engineered strain inhibits tumor growth, improves survival in syngeneic tumor models, and leads to long-lasting immunity in a tumor rechallenge experiment. Further investigation indicates that this immune modulation is driven by the direct activation of AhR by indole-3-acetic acid, leading to differential cytokine expression and a shift in immune cell composition within the tumor. This study highlights the importance of microbial metabolites in immune modulation and supports exploring microbiome-based therapies in oncology.},
}

@article {pmid40054578,
year = {2025},
author = {Zeng, Y and Lu, X and Wang, M and Chen, R and Li, Q and Zhu, J and Su, Z and Lin, F},
title = {Endophyte Acrocalymma vagum establishes the holobiont with rice to attract beneficial microorganisms and promote disease resistance.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.03.008},
pmid = {40054578},
issn = {2090-1224},
abstract = {INTRODUCTION: Endophytic fungi are essential microorganisms in promoting plant health. However, the mechanism of endophytic fungi regulating root microbiota to enhance crop production and resistance remains unclear.

OBJECTIVES: We aimed i) to explore the microbial alteration driven by endophytic Acrocalymma vagum in developing crop yield and rice resistance; ii) to reveal the mechanism of root-released compound stimulated by A. vagum in recruiting benefit microbes.

METHODS: The microbiome was applied in a culture-dependent and culture-independent method to study the microbial communities of the A. vagum-rice holobiont using 16S rRNA and ITS gene metabarcoding. Non-target metabolome identified distinct metabolites responsible for community variations. Label-free proteomic analyses investigated the association between primary genes related to the holobiont formation. CRISPR/Cas9 technique and homologous recombination replacement were used to characterize the functions of putative genes.

RESULTS: A. vagum enhanced cultivated rice yield by 5.73 ± 1.76 % and induced 83.24 ± 9.86 % control efficiency against rice blast. We discovered that A. vagum simplified rice microbial structure based on co-occurrence networks, by lowering the proportion of potentially pathogenic predominant Burkholderia and driving rice to recruit beneficial Lactobacillus, Sarocladium and Nigrospora to promote rice growth with the increases of 44.41 ± 5.10 % shoot height and 70.21 ± 9.57 % shoot biomass. Moreover, the holobiont released coumaric and trans-ferulic acids to attract beneficial microbes. 206 rice proteins were notably up-regulated in the holobiont, particularly the OsPrxs. CRISPR/Cas9-edited mutants of OsPRX70 and OsPRX95 reduced the promotion effect of A. vagum on rice growth. Furthermore, the pathways of 39 overexpressed proteins in A. vagum were enriched in invading the host and inducing resistance. The knockouts of AvGH3, AvGH7, AvMFS1, and AvCBA transformed A. vagum role from endophyte to pathogen.

CONCLUSIONS: The A. vagum-rice holobiont releases recruitment signals and improves the rice community structure. We provide ecological and molecular evidence to confirm the mutualism of endophyte-plant-promoting growth and disease resistance.},
}

@article {pmid40054511,
year = {2025},
author = {Yang, S and He, Y and Ma, Y and Wang, R and Wu, Y and Wu, W},
title = {Associations between the oral microbiome, number of teeth and frailty among American adults: A cross-sectional study from NHANES 2009-2012.},
journal = {Experimental gerontology},
volume = {},
number = {},
pages = {112727},
doi = {10.1016/j.exger.2025.112727},
pmid = {40054511},
issn = {1873-6815},
abstract = {BACKGROUND: The intricate interrelationship between oral health, the number of teeth, oral microbiota, and frailty remains largely unexplored in clinical research. This study aimed to investigate the interrelationship between oral microbiome, the number of teeth, and frailty.

METHODS: Data from 4518 participants in NHANES 2009-2012 were analyzed. Frailty was measured using the 48-item Frailty Index (FI), oral microbiota diversity through 16S rRNA sequencing, and tooth retention via clinical examination. Multivariable logistic regression and restricted cubic spline (RCS) evaluated associations between alpha diversity and frailty. Mediation analysis assessed tooth retention's role. Mortality associations were analyzed using Kaplan-Meier survival curves and Cox regression. Beta diversity was examined with PCoA and PERMANOVA.

RESULTS: The prevalence of frailty was 39.73 %. Univariate analysis showed that alpha diversity indices except for the Simpson index were significantly lower in frailty, and after adjusted for confounders, observed ASVs (adjusted OR: 0.80 [0.73, 0.87], p < 0.001), Faith's PD (adjusted OR: 0.81 [0.74, 0.88], p < 0.001) and Shannon-Weiner index (adjusted OR: 0.88 [0.81, 0.95], p = 0.002) were remained significantly associated with frailty. The reduced number of teeth partially mediated the relationship (for Faith's PD: βindirect = -0.001 [-0.003, 0.000], p = 0.036, proportion: 8.33 % [0.00 %, 37.50 %]; for Shannon-Weiner index, βindirect = -0.007 [-0.013, -0.002], p = 0.007, Proportion = 17.07 % [3.39 %, 65.00 %]). Univariable Cox proportional hazard regression showed that all alpha diversity indices were significantly associated with all-cause mortality in frail population, and in multivariable analysis, Shannon-Weiner index (HR: 0.72 [0.55, 0.94], p = 0.017) and Simpson index (HR: 0.71 [0.60, 0.83], p < 0.001) remained statistically significant. PCoA showed that beta diversity was also significantly associated with frailty.

