@article {pmid40634580,
year = {2025},
author = {},
title = {Workouts can help gut microbes to quell cancer.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40634580},
issn = {1476-4687},
}

@article {pmid40634535,
year = {2025},
author = {Ondee, T and Pongpirul, K and Wongsaroj, L and Senaprom, S and Wattanaphansak, S and Leelahavanichkul, A},
title = {Lactiplantibacillus plantarum dfa1 reduces obesity caused by a high carbohydrate diet by modulating inflammation and gut microbiota.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24801},
pmid = {40634535},
issn = {2045-2322},
support = {FOODF67300006//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; FOODF67300006//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; N/A//Second Century Fund (C2F)/ ; N/A//Second Century Fund (C2F)/ ; N/A//Second Century Fund (C2F)/ ; N/A//Second Century Fund (C2F)/ ; },
mesh = {Animals ; *Obesity/etiology/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Probiotics/pharmacology/administration & dosage ; *Inflammation ; Male ; *Dietary Carbohydrates/adverse effects ; Mice, Inbred C57BL ; *Lactobacillaceae ; },
abstract = {Given the potential of probiotics to counteract obesity induced by high glucose diets (HGD) and the beneficial effects of high-fiber diets, this study explored the impact of Lactiplantibacillus plantarum dfa1 (Lp dfa1) in mice consuming modified diets, including a unique high-carbohydrate biscuit diet (HBD) featuring Prachuap Khiri Khan's Pineapple Cheese Cake Biscuit for its rich fiber content. Notably, the fruit-derived soluble fiber HBD might have a synbiotic effect (the enhanced beneficial bacteria in the gut) different from HGD. in The standard mouse diet (RD) with a carbohydrate: protein: fat (C: P:F) ratio of 56:13:31 served as the base, which was then modified with either glucose to form the HGD (C: P:F at 60:25:15) or blended with the high-fiber dessert to create the HBD (C: P:F at 70:9:21). Over 12 weeks, mice were fed HGD or HBD with and without daily oral administration of Lp dfa1 at 1 × 10[9] CFU. This study aimed to assess the effects on obesity indicators (weight gain, lipid profiles, fat deposition), prediabetes markers (fasting glucose, insulin, oral glucose tolerance test, and Homeostatic Model Assessment for Insulin Resistance (HOMA-IR)), intestinal health (FITC-dextran assay for enterocyte injury, serum cytokines TNF-α, IL-10, and IL-6), and liver health (enzymes, weight, histology, carbohydrate and fat components, and oxidative stress). Both HGD and HBD induced similar obesity metrics, prediabetic conditions, enterocyte injury, altered serum cytokines, and liver damage. Remarkably, Lp dfa1 administration mitigated these adverse effects with an elevation in fecal short-chain fatty acids. Microbiome analysis revealed diet-induced dysbiosis, with a notable difference between HGD and HBD impacts, particularly in the Fermicutes/Bacteroides ratio and Akkermansia spp. abundance, which was significantly elevated in the HBD + Lp group. Actinomycota with a lower Proteobacteria in HBD compared with HGD group indicate the possible different impacts between the mixed sugar with fruit-derived soluble fiber versus pure glucose. Interestingly, Lp dfa1 elevated Akkermansia spp. (a well-known beneficial probiotic against obesity) only in mice with HBD but not HGD, despite an obesity attenuation by Lp dfa1 in both HGD and HBD groups, implying the different anti-obesity mechanisms. In vitro experiments revealed Lp dfa1's supernatant reduced inflammation in Caco-2 and HepG2 cell lines, evidenced by improved transepithelial electrical resistance (TEER), expression of occludin-1 (a tight junction molecule), decreased inflammatory mediators (NF-κB, TNF-α, IL-8, IL-6, and IL-10), and elevated mucin gene. Conclusively, Lp dfa1 demonstrates a dual mechanism in preventing sugar-induced intestinal injury and supporting metabolic health: direct cellular protection and microbiome modulation. These findings highlight the additive effects of Lp dfa1 and high-fiber diets, particularly emphasizing the Pineapple Cheese Cake Biscuit-based diet's role in enhancing gut microbiota and addressing diet-induced health issues.},
}

Animals
*Obesity/etiology/microbiology/therapy
*Gastrointestinal Microbiome/drug effects
Mice
*Probiotics/pharmacology/administration & dosage
*Inflammation
Male
*Dietary Carbohydrates/adverse effects
Mice, Inbred C57BL
*Lactobacillaceae

@article {pmid40634526,
year = {2025},
author = {Tarriño, M and Gutiérrez-Bautista, JF and Durán, MJO and Garcia-Diaz, A and Cabrera-Serrano, AJ and Sainz, J and Cobo, F and Rodriguez, T and Reguera, JA and Bernal, M and López-Nevot, MÁ and Sampedro, A},
title = {The role of intestinal microbiota in the humoral response to SARS-CoV-2 after mRNA-1273 vaccination.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24731},
pmid = {40634526},
issn = {2045-2322},
support = {PI21/01708//Instituto de Salud Carlos III/ ; PI21/01708//Instituto de Salud Carlos III/ ; PI21/01708//Instituto de Salud Carlos III/ ; PI21/01708//Instituto de Salud Carlos III/ ; PI21/01708//Instituto de Salud Carlos III/ ; PI21/01708//Instituto de Salud Carlos III/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Female ; Male ; *SARS-CoV-2/immunology ; *COVID-19/prevention & control/immunology/microbiology ; *Immunity, Humoral ; Adult ; 2019-nCoV Vaccine mRNA-1273/immunology ; Immunoglobulin G/immunology/blood ; Middle Aged ; Antibodies, Viral/immunology/blood ; *COVID-19 Vaccines/immunology ; Vaccination ; Feces/microbiology ; },
abstract = {The gut microbiota plays a key role in shaping immune responses, including those induced by vaccination. Its impact on the humoral response to mRNA-based SARS-CoV-2 vaccines, however, remains underexplored. We analyzed gut microbiota composition and anti-Spike (S) IgG levels in 50 healthcare workers vaccinated with the mRNA-1273 SARS-CoV-2 vaccine. Participants were stratified into low, medium, and high responders based on IgG titers 30 days post-vaccination. Stool samples were collected at baseline, and 16 S rRNA sequencing was used to assess microbiota diversity and taxonomic profiles. Alpha diversity indices showed no significant differences across response groups. However, specific microbial signatures were associated with vaccine response. Higher relative abundance of Clostridia, Clostridiales, Ruminococcaceae, and Odoribacter splanchnicus correlated with stronger IgG responses. Functional microbiome analysis revealed enrichment of acetate-producing pathways in high responders (p = 0.012), suggesting a role for short-chain fatty acids in enhancing vaccine-induced immunity. Logistic regression and Random Forest models identified these taxa as predictors of strong antibody responses. The area under the ROC curve (AUC) for individual taxa ranged from 0.70 to 0.76, indicating moderate predictive performance. Conversely, taxa such as Hallella and Sutterella wadsworthensis were linked to lower responses. These findings support a modulatory role of the gut microbiota in mRNA vaccine immunogenicity and highlight microbial metabolic functions as potential targets to boost vaccine efficacy in personalized immunization strategies.},
}

Humans
*Gastrointestinal Microbiome/immunology
Female
Male
*SARS-CoV-2/immunology
*COVID-19/prevention & control/immunology/microbiology
*Immunity, Humoral
Adult
2019-nCoV Vaccine mRNA-1273/immunology
Immunoglobulin G/immunology/blood
Middle Aged
Antibodies, Viral/immunology/blood
*COVID-19 Vaccines/immunology
Vaccination
Feces/microbiology

@article {pmid40634502,
year = {2025},
author = {},
title = {Tracking microbiome-derived cell-free RNA modifications detects colorectal cancer.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40634502},
issn = {1546-1696},
}

@article {pmid40634391,
year = {2025},
author = {Cullen, JT and Lawlor, PG and Cormican, P and Crispie, F and Slattery, H and Gardiner, GE},
title = {Bacteriome and mycobiome profiling of liquid feed for finisher pigs on commercial pig farms.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24718},
pmid = {40634391},
issn = {2045-2322},
support = {GOIPG/2021/331//Irish Research Council/ ; },
mesh = {Animals ; *Animal Feed/microbiology/analysis ; Swine/microbiology ; *Mycobiome ; Biogenic Amines/analysis/metabolism ; Farms ; *Bacteria/genetics/classification/isolation & purification ; Fermentation ; *Fungi/genetics/classification/isolation & purification ; },
abstract = {The aim was to assess the quality of liquid feed for grow-finisher pigs across commercial pig farms by profiling the bacteriome and mycobiome of samples and determining biogenic amine concentrations. Amplicon sequencing of liquid feed samples revealed that bacterial and fungal community structures were influenced by the farm of origin and sampling location (mixing tank/trough) on a given farm. Decreases in alpha-diversity of liquid feed between the mixing tank and the troughs corresponded with increased relative abundances of bacteria, particularly Lactobacillus, Weissella and Leuconostoc, as well as yeasts, including Kazachstania and Dipodascus, indicative of spontaneous fermentation. The concentration of biogenic amines, resulting from amino acid loss from the feed, which likely plays a role in poorer feed efficiency, also increased between the mixing tank and the troughs. The highest biogenic amine concentrations in the feed were found on the farm that had the highest lactic acid bacteria (LAB) and yeast counts. Both Lactobacillus and Kazachstania were correlated with biogenic amine concentrations in liquid feed, highlighting the unexplored role that LAB and yeast may play in amino acid decarboxylation and biogenic amine formation in liquid feed. Factors including the use of liquid co-products in diets also impacted the liquid feed microbiome.},
}

Animals
*Animal Feed/microbiology/analysis
Swine/microbiology
*Mycobiome
Biogenic Amines/analysis/metabolism
Farms
*Bacteria/genetics/classification/isolation & purification
Fermentation
*Fungi/genetics/classification/isolation & purification

@article {pmid40634281,
year = {2025},
author = {Bagaev, A and Sur, D and Agranyoni, O and Pe'er, N and Savita, BK and Rocha, BGS and Thanos, PK and Navon-Venezia, S and Pinhasov, A},
title = {Maternal oral sodium propionate supplementation restores gut integrity and mitigates stress-induced metabolic and behavioral outcomes in offspring.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {235},
pmid = {40634281},
issn = {2158-3188},
support = {2069/17//Israel Science Foundation (ISF)/ ; },
mesh = {Animals ; *Propionates/administration & dosage/pharmacology ; Female ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; *Behavior, Animal/drug effects ; *Stress, Psychological/metabolism ; Dietary Supplements ; *Maternal Behavior/drug effects ; Pregnancy ; Mice, Inbred C57BL ; Receptors, G-Protein-Coupled/metabolism ; Administration, Oral ; Feces/chemistry/microbiology ; },
abstract = {Maternal attachment is a critical determinant of offspring's postnatal development, significantly influencing their later-life metabolic and behavioral patterns. We previously showed that stress-vulnerable, socially submissive (Sub) mice exhibit significant disruptions in gut physiology including distorted microbiome composition, lower colonic propionate levels, and increased gut permeability. These alterations exacerbated chronic inflammation, caused metabolic imbalances and reduced maternal care. In this study, we revealed a significant reduction in bacterial diversity and fecal propionate levels in Sub dams. To investigate whether maternal gut integrity could mitigate adverse offspring outcomes, we provided oral sodium propionate (SP) supplementation to Sub dams via drinking water from postpartum day (PD) 0, until weaning (PD21). SP supplementation notably improved maternal care, reflected by faster pup retrieval times and better nesting. Beneficial effects were particularly pronounced in two-month-old male offspring, demonstrating decreased anxiety-like behavior, improved sociability and enhanced short-term memory accompanied by increased abundance of specific gut bacteria (Roseburia, and Shuttleworthia genus). Additionally, male offspring exhibited significant metabolic improvements, including reduced epididymal white adipose tissue (eWAT) mass, decreased adipocyte diameter accompanied by increased eWAT mRNA expression of GPR43 and PPAR-γ. Moreover, SP supplementation increased colon length linked with increased colonic mRNA expression of GPR43, PPAR-γ and Claudin-7, highlighting the importance of propionate in tight junction regulation and inflammation. Importantly, these positive outcomes exhibited notable sex-dependent differences, with male offspring responding robustly, whereas females showed minimal behavioral or metabolic improvements following maternal SP supplementation. Overall, our findings emphasize that innate stress vulnerability-related metabolic and behavioral alterations in offspring can be mitigated by restoring the dams' gut epithelial barrier integrity, highlighting the critical role of the maternal gut environment and demonstrating clear sex-specific responses to gut microbiota-targeted interventions.},
}

Animals
*Propionates/administration & dosage/pharmacology
Female
*Gastrointestinal Microbiome/drug effects
Male
Mice
*Behavior, Animal/drug effects
*Stress, Psychological/metabolism
Dietary Supplements
*Maternal Behavior/drug effects
Pregnancy
Mice, Inbred C57BL
Receptors, G-Protein-Coupled/metabolism
Administration, Oral
Feces/chemistry/microbiology

@article {pmid40634275,
year = {2025},
author = {Özçam, M and Lin, DL and Gupta, CL and Li, A and Gomez, JC and Wheatley, LM and Baloh, CH and Sanda, S and Jones, SM and Lynch, SV},
title = {Gut microbial bile and amino acid metabolism associate with peanut oral immunotherapy failure.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6330},
pmid = {40634275},
issn = {2041-1723},
support = {AI128482//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI148104//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; UM1AI160040//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI089473//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/immunology/physiology ; *Bile Acids and Salts/metabolism ; *Peanut Hypersensitivity/therapy/immunology/microbiology ; Feces/microbiology/chemistry ; *Arachis/immunology ; *Amino Acids/metabolism ; Male ; Administration, Oral ; Female ; Child ; *Desensitization, Immunologic/methods ; Double-Blind Method ; Child, Preschool ; Treatment Failure ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Antigens, Plant/immunology ; },
abstract = {Peanut Oral Immunotherapy (POIT) holds promise for remission of peanut allergy, though treatment is protracted and successful in only a subset of patients. Because the gut microbiome has been linked to food allergy, we sought to identify fecal predictors of POIT efficacy and mechanistic insights into treatment response. Here, we conducted a secondary analysis of the IMPACT randomized, double-blind, placebo-controlled POIT trial (NCT01867671), using longitudinal fecal samples from 90 children, and performed 16S rRNA sequencing, shotgun metagenomics, and untargeted metabolomics. Integrated multi-omics analyses revealed a relationship between gut microbiome metabolic capacity and treatment outcomes. Five fecal bile acids present prior to treatment initiation predicted POIT efficacy (AUC 0.71). Treatment failure was associated with a specific bile acid profile, enhanced amino acid utilization, and higher copy number of the ptpA gene encoding a bacterial hydrolase that cleaves tripeptides containing proline residues - a feature of immunogenic peanut Ara h 2 proteins. In vitro, peanut-supplemented fecal cultures of children for whom POIT failed to induce remission evidenced reduced Ara h 2 concentrations. Thus, distal gut microbiome metabolism appears to contribute to POIT failure.},
}

Humans
*Gastrointestinal Microbiome/genetics/immunology/physiology
*Bile Acids and Salts/metabolism
*Peanut Hypersensitivity/therapy/immunology/microbiology
Feces/microbiology/chemistry
*Arachis/immunology
*Amino Acids/metabolism
Male
Administration, Oral
Female
Child
*Desensitization, Immunologic/methods
Double-Blind Method
Child, Preschool
Treatment Failure
RNA, Ribosomal, 16S/genetics
Metagenomics
Antigens, Plant/immunology

@article {pmid40634132,
year = {2025},
author = {Nijat, D and Zhao, Q and Abdurixit, G and He, J and Liu, H and Li, J},
title = {An Up-to-Date Review of Traditional Chinese Medicine in the Treatment of Atherosclerosis: Components, Mechanisms, and Therapeutic Potentials.},
journal = {Phytotherapy research : PTR},
volume = {},
number = {},
pages = {},
doi = {10.1002/ptr.70037},
pmid = {40634132},
issn = {1099-1573},
support = {2023B02030//Key Research and Development Program in Xinjiang Uygur Autonomous Region/ ; 2024B02005//Key Research and Development Program in Xinjiang Uygur Autonomous Region/ ; 2023TSYCLJ0043//Tianshan Talent Training Program/ ; },
abstract = {Atherosclerosis is a chronic inflammatory disease and a major global health concern. In recent years, traditional Chinese medicines (TCMs) have demonstrated multi-target therapeutic potential against atherosclerosis by modulating inflammatory responses, oxidative stress, lipid metabolism, and gut microbiota interactions. This review systematically evaluates (1) the anti-atherogenic mechanisms of key TCM herbs (e.g., Panax ginseng, Salvia miltiorrhiza) and bioactive compounds (e.g., ginsenosides, tanshinones), (2) their synergistic effects in proprietary formulations, and (3) clinical evidence for cardiovascular protection. Notably, we highlight how TCM compounds like berberine and resveratrol target the gut-vascular axis by regulating microbiota-derived metabolites (e.g., TMAO) and improving endothelial function. While preclinical studies show promising results through Nrf2/HO-1 activation, NF-κB inhibition, and plaque stabilization, translational challenges persist, including the lack of standardization and microbiome-dependent efficacy variations. We conclude that integrating TCM's multi-component advantages with cutting-edge technologies such as bioinformatics, nanotechnology, and patient-specific multiomics including microbiome profiling could revolutionize atherosclerosis management, though rigorous clinical validation and standardization remain imperative.},
}

@article {pmid40633803,
year = {2025},
author = {Xie, D and Wang, Y and Li, J and Yang, T and Zhang, Y and Zhang, W and Doherty, M and Zhu, Y and Yang, Z and Wang, Y and Wei, J and Lei, G and Zeng, C},
title = {Correlation between Gut Dysbiosis, Metabolite Alterations and Erosive Hand Osteoarthritis - an observational study within the community-based Xiangya Osteoarthritis (XO) cohort.},
journal = {Osteoarthritis and cartilage},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joca.2025.07.004},
pmid = {40633803},
issn = {1522-9653},
abstract = {OBJECTIVES: Erosive hand osteoarthritis (EHOA) is an aggressive subtype of hand osteoarthritis (HOA) with unclear pathogenesis. Since gut dysbiosis and related metabolite alterations may exacerbate inflammation and accelerate bone destruction, we investigated whether these abnormalities were involved in EHOA.