CONCLUSION: Lower oral microbiome diversity is associated with higher frailty and reduced survival. Tooth retention partially mediates this link, emphasizing the importance of oral health in mitigating frailty and promoting healthy aging.},
}

@article {pmid40054458,
year = {2025},
author = {O'Riordan, KJ and Moloney, GM and Keane, L and Clarke, G and Cryan, JF},
title = {The gut microbiota-immune-brain axis: Therapeutic implications.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {101982},
doi = {10.1016/j.xcrm.2025.101982},
pmid = {40054458},
issn = {2666-3791},
abstract = {The microbiota-gut-brain axis has major implications for human health including gastrointestinal physiology, brain function, and behavior. The immune system represents a key pathway of communication along this axis with the microbiome implicated in neuroinflammation in health and disease. In this review, we discuss the mechanisms as to how the gut microbiota interacts with the brain, focusing on innate and adaptive immunity that are often disrupted in gut-brain axis disorders. We also consider the implications of these observations and how they can be advanced by interdisciplinary research. Leveraging an increased understanding of how these interactions regulate immunity has the potential to usher in a new era of precision neuropsychiatric clinical interventions for psychiatric, neurodevelopmental, and neurological disorders.},
}

@article {pmid40054278,
year = {2025},
author = {Wang, YC and Wang, S and Lv, YH and Wang, JY and Yang, WX and Deng, Y and Ju, F and Wang, C},
title = {Diversity, influential factor, and communication network construction of quorum sensing bacteria in global wastewater treatment plants.},
journal = {Water research},
volume = {279},
number = {},
pages = {123437},
doi = {10.1016/j.watres.2025.123437},
pmid = {40054278},
issn = {1879-2448},
abstract = {Quorum sensing (QS) is widespread in the microbial world and mediates microbial relationships in communities. However, the existing knowledge is far from a full description of the complex communication-based microbial interactions in engineered ecosystems, i.e., wastewater treatment plants (WWTPs). Herein, we conducted a systematic analysis of the diversity and influential factors of the QS-related microflora through the collection of global 1186 activated sludge microbiome samples. We found that the richness of bacteria associated with the universal bacterial secondary messenger presented the highest in QS system, whereas the bacteria related to the degradation of N-Acyl-homoserine lactones occupied the main position in the quorum quenching system. The community turnover of QS microflora was found more likely to be dominated by the deterministic process, such as the dissolved oxygen and resource availability (the ratio of organic matter to microorganisms). Meanwhile, these QS microflora in turn have a profound impact on the functions of WWTPs, especially multilingual intelligencers involving various language systems, such as Nitrospira. By connecting the signal molecule synthesis and acceptance bacteria, we constructed a QS communication network, which can be a robust tool for initial investigation of signaling molecule-mediated microbial interactions. The above results were further integrated into an online access website, named Quorum Sensing Communication Network in Activated Sludge (QSCNAS) (https://www.qscnas.cn/), which allowed users to browse and capture possible QS-based interactions of target bacterium. This work contributes to the understanding of bacterial communication in WWTPs and provides a platform to help in developing potential regulation strategies.},
}

@article {pmid40054134,
year = {2025},
author = {Jiang, T and Ren, J and Li, D and Luo, Y and Huang, Y and Gao, T and Yang, J and Yu, J and Liu, L and Yuan, H},
title = {Pseudomonas syringae exacerbates apple replant disease caused by Fusarium.},
journal = {Microbiological research},
volume = {296},
number = {},
pages = {128124},
doi = {10.1016/j.micres.2025.128124},
pmid = {40054134},
issn = {1618-0623},
abstract = {Apple replant disease (ARD) causes significant economic losses globally, including in China. Analyzing the causes of this replant disease from the perspective of rhizosphere microecology is therefore essential. In this study, we examined rhizosphere soils from apple trees subjected to continuous cropping. The mechanisms underlying ARD were elucidated through high-throughput sequencing of the soil microbiome, co-occurrence network analysis using NetShift, and correlation analyses. Core bacterial microbes were isolated, and their roles in altering the microecological environment were verified through reinoculation experiments. The results indicated that the disease indices for apple seedlings cultivated increased in continuously cropped soils. Bacterial diversity decreased in continuously cropped apple orchards for 10 years (R10) and 15 years (R15), but the relative abundance of Pseudomonas increased. In contrast, fungal diversity increased, with the relative abundance of Fusarium also increasing. As a dominant genus, Pseudomonas exhibited significant network variation after 10 years of consecutive cultivation, suggesting that this microorganism may play a key role in the occurrence of ARD. Moreover, the correlation analysis revealed, for the first time, that Pseudomonas is negatively correlated with bacterial diversity but positively correlated with the relative abundance of Fusarium, indicating a close relationship between Pseudomonas and Fusarium in continuously cropped soil. Four key Pseudomonas amplicon sequence variants (ASVs) strains were isolated from the continuously cropped rhizosphere soil of apple trees, and reinoculation experiments verified that introducing Pseudomonas exacerbated the occurrence of replant diseases in both strawberry and apple, with significantly higher disease indices compared to single Fusarium inoculation. The findings of this study provide new and timely insights into the mechanism underlying the occurrence of ARD.},
}