METHODS: Participants were drawn from the Xiangya Osteoarthritis Study. We compared gut microbial α-diversity and β-diversity between EHOA and controls (neither EHOA nor non-erosive HOA), and analyzed associations between microbial species abundance, functions, and EHOA. Targeted blood metabolomics were performed to identify microbiome-associated metabolites in EHOA. The associations between EHOA-related microbial species and blood metabolites were examine through multi-omics analyses.

RESULTS: Among 1,324 participants, significant differences in α-diversity (EHOA: median=4.53, non-HOA control: median=4.16; median difference=0.37 [95%CI: 0.09-0.57], P=0.016) and β-diversity (R²=0.002 [95%CI: 0.0018-0.006], P=0.015) were observed at the species level between EHOA and controls. Participants with EHOA had a higher relative abundance of Alistipes senegalensis (β coefficient:0.17 [95%CI:0.07-0.26]) and Fournierella massiliensis (β coefficient:0.39 [95%CI:0.28-0.49]). Tryptophan metabolism was the main altered metabolic pathway. Targeted blood metabolomics showed higher levels of L-5-hydroxytryptophan (β coefficient:0.38 [95%CI:0.15-0.61]), 3-indoleglyoxylic acid (β coefficient:0.35 [95%CI:0.01-0.69]), 5-hydroxyindoleacetic acid (β coefficient:0.27 [95%CI:0.09-0.45]), indoleacrylic acid (IA) (β coefficient:0.23 [95%CI:0.001-0.46]), and serotonin (β coefficient: 0.20 [95%CI: 0.004-0.40]), alongside lower levels of L-tryptophan (β coefficient:-0.41 [95%CI:-0.75 to -0.06]) and indole-3-acetyl-aspartate (β coefficient:-1.05 [95%CI:-1.79 to -0.32]) in EHOA. IA was positively correlated with EHOA-related microbial species, particularly Alistipes senegalensis (β coefficient:0.20 [95%CI:0.14-0.27]).

CONCLUSIONS: A higher relative abundance of Alistipes senegalensis and alterations in tryptophan metabolites, particularly higher levels of IA, are associated with EHOA.},
}

@article {pmid40633656,
year = {2025},
author = {Chakraborty, S and Banerjee, S and Kumar, S and Ghosh, S and Mukherjee, P and Das, S and Bhattacharyya, P},
title = {Biofortified Vermicompost: Exploring Bacterial Community Dynamics and Enzymatic Pathways through Bacteriome Analysis for Arsenic Bioremediation in Mine Waste.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126795},
doi = {10.1016/j.envpol.2025.126795},
pmid = {40633656},
issn = {1873-6424},
abstract = {The extraction of mica from open-cast mines generates substantial waste, often laden with arsenic, posing severe environmental risks. Addressing this waste is essential to mitigate co-contamination. Vermitechnology offers a promising solution by converting toxic waste into nutrient-enriched, sanitized compost suitable for agriculture. This study explored bioremediation of toxic mine tailings (MT) through aerobic composting, vermicomposting and enriched vermicomposting (with Bacillus subtilis K5BGRD). Earthworm fecundity was impaired in dense MT settings but improved in MT+CD (1:1) treatments. Vermicomposting stabilized pH, enhanced nutrient mineralization and increased potassium bioavailability compared to aerobic composting. Enriched vermicompost reduced bioavailable arsenic by 58-88% post-maturity, alongside increased microbial diversity and enzymatic activity. Earthworms bioaccumulated arsenic, contributing to a total reduction of 14.25%. Pearson correlation and PLS-SEM analyses highlighted reduced arsenic-induced stress upon compost maturity. Metataxonomic analysis revealed microbial similarities between V1 (MT+CD [1:1]) and EV1 (MT+CD+B [1:1:1]) composts, with enrichment of stress-resistant, bioremediating and plant growth-promoting taxa. Upon crop trial it was deduced that microbe-mediated vermicomposting, particularly when combined with recommended fertilizer doses (as in T2), not only minimized arsenic accumulation in tomato plants but also significantly enhanced yield, highlighting its potential as a sustainable and effective strategy for safe crop production in contaminated soils. The study demonstrated the symbiotic relationship between earthworms and microbes in waste-treated settings, establishing a novel feedstock combination to remediate hazardous mine waste. Ultimately, this approach has the potential to replace chemical fertilizers, improve crop yields and reduce arsenic exposure - offering a cost-effective and eco-friendly solution to mining waste management.},
}

@article {pmid40633607,
year = {2025},
author = {Linh, NV and Khang, LTP and Dinh-Hung, N and Wisetkaew, S and Therdtatha, P and Sangsawad, P and Wannavijit, S and Jitjumnong, J and Permpoonpattana, P and Van Doan, H},
title = {Effects of dietary corn silk (Zea mays L.) on growth, immune and antioxidant pathways, histological morphology, gut microbiome, and sensitivity to acute ammonia exposure in the koi carp (Cyprinus carpio var. koi).},
journal = {Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology},
volume = {},
number = {},
pages = {111127},
doi = {10.1016/j.cbpb.2025.111127},
pmid = {40633607},
issn = {1879-1107},
abstract = {Corn silk is a promising aquafeed additive due to its antioxidant, antibacterial, and anti-inflammatory properties. This study evaluated the impact of graded dietary levels of powdered corn silk (PCS) on growth, immunity, antioxidant enzyme activities, histology, gut microbiota composition, gene expression profiles, and sensitivity to acute ammonia exposure in koi carp (Cyprinus carpio var. koi). A total of 300 fish were assigned to five dietary treatments (0, 5, 10, 20, and 30 g/kg PCS) for eight weeks. Fish fed the PCS-30 diet showed significant improvements in growth parameters, including weight gain (WG) and specific growth rate (SGR) (p < 0.05). Antioxidant capacity (2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid); ABTS) and superoxide dismutase (SOD) activity, increased dose-dependently, while malondialdehyde (MDA) levels remained unchanged (p > 0.05). Expression of the immune and antioxidant genes interleukin 8 (il-8), lysozyme (lyz), catalase (cat), nuclear factor-κB (Nf-κB), and toll-like receptor 4 (tlr4) was significantly upregulated in the PCS-20 and PCS-30 groups (p < 0.05). Histological analysis revealed progressive improvements in anterior intestinal morphology, with the PCS-30 group exhibiting the greatest villus height and width. Gut microbiota analysis showed increased relative abundance of beneficial taxa (Gammaproteobacteria, Lactobacillales, Prevotella), which positively correlated with growth and antioxidant markers, and negatively with MDA levels. Survival under acute ammonia exposure was highest in the PCS-20 and PCS-30 groups. These findings demonstrate the efficacy of PCS, particularly at 30 g/kg, in enhancing growth, immunity, and stress resilience.},
}

@article {pmid40633493,
year = {2025},
author = {Sibinga, NA and Werner, E and Tegtmeier, D and De Smet, J},
title = {Animal board invited review: The need for, and the path towards, a functional understanding of the farmed insect microbiome.},
journal = {Animal : an international journal of animal bioscience},
volume = {19},
number = {8},
pages = {101575},
doi = {10.1016/j.animal.2025.101575},
pmid = {40633493},
issn = {1751-732X},
abstract = {The rapid growth of research on industrially produced insect species over the past two decades has coincided with breakthroughs in the speed and affordability of DNA sequencing. This has allowed researchers to rapidly generate data on the microbial communities associated with farmed insects, especially the gut-residing bacteria of the two cornerstone production species: black soldier fly (BSF, Hermetia illucens) and yellow mealworm (Tenebrio molitor). A picture of the most prevalent and abundant microbes associated with these species has rapidly come into focus. Specific microbial functions have been suggested under extreme or challenging rearing settings, but less is known about the contributions of the microbiome to insect rearing under realistic production conditions. There is limited understanding of how microbial communities of farmed insects arise, are maintained, and change in response to stimuli. Likewise for seemingly basic questions: what functions do insect-associated microbes perform for the host? Which (if any) taxa are essential for healthy insects? This is not intended as a criticism of existing research; indeed, these questions turn out not to be simple. Answering them requires targeted research approaches testing specific hypotheses about farmed insect microbiome function. This review aims to recalibrate the state of knowledge by critically assessing common and emerging strategies to study these microbiomes and existing knowledge gaps about the functional role of the microbiome for BSF and mealworm. Overall, it is clear that microbes are an intrinsic part of the ecology of these two farmed insects. Reciprocal interactions between microbes and insects are extensive, though microbiome community composition depends to a large extent on environmental conditions. To date, it remains unclear how taxonomical shifts correspond to functional shifts and to what extent such changes impact insect physiology. For example, when mealworms are fed plastics, their microbiomes undergo significant changes in microbial composition. These changes are presumed to increase the ability of mealworms and their microbiota to degrade plastic, but this change in function is hard to conclusively demonstrate with current tools. Furthermore, analysis of the literature shows that taxonomically disparate microbial communities may provide similar functional benefits, e.g. lignocellulose breakdown in BSF larvae. This review therefore aims to critically assess the state of the art with regard to functional analysis of the farmed insect microbiome and how available experimental methods can be best applied to identify links between microbial functions and insect physiology and improve the efficiency and sustainability of the farmed insect industry.},
}

@article {pmid40633399,
year = {2025},
author = {Criscuolo, A and Czepiel, A and Schwartze, M and Kotz, SA},
title = {A body-brain (dis)equilibrium regulating transitions from health to pathology.},
journal = {Physics of life reviews},
volume = {54},
number = {},
pages = {94-111},
doi = {10.1016/j.plrev.2025.07.003},
pmid = {40633399},
issn = {1873-1457},
abstract = {Recent empirical evidence and theoretical propositions motivate a paradigm shift in how we investigate neurocognitive functions. Rather than looking at the brain-behaviour relationship in isolation, research shows that cognition is shaped by reciprocal, dynamical interactions between the brain and the body across multiple timescales: from ultra-slow circadian rhythm to gastrointestinal and cardiorespiratory activity. This interest in body-brain-behaviour dynamics has raised new questions about if and how autonomic functioning, the coordination of intero- and exteroception, lifestyle and dietary choices, gut microbiome composition, hormonal cycles, and inflammation can impact behaviour, general health and well-being. We carefully reviewed existing theoretical accounts and empirical evidence on the body-brain-behaviour interface and delineated new emerging avenues for multimodal, functional, ecologically valid, and personalized research that also integrates smart sensing technologies. In a synopsis, we propose the concept of a body-brain (dis)equilibrium regulating transitions from health to pathology.},
}

@article {pmid40633350,
year = {2025},
author = {Huang, C and Wang, T and Chen, W and Wang, J and Cui, M and Zheng, C and Qiu, M and Shan, M and Li, B and Zhang, L and Yu, Y and Xu, L and Fang, H},
title = {Sheep and rapeseed cake manure promote antibiotic resistome in agricultural soil.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139157},
doi = {10.1016/j.jhazmat.2025.139157},
pmid = {40633350},
issn = {1873-3336},
abstract = {The application of manure in agriculture caused the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil environments. However, the co-occurrence pattern and host diversity of ARGs and MGEs in soils amended with animal and green manures remains unclear. In this study, metagenomic assembly and binning techniques were employed to comprehensively explore the effects of sheep manure and green manure on soil microbiome, antibiotic resistomes, and ARG hosts. Both rapeseed cake manure and sheep manure increased the abundance and diversity of ARGs, with sheep manure particularly enhancing the abundance of ARGs conferring resistant to multidrug, quinolone, rifampicin, and macrolide-lincosamide-streptogramin (MLSB). Mobile genetic elements (MGEs), such as plasmids, transposases, and integrases, preferentially enhanced the potential mobility of some ARGs subtypes (i.e. sul2, aadA, qacH, and folp), facilitating the spread of ARGs. Additionally, sheep manure reshaped the bacterial community structure and composition as well as ARG hosts, some opportunistic pathogens (i.e. Staphylococcus, Streptococcus, and Pantoea) acquired antibiotic resistance and remained recalcitrant. It is concluded that rapeseed cake manure and sheep manure increased the co-occurrence of ARGs and MGEs, enriched the potential ARG hosts, and promoted the dissemination of ARGs in agricultural soils.},
}

@article {pmid40633153,
year = {2025},
author = {Missawi, O and Vaccari, F and Zhang, L and Miras-Moreno, B and Boughattas, I and Bandini, F and Lucini, L and Puglisi, E and Banni, M},
title = {Unleashing multi-omic approaches to address environmental microplastic hazards in marine polychaetes.},
journal = {Marine pollution bulletin},
volume = {220},
number = {},
pages = {118345},
doi = {10.1016/j.marpolbul.2025.118345},
pmid = {40633153},
issn = {1879-3363},
abstract = {The impact of an environmental microplastic mixture (< 100 μm) on marine polychaete was explored to simulate the plastic exposure patterns in the natural habitat. In this study, Hediste diversicolor was used to mimic a real scenario exposure model of five common types of widely distributed microplastics sampled from the southern Mediterranean Sea. Sediment and polychaete gut were collected for microbiome and metabolomic analysis. Interestingly, high-throughput sequencing revealed a shift in bacterial diversity depending on microplastic concentration (10, 100 and 1000 μg kg[-1]). Noteworthy, sediment revealed similar diversity with respect to the polychaete gut microbiome. Specific bacterial taxa, particularly Mesoflavibacter zeaxanthinifaciens and Vibrio cortegadensis, were notably affected, indicating adaptive responses to altered environments. The identification of different clusters of markedly altered metabolites, including indoles, benzene derivatives, coumarins, pyrones, flavonoids, cinnamates, diterpenes and sesquiterpenes, offered an insight into the physiological and pathological changes observed within the polychaete following microplastics exposure. These novel findings enhance our understanding of the intestinal hazards of environmental microplastics and underscore the potency of multi-omics investigations in unraveling the intricate mechanisms underlying microplastic toxicity.},
}

@article {pmid40632920,
year = {2025},
author = {Olsson, A and Steel, K and Cooper, R and Jones, AP and Chan, KR and Ogg, G and Irvine, AD and Flohr, C and Taams, LS},
title = {Methotrexate and ciclosporin both reduce levels of circulating IL-4 and IL-13 expressing CD4+ memory T-cells in childhood atopic dermatitis.},
journal = {Clinical and experimental dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/ced/llaf301},
pmid = {40632920},
issn = {1365-2230},
abstract = {Atopic dermatitis (AD) is a chronic dermatosis characterised by type-2 inflammatory responses, skin barrier anomalies, and microbiome dysregulation. The variation of AD presentation necessitates a better understanding of the underlying disease mechanisms and the modulation of immune markers over a treatment course. Globally the most used systemic therapies for moderate-to-severe AD are methotrexate (MTX) and ciclosporin (CyA). The TReatment of severe Atopic Eczema in children Trial (TREAT) was a randomised controlled trial assessing the efficacy and safety of methotrexate and ciclosporin. Peripheral blood samples from n=18 TREAT participants were analysed in a longitudinal immunological study with a focus on cytokine-expressing CD4+ T-cells. The analysis showed that both MTX and CyA were associated with a decreased percentage of IL-4 and IL-13 expressing CD4+ memory T-cells, corresponding to improved disease severity. Patients receiving MTX experienced a more sustained decrease in IL-4 expressing T-cells, which corresponds to the longer-term improved disease control observed in the MTX arm.},
}

@article {pmid40632657,
year = {2025},
author = {Bajaj, JS and Reddy, KR and Tandon, P and Lai, JC and O'Leary, JG and Wong, F and Garcia-Tsao, G and Vargas, HE and Kamath, PS and Biggins, SW and Vutien, P and Shaw, J and Limon Miro, AT and Bera, C and McGinley, JP and Sikaroodi, M and Bush, BJ and Thacker, LR and Gillevet, PM},
title = {Salivary microbiome and serum metabolomics add to clinical biomarkers to predict 6-month hospitalizations in a multi-center cirrhosis outpatient cohort.},
journal = {Hepatology (Baltimore, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/HEP.0000000000001462},
pmid = {40632657},
issn = {1527-3350},
abstract = {BACKGROUND AIMS: Prognosticating outcomes such as hospitalizations in cirrhosis outpatients is challenging, especially with changing etiologies and demographics. Aim: Determine impact of multi-omic strategies on outcome prediction.