@article {pmid40053783,
year = {2025},
author = {Ram, S and Corbin, M and 't Mannetje, A and Eng, A and Kvalsvig, A and Baker, MG and Douwes, J},
title = {Antibiotic Use In Utero and Early Life and Risk of Chronic Childhood Conditions in New Zealand: Protocol for a Data Linkage Retrospective Cohort Study.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e66184},
doi = {10.2196/66184},
pmid = {40053783},
issn = {1929-0748},
mesh = {Humans ; Female ; Retrospective Studies ; *Anti-Bacterial Agents/adverse effects/therapeutic use ; Pregnancy ; *Prenatal Exposure Delayed Effects/epidemiology ; New Zealand/epidemiology ; Child, Preschool ; *Diabetes Mellitus, Type 1/drug therapy/epidemiology ; Infant ; Cohort Studies ; Chronic Disease/epidemiology ; Male ; Inflammatory Bowel Diseases/drug therapy/epidemiology ; Child ; Information Storage and Retrieval ; Attention Deficit Disorder with Hyperactivity/drug therapy/epidemiology ; Infant, Newborn ; },
abstract = {BACKGROUND: The incidence of many common chronic childhood conditions has increased globally in the past few decades, which has been suggested to be potentially attributed to antibiotic overuse leading to dysbiosis in the gut microbiome.

OBJECTIVE: This linkage study will assess the role of antibiotic use in utero and in early life in the development of type 1 diabetes (T1D), attention-deficit/hyperactive disorder (ADHD), and inflammatory bowel disease.

METHODS: The study design involves several retrospective cohort studies using linked administrative health and social data from Statistics New Zealand's Integrated Data Infrastructure. It uses data from all children who were born in New Zealand between October 2005 and December 2010 (N=334,204) and their mothers. Children's antibiotic use is identified for 4 time periods (at pregnancy, at ≤1 year, at ≤2 years, and at ≤5 years), and the development of T1D, ADHD, and inflammatory bowel disease is measured from the end of the antibiotic use periods until death, emigration, or the end of the follow-up period (2021), whichever came first. Children who emigrated or died before the end of the antibiotic use period are excluded. Cox proportional hazards regression models are used while adjusting for a range of potential confounders.

RESULTS: As of September 2024, data linkage has been completed, involving the integration of antibiotic exposure and outcome variables for 315,789 children. Preliminary analyses show that both prenatal and early life antibiotic consumption is associated with T1D. Full analyses for all 3 outcomes will be completed by the end of 2025.

CONCLUSIONS: This series of linked cohort studies using detailed, complete, and systematically collected antibiotic prescription data will provide critical new knowledge regarding the role of antibiotics in the development of common chronic childhood conditions. Thus, this study has the potential to contribute to the development of primary prevention strategies through, for example, targeted changes in antibiotic use.

DERR1-10.2196/66184.},
}

Humans
Female
Retrospective Studies
*Anti-Bacterial Agents/adverse effects/therapeutic use
Pregnancy
*Prenatal Exposure Delayed Effects/epidemiology
New Zealand/epidemiology
Child, Preschool
*Diabetes Mellitus, Type 1/drug therapy/epidemiology
Infant
Cohort Studies
Chronic Disease/epidemiology
Male
Inflammatory Bowel Diseases/drug therapy/epidemiology
Child
Information Storage and Retrieval
Attention Deficit Disorder with Hyperactivity/drug therapy/epidemiology
Infant, Newborn

@article {pmid40053776,
year = {2025},
author = {Abu El Kheir-Mataria, W and Mahmoud Abdelraheem, O and Chun, S},
title = {Genetic, Socioecological, and Health Determinants of Extreme Longevity in Semi-Supercentenarians and Supercentenarians: Protocol for a Scoping Review.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e63900},
doi = {10.2196/63900},
pmid = {40053776},
issn = {1929-0748},
mesh = {Humans ; *Longevity/genetics ; Aged, 80 and over ; Quality of Life ; Female ; Male ; },
abstract = {BACKGROUND: The study of supercentenarians (individuals aged 110 years or older) offers valuable insights into aging, longevity, and the factors contributing to exceptional lifespans. These individuals often exhibit extraordinary cognitive and physical performance, which can inform strategies to improve the health of the general population. Research on centenarians (individuals aged 100 years or older), semi-supercentenarians (individuals aged 105-109 years), and supercentenarians covers themes like genetic factors, microbiome, inflammation, diet, lifestyle, and psychological aspects. These studies often focus on various aspects of extreme longevity, using varied objectives and methodologies, highlighting the need for a comprehensive synthesis to map the breadth of research and identify gaps in understanding this demographic.

OBJECTIVE: This scoping review aims to map and synthesize existing evidence on the determinants of extreme longevity, focusing on individuals living beyond 105 years. This review seeks to categorize genetic factors associated with semi-supercentenarians and supercentenarians; explore the range of socioecological factors contributing to their longevity; and identify common themes such as health, functional capacity, cognition, mental health, behaviors, social support, quality of life, personality traits, environmental factors, and religiosity. Additionally, it aims to examine and describe the methodologies and assessment tools used in studies on extreme longevity and provide an overview of global demographic trends and patterns among supercentenarians, including geographic distribution, gender prevalence, and socioeconomic characteristics.