APPROACH RESULTS: NACSELD3 enrolls cirrhosis outpatients with controlled/eradicated etiologies from 10 centers and follows them systematically. At baseline, clinical/demographic and cirrhosis details were recorded and saliva and serum samples were collected for microbiome and metabolome analysis respectively. Multi-omic bioinformatic studies to determine interaction of microbiota and metabolites with clinical prediction of 6-month hospitalizations were performed. 565 patients (60.2 years, 68% men, 35% alcohol, 33% MASH, 21%, eradicated HCV with MELD3.0 12) were enrolled. 163 (29%) required 6-month hospitalizations; most (75%) were liver-related. Those hospitalized had worse cirrhosis severity, co-morbidity indices, but similar demographics and oral health variables. Salivary microbiome alpha-diversity was lower (1.96±0.48 vs. 2.09±0.45, p=0.018) with greater pathobionts (Streptococcus, Treponema, Enterococcaceae) and lower commensal genera (Veillonella, Prevotella, Haemophilus, Lachnospiraceae spp) at baseline. Serum metabolomics showed significant separation at baseline between hospitalized/not patients using supervised analyses with microbial-origin (phenyllactate, secondary bile acids, indoles), choline moieties, and polyamine/GABA (3-ureidopropionate/spermidine) metabolites being most prominent. Area-under-the curve using random forest for clinical, microbial, and metabolomic variables were higher than that of these individually. Latent factor analysis showed clinical variables (MELD3.0, hemoglobin and albumin) with the greatest impact followed by salivary microbiota and then serum microbiome for hospitalization prediction.

CONCLUSION: In a multi-center North American outpatient cirrhosis cohort with controlled etiologies, serum metabolomics and salivary microbiome add to clinical variables to prognosticate 6-month hospitalization.},
}

@article {pmid40632459,
year = {2025},
author = {Ding, Y and Hou, Y and Lao, X},
title = {The Role of Akkermansia muciniphila in Disease Regulation.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40632459},
issn = {1867-1314},
abstract = {In recent years, Akkermansia muciniphila (A. muciniphila), as a representative of the core gut commensal bacteria, has shown outstanding therapeutic potential in the field of microecological interventions due to its unique mucin degrading ability and host-interaction mechanism. A. muciniphila is first isolated from human feces in 2004. It colonizes the intestinal mucus layer, utilizing mucin secreted by goblet cells as its primary carbon and nitrogen source. In 2013, researchers found that supplementation with A. muciniphila could improve obesity, demonstrating the potential of A. muciniphila in the treatment of disease. Recent studies show that A. muciniphila strengthens intestinal barrier integrity, improves metabolic diseases, and mitigates inflammation through multiple mechanisms, including adenosine monophosphate-activated protein kinase (AMPK) pathway activation via Toll-like receptor (TLR) 2 stimulation and NOD-like receptor family, pyrin domain containing 3 (NLRP3) activation. A. muciniphila and its derivatives also exhibit potent anti-tumor effects. They induce tumor-necrosis-factor-related apoptosis-inducing ligand (TRAIL) upregulation, triggering extrinsic (death receptor-mediated) and intrinsic (mitochondrial) apoptosis pathways in tumor cells. Additionally, A. muciniphila promotes M1-like tumor-associated macrophages (TAMs) through NLRP3 activation and remodels the tumor microenvironment via metabolic crosstalk with intratumoral microbiota. Notably, A. muciniphila combined with programmed death-1 (PD-1) antibody boost CD8[+] T cell infiltration, thereby overcoming host resistance to PD-1 blockade. Moreover, A. muciniphila contributes to the growth of butyric acid-producing bacteria and suppresses the growth of specific bacterial populations, playing an important role in the gut microbiome network. This review evaluates recent discoveries regarding A. muciniphila's multifaceted roles in maintaining intestinal barrier integrity, ameliorating metabolic and inflammatory disorders, and enhancing anti-tumor immune responses. We also discuss its ecological effect on the gut microbiota flora and point out the therapeutic limitations and prospect which provides theoretical references to promote the development of Akkermansia muciniphila in clinical diseases, especially in tumor therapy.},
}

@article {pmid40632357,
year = {2025},
author = {Arif, TB and Damianos, JA and Rahman, AU and Hasnain, N},
title = {Fecal Microbiota Transplantation for Disorders of Gut-Brain Interaction: Current Insights, Effectiveness, and Future Perspectives.},
journal = {Current gastroenterology reports},
volume = {27},
number = {1},
pages = {50},
pmid = {40632357},
issn = {1534-312X},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Dysbiosis/therapy/complications/microbiology ; *Gastrointestinal Microbiome ; *Brain-Gut Axis ; *Gastrointestinal Diseases/therapy/microbiology ; },
abstract = {PURPOSE OF REVIEW: Dysbiosis can disrupt intestinal barrier integrity and impact the immune and nervous systems, playing a significant role in developing disorders of gut-brain interaction (DGBI). This review aims to provide a comprehensive understanding of dysbiosis and its role in DGBI while examining the latest advancements in fecal microbiota transplantation (FMT). It also highlights key challenges in the field and outlines critical directions for future research to optimize FMT strategies, ultimately improving patient outcomes in this evolving treatment area.

RECENT FINDINGS: In DGBI, dysbiosis triggers immune responses, increases gut permeability, and disrupts nervous system signaling, with contributing factors including diet, antibiotics, stress, and infections. Individuals with DGBI exhibit distinct microbial imbalances, such as an increased Firmicutes-to-Bacteroidetes ratio and reduced beneficial bacteria. FMT has shown mixed results, with factors like patient selection, treatment protocols, and microbiome diversity influencing outcomes. While FMT can improve symptoms in refractory irritable bowel syndrome (IBS), effects may fade over time, requiring repeat treatments. Future FMT approaches should focus on targeted microbial interventions, considering the role of archaea, fungi, and microbial metabolites, while prioritizing optimal donor selection and large-scale trials for long-term efficacy. Despite the promising findings, FMT has not yet been widely endorsed in clinical guidelines due to the variability and heterogeneity of the data available. While much of the research has focused on IBS, studies have also explored the impact of FMT on other conditions such as functional diarrhea, functional constipation, and functional dyspepsia, which all exhibit altered microbial profiles.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Dysbiosis/therapy/complications/microbiology
*Gastrointestinal Microbiome
*Brain-Gut Axis
*Gastrointestinal Diseases/therapy/microbiology

@article {pmid40631920,
year = {2025},
author = {Wang, X and Jun, F and Lin, C and Wang, X},
title = {Psychedelics and the Gut Microbiome: Unraveling the Interplay and Therapeutic Implications.},
journal = {ACS chemical neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschemneuro.5c00418},
pmid = {40631920},
issn = {1948-7193},
abstract = {Classic psychedelics and the gut microbiome interact bidirectionally through mechanisms involving 5-HT2A receptor signaling, neuroplasticity, and microbial metabolism. This viewpoint highlights how psychedelics may reshape microbiota and how microbes influence psychedelic efficacy, proposing microbiome-informed strategies─such as probiotics or dietary interventions─to personalize and enhance psychedelic-based mental health therapies.},
}

@article {pmid40631910,
year = {2025},
author = {Deng, Y and Leib, N and Schnautz, S and Benfadal, S and Oldenburg, J and Bieber, T and Herrmann, N},
title = {Langerhans Cell Modulation in Atopic Dermatitis Is TLR2/SOCS1-Dependent and JAK Inhibitor-Sensitive.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16641},
pmid = {40631910},
issn = {1398-9995},
support = {//Christine Kühne - Center for Allergy Research and Education/ ; EXC2151-390873048//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Langerhans cells (LC) are epidermal dendritic cells building the skin's outermost immunological barrier and bridging innate and adaptive immune responses. Their sensing property of the microbiome via Toll-like receptors (TLR) is impaired in atopic dermatitis (AD). We hypothesize a desensitization of LC because of persistent Staphylococcus aureus exposure in AD and underlying mechanisms being TLR2-related.

METHODS: Human LC generated from hematopoetic stem cells were desensitized via repetitive exposure to TLR2-ligands (priming) and compared to unprimed cells for their TLR-responsiveness. JAK inhibitors impact was evaluated. Maturation marker, migration marker and behavior, cytokine release, and downstream molecule regulation were addressed by flow cytometry, qPCR, and transwell and multiplex assays.

RESULTS: Primed LC mimicked the LC behavior in AD skin, exhibiting desensitization toward TLR2-mediated activation monitored by impaired CD83/CD80/CD86 and MHCII expression as well as impaired regulation of chemokines CCR6 and CCR7, migration competence, and Th17-driving cytokines. IL-18 and IL-1β were elevated under these conditions. Negative regulators of the TLR2 pathway, specifically SOCS1 and IRAKM, were significantly upregulated, whereas activating molecules were hardly affected. JAK inhibitors reduced SOCS1 expression in primed cells and restored activation markers CD83/80/86 and MHCII upon TLR2 engagement, but had no effect on IRAKM expression.

CONCLUSION: Primed LC mimic the impaired LC-responsiveness toward TLR2 in AD skin. Our findings unravel a new direct contribution of LC to AD-associated IL-1β and IL-18 under these conditions and shed light on the mechanistical role of SOCS1 and the mode of action of JAK inhibitors.},
}

@article {pmid40631899,
year = {2025},
author = {Zhao, N and Geng, P and Perez, AG and Maya, AC and Yadav, B and Du, Y and Ge, Y},
title = {Genomic and functional characterization of a Butyricicoccus porcorum strain isolated from human gut microbiota.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0079025},
doi = {10.1128/msystems.00790-25},
pmid = {40631899},
issn = {2379-5077},
abstract = {The gut is the most complex microbial ecosystem in the body that greatly influences human immune and metabolic health. However, the functional understanding of gut microbiome is hampered by our limited ability to obtain bacterial cultures for experimental validation, particularly low-abundant species that may carry specific functions but are often overlooked by population-based analyses. Here, we isolated and characterized a novel strain of Butyricicoccus porcorum (named Bp 531D) from human gut microbiota, representing the first butyrate-producing human isolate within a phylogenetic clade of Butyricicoccus complex. Comparative whole-genome analysis revealed a unique capability of Bp 531D for one-carbon metabolism and a high abundance of mobile genetic elements, including six prophages and plentiful transposons, reflecting its evolutionary flexibility. Oral administration of the bacterium profoundly altered gut microbiome composition in C57BL/6 mice, leading to controlled microbial oxidative signaling and calibrated carbohydrate metabolic function in the gut. RNA sequencing (RNA-seq) analysis demonstrated notable functional programming of colonic ECs, whereupon Bp 531D primarily restricted the biosynthesis of cholesterols and activated the pathway of antigen processing and presentation. Furthermore, the expression of MHC class II was correlatively heightened in colonic dendritic cells (DCs), and the frequencies of interleukin-10- (IL-10) and IL-22-producing T helper 17 (Th17) cells were significantly elevated in mice treated with Bp 531D compared to controls. Our findings uncover the crucial roles of B. porcorum in supporting intestinal homeostasis and provide a novel functional modulator to potentially optimize microbial strategies for improving intestinal health.IMPORTANCEReduced abundance of the Butyricicoccus genus has been associated with human intestinal disorders, including inflammatory bowel diseases. While supplementation of B. pullicaecorum mitigates intestinal inflammation, it is unclear whether other Butyricicoccus species critically contribute to intestinal microbial and immune homeostasis. We identified a novel Butyricicoccus species within human gut microbiota and characterized its detailed intestinal functions using the C57BL/6 mouse model. Our findings may further highlight the genetic and functional diversities of the gut microbiome.},
}

@article {pmid40631880,
year = {2025},
author = {Stanojević, M and Kociszewska-Najman, B and Grünebaum, A and Chervenak, F and Kurjak, A},
title = {Quo vadis neonatologia? Where is neonatology heading in the 21st century?.},
journal = {Journal of perinatal medicine},
volume = {},
number = {},
pages = {},
pmid = {40631880},
issn = {1619-3997},
abstract = {INTRODUCTION: This comprehensive narrative review examines current paradigms, emerging trends, and future directions in neonatology through systematic analysis of contemporary literature, clinical practice patterns, and expert consensus. We synthesized evidence from recent publications, international guidelines, and clinical innovations to identify key transformation areas.

CONTENT: Several critical areas are reshaping neonatology. Gestational age has emerged as a lifelong health determinant with implications extending far beyond the neonatal period, affecting cardiovascular, metabolic, and neurodevelopmental outcomes throughout life. Global disparities in neonatal care remain unconscionably large, with survival rates for 28-week infants exceeding 90 % in high-income countries while similar infants in low-resource settings often die from preventable causes. Artificial intelligence applications are revolutionizing predictive analytics, real-time monitoring, and decision support systems, though implementation requires careful attention to bias, transparency, and human oversight. The neonatal microbiome's crucial role in immune development and long-term health has prompted interventions targeting healthy colonization. Salutogenic approaches emphasizing health promotion rather than disease treatment are gaining recognition. Most significantly, the systematic marginalization of mothers in neonatal care is being challenged, with growing recognition of the mother-infant dyad as the fundamental unit of care.

SUMMARY AND OUTLOOK: Future neonatal care must balance technological advancement with humanistic values, addressing global disparities while maintaining scientific rigor. Success requires committing to global health equity, embracing ethical complexity at viability margins, recognizing maternal centrality, thoughtfully integrating emerging technologies, implementing salutogenic principles, and adopting lifelong health perspectives. The field's future depends on interdisciplinary collaboration, ethical reflection, and unwavering commitment to ensuring every newborn receives compassionate, high-quality care.},
}

@article {pmid40631858,
year = {2025},
author = {Qu, S and Gu, Y and Hou, X and Wei, M and Wang, M and Su, Y and Miao, Y and Yang, J and Sun, Y and Zeng, Z},
title = {Dual associations of gut and oral microbial networks with kidney transplantation.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0025225},
doi = {10.1128/msystems.00252-25},
pmid = {40631858},
issn = {2379-5077},
abstract = {UNLABELLED: Gut and oral microbiomes play an essential role in the occurrence and development of kidney disease, but their changes after kidney transplantation in patients with end-stage renal disease and their relationships with host health remain unclear. Through shotgun metagenomic sequencing of fecal and saliva samples, we found that for both gut and oral microbiome, the initial loss of species diversity after kidney transplantation led to a reduction in network nodes and interactions, but strengthened the connections among the remaining species, which started to get a recovery approximately 7-14 days later. Different network modules tended to exhibit unique functions and showed different responses to transplantation. These network changes were significantly correlated with clinical indicators, especially with estimated glomerular filtration rate, suggesting that microbial networks contributed to regulating kidney function and host health from dual dimensions. Our study provides novel insights into associating microbiomes with patient recovery after kidney transplantation and offers new diagnostic strategies.

IMPORTANCE: Understanding the dynamics of gut and oral microbiomes after kidney transplantation is crucial for improving post-transplant outcomes and managing potential complications. Through shotgun metagenomic sequencing of fecal and saliva samples from patients following kidney transplantation, our study emphasizes that, in addition to focusing on the various microbial species themselves, the topological properties of gut and oral microbial networks are also critically important for kidney function. We aim to explore the relationship between host health and the oral and gut microbiomes following kidney transplantation from an ecological perspective and extend to other diseases to advance the study of the microbiome and its clinical impact.},
}

@article {pmid40631371,
year = {2025},
author = {Billet, LS and Hernández-Gómez, O and Skelly, DK},
title = {Ranavirus Epizootics and Gut Bacteriome Dysbiosis in Tadpoles: Evidence for the Anna Karenina Principle?.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70022},
doi = {10.1111/mec.70022},
pmid = {40631371},
issn = {1365-294X},
support = {//Yale University/ ; //Sigma Xia/ ; //American Museum of Natural History/ ; },
abstract = {The microbiome plays a critical role in animal health, yet its responses to pathogens under natural conditions remain poorly understood. We investigated gut bacterial community (bacteriome) dynamics in wood frog (Rana sylvatica [Lithobates sylvaticus]) tadpoles during natural ranavirus outbreaks to understand how pathogen-induced disturbances shape the bacteriome. Using 16S rRNA sequencing, we compared the bacteriomes of tadpoles in ponds experiencing ranavirus die-offs with those from unaffected ponds before, during and after die-offs. Ranavirus infection significantly altered gut bacteriome composition and increased variability (dispersion), consistent with the Anna Karenina principle. Tadpoles with high infection intensities exhibited reduced bacterial diversity and shifts in community structure, including enrichment of some genera that have been linked previously to antiviral immunity. The predicted functional pathway analyses revealed shifts toward carbohydrate metabolism pathways during die-offs, suggesting microbial adaptation to altered host physiology under infection stress. Some bacteriome changes were detectable even before die-offs occurred, highlighting potential early indicators of infection in the gut bacteriome. In a pond that recovered after an epizootic, we observed partial recovery of some of the bacteria that shifted in relative abundance during the die-off, a pattern that may reflect microbial resilience within hosts, selective survival of tadpoles that never developed severe infections, or a combination of both mechanisms. Our findings demonstrate that ranavirus epizootics disrupt gut bacteriomes in amphibians while simultaneously eliciting potentially adaptive microbial responses. These insights underscore the complex interplay between immunity, microbiome dynamics, and environmental conditions during disease outbreaks, highlighting opportunities for microbiome-based interventions to support amphibian conservation.},
}

@article {pmid40631329,
year = {2025},
author = {Magossi, G and Amat, S},
title = {Optimizing bacteriophage screening and isolation methods for microbial samples derived from different body sites of cattle.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.04.663187},
pmid = {40631329},
issn = {2692-8205},
abstract = {Bacteriophages are gaining increased research attention as alternatives to antibiotics and microbiome manipulation tools to enhance feed efficiency and animal health in cattle. However, challenges associated with phage specificity, microbial ecosystem variations, and the absence of effective screening methods have hindered harnessing the power of phage application in cattle. The objectives of this study were to (i) optimize phage screening method for microbial samples obtained from different cattle body sites, (ii) isolate lytic phages against key bovine pathogens and commensal bacteria, and (iii) characterize the isolated phages and their bacterial hosts. A total of 1,214 samples from different cattle body sites (n = 1194) and environmental sources were screened using 13 phage detection methods, including one high-throughput approach. Eighty-three phages were isolated, primarily from ruminal fluid (59), feces (15), vaginal (7) and nasopharyngeal swabs (1), and fetal ruminal fluid (1). The bacterial hosts inhibited by these phages were from 29 genera, with Bacillus (34), Escherichia/Shigella (8), Shouchella (5), Corynebacterium (4), and Lysinibacillus (4) being the most common. No phages were identified against bovine pathogens including Trueperella pyogenes, Mannheimia haemolytica, Pasteurella multocida, or Moraxella bovis. Method 12 demonstrated the highest efficiency in phage recovery, particularly from ruminal samples. The isolation of phages against commensal bacteria from the gastrointestinal, reproductive, and respiratory tracts, and fetal gut highlights their potential for microbiome modulation to improve cattle health and feed efficiency. These findings underscore the need for further research into pathogen-targeting phage isolation in cattle.},
}