METHODS: This scoping review follows the PRISMA-P (Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols) 2015 guidelines and the Population, Exposure, and Outcome framework. It includes observational and interventional, quantitative and qualitative studies on supercentenarians and semi-supercentenarians. Data will be sourced from databases like Scopus, PubMed, ProQuest, PsycINFO, and The Cochrane Library. The selection process involves abstract and full-text screening by two independent reviewers, with data extraction focusing on study characteristics, participant demographics, interventions or exposures, and key findings. A thematic analysis will identify patterns across various themes.

RESULTS: As of October 2, 2024, five databases were searched, yielding 844 studies. After removing duplicates, 706 studies remained. Following the first and second screening stages, 135 studies were found to be eligible. The study is expected to be completed by the end of February 2025.

CONCLUSIONS: By synthesizing evidence, this study will understand the global scope of supercentenarians, describe the main themes of research interest, and identify gaps. The findings are expected to contribute significantly to the body of knowledge on longevity, informing future research and public health policies. This scoping review aims to enhance the understanding of factors promoting healthy aging and extreme longevity, benefiting broader public health initiatives.

TRIAL REGISTRATION: PROSPERO CRD42024512298; https://tinyurl.com/4cmux7h4.},
}

Humans
*Longevity/genetics
Aged, 80 and over
Quality of Life
Female
Male

@article {pmid40053318,
year = {2025},
author = {Nihalani, R and Zola, J and Aluru, S},
title = {Disambiguating a Soft Metagenomic Clustering.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/cmb.2024.0825},
pmid = {40053318},
issn = {1557-8666},
abstract = {Clustering is a popular technique used for analyzing amplicon sequencing data in metagenomics. Specifically, it is used to assign sequences (reads) to clusters, each cluster representing a species or a higher level taxonomic unit. Reads from multiple species often sharing subsequences, combined with lack of a perfect similarity measure, make it difficult to correctly assign reads to clusters. Thus, metagenomic clustering methods must either resort to ambiguity, or make the best available choice at each read assignment stage, which could lead to incorrect clusters and potentially cascading errors. In this article, we argue for first generating an ambiguous clustering and then resolving the ambiguities collectively by analyzing the ambiguous clusters. We propose a rigorous formulation of this problem and show that it is NP-Hard. We then propose an efficient heuristic to solve it in practice. We validate our approach on several synthetically generated datasets and two datasets consisting of 16S rDNA sequences from the microbiome of rat guts.},
}

@article {pmid40053288,
year = {2025},
author = {Melese, K and Alemu, T and Desalegn, A},
title = {Probiotic effects of Lactobacillus reuteri and Pediococcus pentosaceus on growth performance, blood biochemistry, and antibody response in broiler chickens.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {40053288},
issn = {1678-4405},
support = {1/CX/CSRD VA/United States ; 2//Addis Ababa University/ ; },
abstract = {The gut microbiome, consisting of a diverse community of beneficial bacteria, supports broiler health and performance. This study aimed to assess the impact of probiotic lactic acid bacteria supplementation on growth performance, blood parameters, and antibody response in broiler chickens. The experiment involved 108 Cobb 500 breed chicks, which were allocated into three groups: T1 (received basal diets + L. reuteri at 1 × 10[8] CFU/mL), T2 (received basal diets + P. pentosaceus at 1 × 10[8] CFU/mL), and T3 (control group receiving only basal diets). The chicks were assigned to these groups randomly, following a completely randomized design. The results showed that the broiler groups supplemented with either L. reuteri or P. pentosaceus probiotics exhibited significant improvements (p < 0.05) in body weight, weight gain, and feed conversion ratio throughout the study. There were no significant differences (p > 0.05) in total protein and albumin levels. At the same time, cholesterol levels were lower in the L. reuteri and P. pentosaceus-treated groups compared to the control group. Furthermore, the hemagglutination inhibition titer of Newcastle disease was significantly (p < 0.05) higher in the groups supplemented with L. reuteri and P. pentosaceus. The study also found that the lymphoid organ weight/body weight ratio was significantly higher in the L. reuteri and P. pentosaceus groups. In conclusion, the oral administration of the probiotic strains L. reuteri DSM 20016T and P. pentosaceus DSM 20206 to broiler chickens improved growth performance, reduced blood cholesterol levels, and enhanced immune function. These findings indicate that these lactic acid bacteria could be beneficial as both immunomodulators and growth promoters in broiler production.},
}