@article {pmid40631287,
year = {2025},
author = {Zuffa, S and Thomas, SP and Mohanty, I and El Abiead, Y and Deleray, V and Kvitne, KE and Kousha, A and Suzuki, E and Tsai, CM and Nguyen, G and Ho, B and Liu, GY and Nizet, V and Dorrestein, PC and Askarian, F and Tsunoda, SM},
title = {Influence of perinatal ampicillin exposure on maternal fecal microbial and metabolic profiles.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.30.662372},
pmid = {40631287},
issn = {2692-8205},
abstract = {UNLABELLED: Indirect exposure to antibiotics during early life, via maternal intrapartum antibiotic prophylaxis (IAP) or postpartum maternal antibiotic usage, is increasingly common and has been epidemiologically linked to altered growth and immune developmental trajectories in offspring. Nevertheless, the underlying mechanisms remain poorly understood. Here, we explored the effects of antepartum and postpartum maternal ampicillin administration on the dams' fecal microbiome and metabolic profiles in vivo . Ampicillin caused a reproducible depletion of beneficial bacterial species belonging to the Muribaculaceae family, including Muribaculum intestinale and Duncaniella dubosii , and led to cohort-dependent enrichments of Enterococcus and Prevotella species. These microbial alterations were accompanied by substantial metabolic remodeling, characterized by elevated fecal acylcarnitines and dysregulation of the bile acids profile. Intriguingly, we identified two previously uncharacterized trihydroxylated bile acids conjugated to a hexose moiety, which appeared to be associated with antibiotic exposure across public metabolomics repositories. These alterations in the fecal maternal microbiome and metabolome coincided with increased weight gain in offspring, suggesting a possible role for maternal antibiotic exposure in shaping early developmental trajectories. Further studies are warranted to elucidate the long-term implications of these changes in infant health.

IMPORTANCE: Perinatal antibiotic administration is a critical intervention to reduce maternal and neonatal infections, including early-onset group B Streptococcus (GBS) disease, a major cause of neonatal mortality. Nevertheless, mounting evidence suggests that the use of broad-spectrum antibiotics during the perinatal period in mothers can affect infant gut microbiome development, with potential consequences for immune maturation and early development. Understanding how maternal antibiotic exposure affects the gut microbiome and metabolome is essential for uncovering the potential pathways by which maternal intervention may influence offspring outcomes and for guiding strategies that balance infection control with long-term infant health.},
}

@article {pmid40631266,
year = {2025},
author = {Villa Soto, VS and Degraeve, AL and Heath, CM and Orellana, DA and Reilly, ER and Mukherjee, M and Brockert, JG and Dumlao, DS and Blank, RB and Perlmutter, N and Yu, S and Ashouri, J and Scher, JU and Patterson, AD and Turnbaugh, PJ and Nayak, RR},
title = {The gut microbiome shapes pharmacology and treatment outcomes for a key anti-inflammatory therapy.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.26.661733},
pmid = {40631266},
issn = {2692-8205},
abstract = {UNLABELLED: The human gut microbiome encodes a formidable metabolic repertoire that harvests nutrients from the diet, but these same pathways may also metabolize medications. Indeed, large screens have revealed extensive microbial metabolism of drugs in vitro , but the pharmacologic and clinical repercussions of microbiota-mediated metabolism in vivo remain to be discerned. As a proof-of-concept, we investigate how human gut microbes contribute to in vivo pharmacology and efficacy of a key anti-inflammatory drug, methotrexate (MTX). Specifically, we demonstrate that the gut microbiome shapes drug pharmacology in vivo in mice, both by directly metabolizing the drug and by inducing host pathways that promote drug metabolism. Moreover, interindividual variation in the human gut microbiome contributes to variation in pharmacokinetic (PK) profiles. When we quantified metabolites produced by microbes, we unexpectedly identified novel MTX metabolites, one of which, p-methylaminobenzoyl-L-glutamic acid (pMABG), was a major byproduct of microbial metabolism both in vitro and in vivo . Further, we find that a large proportion of patient-associated microbes are capable of metabolizing MTX. Finally, we show that microbial metabolism of MTX is linked to PK profiles and disease outcomes in a mouse model of inflammatory arthritis. Taken together, these findings provide evidence that the human gut microbiome causally contributes to drug pharmacology in vivo for a key anti-inflammatory drug through known and novel mechanisms. Our studies provide a framework for elucidating the clinical relevance of drug microbial metabolism in the context of treatment response. These results are a first step towards understanding and manipulating the human gut microbiome in the treatment of autoimmunity and the advancement of precision medicine for millions of patients taking MTX for immune or inflammatory conditions.

HIGHLIGHTS: The gut microbiome impacts methotrexate (MTX) pharmacology in miceThe human gut microbiome contributes to interindividual variation in MTX pharmacologyHuman gut microbes produce novel MTX metabolites, pMABG and 6-MPDAMicrobial metabolism of MTX is linked to treatment outcomes.},
}

@article {pmid40631202,
year = {2025},
author = {Palmer, SN and Mishra, A and Gan, S and Liu, D and Koh, AY and Zhan, X},
title = {Identifying Optimal Machine Learning Approaches for Microbiome-Metabolomics Integration with Stable Feature Selection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.21.660858},
pmid = {40631202},
issn = {2692-8205},
abstract = {Microbiome research has been limited by methodological inconsistencies. Taxonomy-based profiling presents challenges such as data sparsity, variable taxonomic resolution, and the reliance on DNA-based profiling, which provides limited functional insight. Multi-omics integration has emerged as a promising approach to link microbiome composition with function. However, the lack of standardized methodologies and inconsistencies in machine learning strategies has hindered reproducibility. Additionally, while machine learning can be used to identify key microbial and metabolic features, the stability of feature selection across models and data types remains underexplored, despite its importance for downstream experimental validation and biomarker discovery. Here, we systematically compare Elastic Net, Random Forest, and XGBoost across five multi-omics integration strategies: Concatenation, Averaged Stacking, Weighted Non-negative Least Squares (NNLS), Lasso Stacking, and Partial Least Squares (PLS), as well as individual 'omics models. We evaluate performance across 588 binary and 735 continuous models using microbiome-derived metabolomics and taxonomic data. Additionally, we assess the impact of feature reduction on model performance and feature selection stability. Among the approaches tested, Random Forest combined with NNLS yielded the highest overall performance across diverse datasets. Tree-based methods also demonstrated consistent feature selection across data types and dimensionalities. These results demonstrate how integration strategies, algorithm selection, data dimensionality, and response type impact both predictive performance and the stability of selected features in multi-omics microbiome modeling.},
}

@article {pmid40631189,
year = {2025},
author = {Shahmohamadloo, RS and Gabidulin, AR and Andrews, ER and Rudman, SM},
title = {Microbiome evolution plays a secondary role in host rapid adaptation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.27.661976},
pmid = {40631189},
issn = {2692-8205},
abstract = {UNLABELLED: Understanding how populations adapt to environmental change is a central goal in evolutionary biology. Microbiomes have been proposed as a source of heritable variation that is central to rapid adaptation in hosts, yet empirical evidence supporting this remains limited, particularly in naturalistic settings. We combined a field evolution experiment in Drosophila melanogaster exposed to an insecticide with microbiome manipulations to disentangle the contributions of host standing genetic variation and microbiome evolution to adaptation. Within three generations, independent populations rapidly and repeatedly evolved increased survivorship, a defining feature of resistance evolution. Adaptive changes in sub-lethal traits such as reproductive output, stress tolerance, and body size occurred with a delayed response following the evolution of resistance. Core microbiome taxa declined following insecticide exposure, and resistant populations evolved to house lower microbial abundances. Axenic rearing and microbiome transplant experiments demonstrated that adaptation via host standing genetic variation was the mechanism for resistance evolution. Microbiome evolution played a secondary and cryptic role in host adaptation by masking slowed development rates that evolved in resistant populations. Together, these results reinforce the primacy of adaptation occurring through selection on host standing genetic variation while also demonstrating the contributions of microbiome evolution in host adaptation.