@article {pmid40053245,
year = {2025},
author = {Lukic, I and Ivkovic, S and Glavonic, E and Adzic, M and Mitic, M},
title = {Long-lasting Depressive Behavior of Adolescent Chronically Stressed Mice is Mediated by Gut Microbiota Dysbiosis.},
journal = {Molecular neurobiology},
volume = {},
number = {},
pages = {},
pmid = {40053245},
issn = {1559-1182},
abstract = {Depression is one of the most common mental disorders worldwide, and its prevalence sharply rises during adolescence. Adolescence is a particularly sensitive period to the effects of environmental stressors, which can cause persistent depressive behavior extending into adulthood. However, the studies assessing if changes in gut microbiota could be one of the mediators of long-term effects of adolescent stress are scarce. In the present study, we examined enduring effects of adolescent chronic unpredictable stress (CUS) on mice behavior along with alterations in their gut microbiome, by using 16 s rRNA gene sequencing and fecal microbiota transplantation (FMT). CUS mice, as well as naïve mice receiving FMT from stressed animals, showed long-lasting anxiety and depressive-like behavior extending into adulthood. The microbiota dysbiosis in adolescence was characterized by higher abundance of Alloprevotella and lower abundance of Paraprevotella, Parasutterella, Parabacteroides, and undefined genus Rikenellaceae_RC9_gut_group. On the contrary, microbiota dysbiosis in adulthood was characterized by higher abundance of Bacteroides, Enterorhabdus, Marvinbriantia, and Parabacteroides and lower abundance of Akkermansia, Odoribacter, and Rikenella. In particular, depressive-like behavior in adolescence was negatively correlated with Paraprevotella, while depressive-like behavior in adulthood was negatively correlated with Rikenella abundance, in both CUS and FMT mice. Therefore, the transfer of microbiota from mice stressed in adolescence is able to induce long-lasting depressive-like behavior in naïve mice, clearly showing the importance of gut microbiota dysbiosis in adolescence in shaping enduring depressive behavior. Moreover, our results indicate that changes in specific but different bacteria are related to depressive behavior in adolescence and in adulthood.},
}

@article {pmid40052570,
year = {2025},
author = {Shen, M and Gao, S and Zhu, R and Wang, W and Gao, W and Tao, L and Chen, W and Zhu, X and Yang, Y and Xu, T and Zhao, T and Jiao, N and Zhi, M and Zhu, L},
title = {Multimodal Metagenomic Analysis Reveals Microbial InDels as Superior Biomarkers for Pediatric Crohn's Disease.},
journal = {Journal of Crohn's & colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjaf039},
pmid = {40052570},
issn = {1876-4479},
abstract = {BACKGROUND AND AIMS: The gut microbiome is closely associated with pediatric Crohn's disease (CD), while the multidimensional microbial signature and their capabilities for distinguishing pediatric CD are underexplored. This study aims to characterize the microbial alterations in pediatric CD and develop a robust classification model.

METHODS: A total of 1,175 fecal metagenomic sequencing samples, predominantly from three cohorts of pediatric CD patients, were re-analyzed from raw sequencing data using uniform process pipelines to obtain multidimensional microbial alterations in pediatric CD, including taxonomic profiles, functional profiles, and multi-type genetic variants. Random forest algorithms were used to construct classification models after comparing multiple machine learning algorithms.

RESULTS: We found pediatric CD samples exhibited reduced microbial diversity and unique microbial characteristics. Pronounced abundance differences in 45 species and 1,357 KO genes. Particularly, Enterocloster bolteae emerged as a pivotal pediatric CD-associated species. Additionally, we identified a vast amount of microbial genetic variants linked to pediatric CD, including 192 structural variants, 1,256 insertions/deletions (InDels), and 3,567 single nucleotide variants, with a considerable portion of these variants occurred in non-genic regions. The InDel-based model outperformed other predictive models against multidimensional microbial signatures, achieving an AUC of 0.982. The robustness and disease specificity were further confirmed in an independent CD cohort (AUC=0.996) and five other microbiome-associated pediatric cohorts.

CONCLUSIONS: Our study provided a comprehensive landscape of microbial alterations in pediatric CD and introduced a highly effective diagnostic model rooted in microbial InDels, which contributes to the development of the non-invasive diagnostic tools and targeted therapies.},
}

@article {pmid40052450,
year = {2025},
author = {Qian, Z and Chen, S and Liao, X and Xie, J and Xu, Y and Zhong, H and Ou, L and Zuo, X and Xu, X and Peng, J and Wu, J and Cai, S},
title = {Decreased intestinal abundance of Akkermansia muciniphila is associated with metabolic disorders among people living with HIV.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2474730},
doi = {10.1080/07853890.2025.2474730},
pmid = {40052450},
issn = {1365-2060},
mesh = {Humans ; Male ; *HIV Infections/complications/microbiology ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; *Akkermansia ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism ; Prospective Studies ; Feces/microbiology ; Metagenomics/methods ; Hyperlipidemias/microbiology ; Metabolic Diseases/microbiology/epidemiology ; Verrucomicrobia/isolation & purification ; Overweight/microbiology/complications ; },
abstract = {BACKGROUND: Previous studies have shown changes in gut microbiota after human immunodeficiency virus (HIV) infection, but there is limited research linking the gut microbiota of people living with HIV (PLWHIV) to metabolic diseases.

METHODS: A total of 103 PLWHIV were followed for 48 weeks of anti-retroviral therapy (ART), with demographic and clinical data collected. Gut microbiome analysis was conducted using metagenomic sequencing of fecal samples from 12 individuals. Nonalcoholic fatty liver disease (NAFLD) was diagnosed based on controlled attenuation parameter (CAP) values of 238 dB/m from liver fibro-scans. Participants were divided based on the presence of metabolic disorders, including NAFLD, overweight, and hyperlipidemia. Akkermansia abundance in stool samples was measured using RT-qPCR, and Pearson correlation and logistic regression were applied for analysis.

RESULTS: Metagenomic sequencing revealed a significant decline in gut Akkermansia abundance in PLWHIV with NAFLD. STAMP analysis of public datasets confirmed this decline after HIV infection, while KEGG pathway analysis identified enrichment of metabolism-related genes. A prospective cohort study with 103 PLWHIV followed for 48 weeks validated these findings. Akkermansia abundance was significantly lower in participants with NAFLD, overweight, and hyperlipidemia at baseline, and it emerged as an independent predictor of NAFLD and overweight. Negative correlations were observed between Akkermansia abundance and both CAP values and body mass index (BMI) at baseline and at week 48. At the 48-week follow-up, Akkermansia remained a predictive marker for NAFLD.

CONCLUSIONS: Akkermansia abundance was reduced in PLWHIV with metabolic disorders and served as a predictive biomarker for NAFLD progression over 48 weeks of ART.},
}

Humans
Male
*HIV Infections/complications/microbiology
Female
*Gastrointestinal Microbiome
Middle Aged
Adult
*Akkermansia
*Non-alcoholic Fatty Liver Disease/microbiology/metabolism
Prospective Studies
Feces/microbiology
Metagenomics/methods
Hyperlipidemias/microbiology
Metabolic Diseases/microbiology/epidemiology
Verrucomicrobia/isolation & purification
Overweight/microbiology/complications

@article {pmid40051875,
year = {2025},
author = {De Troyer, L and Audenaert, K and Ommeslag, S and Debode, J and De Gelder, L and De Zutter, N},
title = {The biocontrol agent Streptomyces rimosus subsp. rimosus tempers shifts in the wheat spicosphere microbiome induced by Fusarium Head Blight.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1540242},
pmid = {40051875},
issn = {1664-462X},
abstract = {INTRODUCTION: Fusarium Head Blight (FHB) is a major fungal disease in wheat caused by Fusarium graminearum, inducing severe yield losses. Biological control agents (BCAs) can be an effective and sustainable approach to mitigate this phytopathogen. In this study, Streptomyces rimosus subsp. rimosus LMG19352 was used as a BCA to mitigate F. graminearum on wheat ears. Moreover, we aimed to assess the impact of BCA inoculation on non-target microorganisms present on the wheat spikes. Therefore, we evaluated shifts in the fungal and bacterial spicosphere microbiome (i) over time from flowering to mid-grain filling stage and (ii) across inoculations with F. graminearum and/or S. rimosus subsp. rimosus LMG19352.

METHODS: FHB symptoms were determined by multispectral imaging, and Illumina MiSeq was used to amplify 16S V3-V4 rDNA for bacteria and ITS2 for fungi, whereafter a correlation network analysis was performed.

RESULTS: The biocontrol potential of S. rimosus subsp. rimosus LMG19352 against F. graminearum was confirmed, as FHB symptoms were significantly reduced. Based on the microbial abundances, S. rimosus subsp. rimosus LMG19352 compensated for shifts in the spicosphere microbiome community induced by FHB. These results were supported by a network analysis, revealing a more complex and stable microbiome in the presence of the BCA compared to the infected control.

DISCUSSION: To our knowledge, this study is the first to reveal the potential of a bacterial BCA to temper shifts in the wheat microbiome caused by a phytopathogen, and thereby acting as a promising BCA.},
}

@article {pmid40051835,
year = {2025},
author = {Zhou, J and Sun, Z and Wang, X and Wang, S and Jiang, W and Tang, D and Xia, T and Xiao, F},
title = {Low-temperature cold plasma promotes wound healing by inhibiting skin inflammation and improving skin microbiome.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1511259},
pmid = {40051835},
issn = {2296-4185},
abstract = {Wound healing includes four consecutive and overlapping stages of hemostasis, inflammation, proliferation, and remodeling. Factors such as aging, infection, and chronic diseases can lead to chronic wounds and delayed healing. Low-temperature cold plasma (LTCP) is an emerging physical therapy for wound healing, characterized by its safety, environmental friendliness, and ease of operation. This study utilized a self-developed LTCP device to investigate its biological effects and mechanisms on wound healing in adult and elderly mice. Histopathological studies found that LTCP significantly accelerated the healing rate of skin wounds in mice, with particularly pronounced effects in elderly mice. LTCP can markedly inhibit the expression of pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) and senescence-associated secretory phenotype factors (MMP-3, MMP-9), while significantly increasing the expression of tissue repair-related factors, such as VEGF, bFGF, TGF-β, COL-I, and α-SMA. It also regulated the expression of genes related to cell proliferation and migration (Aqp5, Spint1), inflammation response (Nlrp3, Icam1), and angiogenesis (Ptx3, Thbs1), promoting cell proliferation and inhibit apoptosis. Furthermore, LTCP treatment reduced the relative abundance of harmful bacteria such as Delftia, Stenotrophomonas, Enterococcus, and Enterobacter in skin wounds, while increasing the relative abundance of beneficial bacteria such as Muribaculaceae, Acinetobacter, Lachnospiraceae NK4A136_group, and un_f__Lachnospiraceae, thereby improving the microbial community structure of skin wounds. These research findings are of significant implications for understanding the mechanism of skin wound healing, as well as for the treatment and clinical applications of skin wounds, especially aging skin.},
}

@article {pmid40051690,
year = {2025},
author = {Waller, ME and Gutierrez, A and Ticer, TD and Glover, JS and Baatz, JE and Wagner, CL and Engevik, MA and Chetta, KE},
title = {Profiling the response of individual gut microbes to free fatty acids (FFAs) found in human milk.},
journal = {Journal of functional foods},
volume = {125},
number = {},
pages = {},
pmid = {40051690},
issn = {1756-4646},
abstract = {Preterm infants have an immature intestinal environment featuring microbial dysbiosis. Human milk can improve the composition of the neonatal gut microbiome by supporting commensal species. Milk free fatty acids (FFAs) provide nutritional energy, participate in endogenous signaling, and exert antimicrobial effects. This study examined the growth of individual commensal and pathobiont microbes in response to unesterified unsaturated FFAs found in milk: oleic, linoleic, arachidonic, and docosahexaenoic acid. Select species of commensal and pathobiont genera (Bifidobacterium, Lactobacillus, Streptococcus, Staphylococcus, Enterococcus, Acinetobacter, Pseudomonas, Escherichia, and Klebsiella) were cultured with FFAs. The growth of all commensals, except for L. johnsonii, was significantly inhibited by the highest concentration (1 %) of all FFAs. L. johnsonii was only inhibited by arachidonic acid. In contrast, suppression of pathobionts in response to FFAs was less pronounced. Higher concentrations (0.1 %, 1 %) of docosahexaenoic acid significantly inhibited the growth of five of eight pathobionts. Meanwhile, for oleic, linoleic, and arachidonic acid, only two of eight pathobionts were significantly affected. Intriguingly, the effects for these FFAs were highly complex. For example, S. agalactiae growth was enhanced with 1 % oleic acid but suppressed at 0.01 %; however, the effects were directionally opposite for linoleic acid, i.e., suppressed at 1 % but enhanced at 0.01 %. Our genome analyses suggest that pathobiont survival may be related to the number of gene copies for fatty acid transporters. Overall, the effect of FFAs was dose-dependent and species-specific, where commensal growth was broadly inhibited while pathobionts were either unaffected or exhibited complex, bi-directional responses.},
}

@article {pmid40051624,
year = {2025},
author = {De Martinis, ECP and Alves, VF and Pereira, MG and Andrade, LN and Abichabki, N and Abramova, A and Dannborg, M and Bengtsson-Palme, J},
title = {Applying 3D cultures and high-throughput technologies to study host-pathogen interactions.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1488699},
pmid = {40051624},
issn = {1664-3224},
mesh = {Humans ; *Host-Pathogen Interactions ; *Cell Culture Techniques, Three Dimensional/methods ; Animals ; High-Throughput Screening Assays/methods ; Microbiota ; High-Throughput Nucleotide Sequencing ; },
abstract = {Recent advances in cell culturing and DNA sequencing have dramatically altered the field of human microbiome research. Three-dimensional (3D) cell culture is an important tool in cell biology, in cancer research, and for studying host-microbe interactions, as it mimics the in vivo characteristics of the host environment in an in vitro system, providing reliable and reproducible models. This work provides an overview of the main 3D culture techniques applied to study interactions between host cells and pathogenic microorganisms, how these systems can be integrated with high-throughput molecular methods, and how multi-species model systems may pave the way forward to pinpoint interactions among host, beneficial microbes and pathogens.},
}

Humans
*Host-Pathogen Interactions
*Cell Culture Techniques, Three Dimensional/methods
Animals
High-Throughput Screening Assays/methods
Microbiota
High-Throughput Nucleotide Sequencing

@article {pmid40051478,
year = {2025},
author = {Park, H and Yeo, S and Lee, T and Han, Y and Ryu, CB and Huh, CS},
title = {Culture-based characterization of gut microbiota in inflammatory bowel disease.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1538620},
pmid = {40051478},
issn = {1664-302X},
abstract = {Inflammatory bowel disease (IBD) is characterized by disruptions in the gut microbiome. While most studies on gut dysbiosis in IBD rely on sequencing-based methods, we employed a streamlined culturomics approach to obtain a more comprehensive understanding of gut microbiota imbalance in patients with IBD that may not be captured by sequencing alone. A total of 367 bacteria were identified at the species level, including 211 species from ulcerative colitis patients, 164 species from Crohn's disease (CD) patients, and 263 species from healthy individuals. Consistent with our 16S rRNA gene amplicon sequencing results, a significant decrease in microbial diversity and a severe imbalance, especially in CD patients, were also observed in the culture-based analysis. Our culturomics approach provided additional insights, highlighting dysbiosis in unique anaerobic and Gram-negative species in CD patients. Moreover, species-level findings for Bifidobacterium and Enterobacterales emphasized specific species expansions in IBD patients. Notably, Mediterraneibacter gnavus, Thomasclavelia ramosa, Parabacteroides merdae, and Collinsella aerofaciens are of particular clinical interest due to their correlation with inflammatory biomarkers. This comprehensive analysis underscores the value of integrating a culture-based approach with a genome-based approach to provide complementary insights and therapeutic targets in IBD.},
}

@article {pmid40051134,
year = {2025},
author = {Bi, O and Caballero-Lima, D and Sikkink, S and Westgate, G and Kauser, S and Elies, J and Thornton, MJ},
title = {Do Melanocytes Have a Role in Controlling Epidermal Bacterial Colonisation and the Skin Microbiome?.},
journal = {Experimental dermatology},
volume = {34},
number = {3},
pages = {e70071},
doi = {10.1111/exd.70071},
pmid = {40051134},
issn = {1600-0625},
support = {//Innovate UK/ ; },
mesh = {Humans ; *Melanocytes ; *Microbiota ; *Staphylococcus epidermidis ; *Keratinocytes/microbiology/immunology ; Corynebacterium ; Epidermis/microbiology/immunology ; Fibroblasts/microbiology ; Melanins/metabolism ; Propionibacteriaceae ; Skin/microbiology/immunology ; alpha-MSH/metabolism ; Cells, Cultured ; Immunity, Innate ; },
abstract = {In addition to producing melanin to protect epidermal keratinocytes against DNA damage, melanocytes may have important roles in strengthening innate immunity against pathogens. We have developed a functional, pigmented, human full-thickness 3D skin equivalent to determine whether the presence of melanocytes impacts epidermal bacterial growth and regulates the expression of genes involved in the immune response. We introduced primary epidermal melanocytes to construct a 3-cell full-thickness skin equivalent with primary dermal fibroblasts and epidermal keratinocytes. Immunohistochemistry verified the appropriate ratio and spatial organisation of melanocytes. Alpha-MSH induced melanogenesis, confirming an appropriate physiological response. We compared this 3-cell skin equivalent with the 2-cell version without melanocytes in response to inoculation with 3 species of bacteria: Staphylococcus epidermidis, Corynebacterium striatum, and Cutibacterium acnes. There was a significant decrease in the colonisation of bacteria in the skin equivalents containing functional melanocytes. There was increased expression of immune-response genes (S100A9, DEFB4A, IL-4R) following microorganism exposure; however, there were marked differences between the unpigmented and pigmented skin equivalents. This physiologically relevant human 3D-skin equivalent opens up new avenues for studying complex skin pigmentation disorders, melanoma, and UV damage, as well as the rapidly evolving field of the skin microbiome and the balance between commensal and pathogenic species.},
}

Humans
*Melanocytes
*Microbiota
*Staphylococcus epidermidis
*Keratinocytes/microbiology/immunology
Corynebacterium
Epidermis/microbiology/immunology
Fibroblasts/microbiology
Melanins/metabolism
Propionibacteriaceae
Skin/microbiology/immunology
alpha-MSH/metabolism
Cells, Cultured
Immunity, Innate

@article {pmid40051043,
year = {2025},
author = {Cresci, GAM},
title = {Understanding how foods and enteral feedings influence the gut microbiome.},
journal = {Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/ncp.11285},
pmid = {40051043},
issn = {1941-2452},
support = {//This study funding was provided by a research grant from Nestlé Health Science./ ; },
abstract = {The gut microbiome supports both gut and overall health. Diet is known to be one of the driving factors that influences the gut microbiome. The foods we eat, the dietary and nondietary components they contain, various food consumption patterns, and the ratio of nutrients consumed have been shown to impact gut microbiome composition and function. Studies indicate that many acute and chronic diseases are associated with alterations to the gut microbiome. There are many patients who rely on enteral tube feeding for their nutrition support. More recently, enteral tube feeding formulations of "real food" have become commercially available. However, little is known about how enteral tube feeding impacts the gut microbiome in patients requiring this specialized form of nutrition therapy. This review summarizes the existing evidence regarding the food sources of commonly consumed macronutrients and their impact on the gut microbiome. Also presented is what is known regarding "standard" and real food enteral formulations on the gut microbiome. Existing evidence is suggestive that real food enteral formulations positively impact the gut microbiome. Still, more research is needed on ready-to-feed formulations, particularly in patients with various clinical conditions, and how gut microbiome modulation impacts clinical outcomes.},
}

@article {pmid40050995,
year = {2025},
author = {Garrigues, Q and Apper, E and Mercier, F and Rodiles, A and Rovere, N and Chastant, S and Mila, H},
title = {Composition of the fecal, vaginal and colostrum microbiotas of dams at parturition and their relationship with neonatal outcomes in dogs.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {23},
pmid = {40050995},
issn = {2524-4671},
abstract = {BACKGROUND: Microbial seeding in early life is critical for the host's short- and long-term health, and the mother is the first source of bacteria for the newborn. The objective of this study was to characterize the maternal fecal, vaginal, and colostral microbiotas in the canine species one day after parturition and to evaluate the relationship between the microbial profiles of 36 dams and the neonatal outcomes of 284 newborns.

RESULTS: The first part of the study revealed the presence of 2 fecal, 3 vaginal, and 2 colostral microbial clusters on the basis of the core microbiota of the dams. Among these three maternal microbiotas, only the vaginal microbiome was found to be associated with neonatal outcomes. Compared with those in the other clusters, females in Cluster 1, with the lowest stillbirth and neonatal mortality ratios, presented a greater abundance of Moraxellaceae in their vaginal microbiota; Cluster 2, with a greater abundance of Pasteurellaceae, mostly from the Haemophilus genus; and Cluster 3 (with the highest stillbirth and neonatal mortality ratios), a greater abundance of Enterobacteriaceae, mostly E. coli. Moreover, Cluster 3 dams presented significantly lower species richness according to the Shannon index than did dams from the other clusters.

CONCLUSIONS: This study underscores the strong association between maternal microbiota, particularly the vaginal microbiota, and newborn health. The results of this study call for further research to gain a deeper understanding of the optimal vaginal microbiota composition in canine species and the ways to modulate it to improve neonatal outcomes.},
}