SIGNIFICANCE: Identifying the mechanisms that allow organisms to adapt to environmental stress is a foundational goal in biology. Using field experimental evolution and microbiome manipulations in Drosophila melanogaster , we directly tested the relative contributions of host genomic evolution and microbiome evolution to adaptation. We found that adaptation to environmental stress occurred rapidly and repeatedly, driven primarily by selection on host standing genetic variation, with microbiome evolution acting as a secondary contributor. These findings reinforce the importance of host genetic variation in rapid adaptation and demonstrate that microbiome evolution can contribute to host evolutionary trajectories in a cryptic manner.},
}

@article {pmid40630933,
year = {2025},
author = {Takács, B and Jaksa, G and Qorri, E and Gyuris, Z and Pintér, L and Haracska, L},
title = {Advancing metagenomic classification with NABAS+: a novel alignment-based approach.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {3},
pages = {lqaf092},
pmid = {40630933},
issn = {2631-9268},
mesh = {Humans ; *Metagenomics/methods ; Algorithms ; *Software ; *Sequence Alignment/methods ; *Metagenome ; Microbiota/genetics ; },
abstract = {Microbiome research has expanded rapidly in the last decade due to advances in sequencing technology, resulting in larger and more complex data. This has also led to the development of a plethora of metagenomic classifiers applying different algorithmic principles to classify microorganisms. However, accurate metagenomic classification remains challenging due to false positives and the need for dataset-specific tuning, limiting the comparability of distinct studies and clinical use. In this study, we demonstrate the discrepancy between current, commonly used classifiers and propose a novel classifier, NABAS+ (Novel Alignment-based Biome Analyzing Software+). NABAS+ uses BWA (Burrows-Wheeler aligner) alignment with strict RefSeq curation to ensure one reliable genome per species and filters for genomes with only high-quality reads for precise species-level identification from Illumina shotgun data. The performance of our algorithm and three commonly used classifiers was evaluated on in silico datasets modelling human gastrooral communities, as well as on deeply sequenced microbial community standards. Additionally, we illustrated the usefulness of NABAS+ in detecting pathogens in real-world clinical data. Our results show that NABAS+, due to its extensive alignment process, is superior in accuracy and sensitivity compared to leading microbiome classifiers, particularly in reducing false positives in deep-sequenced microbial samples, making it suitable for clinical diagnosis.},
}

Humans
*Metagenomics/methods
Algorithms
*Software
*Sequence Alignment/methods
*Metagenome
Microbiota/genetics

@article {pmid40630297,
year = {2025},
author = {Hellman, T and Yeo, LF and Palmu, J and Havulinna, A and Jousilahti, P and Laitinen, V and Pärnänen, K and Salomaa, V and Lahti, L and Knight, R and Niiranen, T},
title = {Gut Microbiome as a Risk Factor for Future CKD.},
journal = {Kidney international reports},
volume = {10},
number = {6},
pages = {1673-1682},
pmid = {40630297},
issn = {2468-0249},
abstract = {INTRODUCTION: Gut microbiome has been linked with chronic kidney disease (CKD) in several small cross-sectional studies. However, the relationship between baseline gut microbiome and long-term incident CKD remains unknown.

METHODS: We performed fecal sampling and measured serum creatinine (SCR) (N = 6699) and urine albumin-to-creatinine ratio (UACR) (N = 797) in a population-based cohort examined in the year 2002. We assessed the multivariable-adjusted associations of gut metagenome with baseline SCR, baseline UACR, and register-based incident CKD.

RESULTS: The mean age of the participants was 49.5 ± 12.9 years and 45.8% were men. During a median follow-up of 18.6 years, 108 participants developed incident CKD. In prospective analyses, increased baseline gut microbiome alpha diversity was associated with lower risk of incident CKD (hazard ratio per 1 SD: 0.84; 95% confidence interval [CI]: 0.71-0.99; P = 0.04). Gut microbial beta diversity and taxa were not related to incident CKD (P ≥ 0.09 for all). In cross-sectional analyses, alpha diversity (beta per 1 SD: 1.28; 95% CI: 0.64-1.98; P < 0.001) and beta diversity (P = 0.002; R[2] = 0.12%) were associated with SCR, whereas no associations were observed for UACR. In total, 43 significant species-level associations with SCR were observed and 16 negative associations (37.2%) for species belonging to the Lachnospiraceae family.

CONCLUSION: Our results suggest that decreased gut microbial diversity may be related to risk of future CKD and that a potential link between the Lachnospiraceae family and desirable kidney health exists. Our results extend previous cross-sectional studies and help to establish the basis for examining gut microbiome as a CKD risk factor.},
}

@article {pmid40630283,
year = {2025},
author = {Ness, C and Svistounov, D and Solbu, MD and Petrenya, N and Boardman, N and Ytrehus, K and Jenssen, TG and Holmes, A and Simpson, SJ and Zykova, SN},
title = {Gut Microbiome Diversity and Uric Acid in Serum and Urine.},
journal = {Kidney international reports},
volume = {10},
number = {6},
pages = {1683-1693},
pmid = {40630283},
issn = {2468-0249},
abstract = {INTRODUCTION: An increasing body of evidence has shown the importance of the gut microbiota in modulating serum uric acid (SUA) levels. In this study, we aimed to determine the association between gut microbiome diversity, diet, SUA, and fractional excretion of uric acid (FEUA) in the kidney.

METHODS: A cross-sectional study was conducted in 53 adults with normal or elevated SUA and estimated glomerular filtration rate (eGFR) range from 37 to 124 ml/min per 1.73 m[2]. Fecal microbiome composition was analyzed using 16S ribosomal RNA sequencing; and alpha diversity was expressed as reverse Simpson, Shannon, and Richness indices. Dietary data were collected, and dietary patterns were identified using principal component analysis. Unadjusted linear regression and models adjusted for sex, waist-hip ratio (WHR), and eGFR were used to study the association between gut microbial diversity, dietary pattern scores, and SUA/FEUA.

RESULTS: Shannon index was negatively associated with SUA after multiple adjustment (β -36.4, 95% CI [-66.2 to -6.7], P = 0.017; adjusted R[2] = 0.62, P < 0.001). Sex (standardized β = 0.52) and WHR (standardized β = 0.35) had the highest effect on SUA, followed by Shannon diversity index (standardized β = -0.22). We found that Shannon index (standardized β = 0.49, P < 0.001) was positively associated with FEUA after adjustment for sex and "sweet" dietary pattern. This model explained 40% of the variability in FEUA (P < 0.001). None of the dietary patterns were associated with SUA or FEUA.

CONCLUSION: A higher gut microbial diversity was associated with lower SUA and more efficient elimination of uric acid by the kidneys. There is a need for studies assessing efficacy and safety of interventions on the gut microbiome as a treatment of hyperuricemia.},
}

@article {pmid40630189,
year = {2025},
author = {Zhang, YF and Qin, YT and Liu, ZY and Zheng, HR and Hu, XD and Wang, XL},
title = {Diversity of endophytic bacteria in mulberry (Morus spp.) scions with different genetic resources.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1618773},
pmid = {40630189},
issn = {1664-302X},
abstract = {Endophytic bacteria in plants play crucial roles in promoting plant growth, facilitating nutrient acquisition, and enhancing stress tolerance. Although many studies have recently investigated endophytic bacteria in plants, the characteristics of endophytic bacterial communities in germplasm resource populations have rarely been reported. In this study, we investigated the endophytic bacterial communities of 21 mulberry scions, representing both wild and cultivated resources, all grafted onto a common rootstock and grown under identical cultivation conditions. High-throughput sequencing of 16S rRNA amplicons was performed using the Illumina MiSeq platform. The results revealed a total of 10 phyla, 31 classes, 50 orders, 50 families, and 113 genera of endophytic bacteria in the mulberry scions. The dominant phylum was Proteobacteria (89.07%), followed by Firmicutes (5.20%) and Actinobacteria (3.10%). At the genus level, Sphingomonas (32.84%), Methylobacterium-Methylorubrum (18.64%), and Aureimonas (8.76%) were the predominant genera enriched in the scion. Wild scions exhibited more complex endophytic bacterial communities compared to cultivated scions. Among the wild germplasm, XZBS and XZMK, originating from Tibet, China, displayed distinctive Actinobacteria signatures, suggesting a potential legacy of primitive geographic adaptation. Co-occurrence network analysis indicated that Sphingomonas and Methylobacterium-Methylorubrum acted as keystone taxa, forming critical bridges within the endophytic bacterial community network in the scions. Functional predictions further indicated that endophytic bacteria from wild species showed a greater metabolic capacity for aromatic compounds, amino acids, and carbohydrates compared with those from cultivated species. Moreover, analyses of the mulberry genetic population structure and endophytic bacterial community composition suggested that differentiation between wild and cultivated resources was associated with differences in endophytic bacterial communities. This study provides new insights into the diversity of endophytic bacteria among different mulberry germplasm resources and highlights geographically unique taxa, advancing our understanding of microbiome-driven adaptation in perennial grafted plants. It also offers a valuable reference for the future utilization of functional endophytic bacteria in mulberry improvement.},
}

@article {pmid40629992,
year = {2025},
author = {Saidu, MB and Moreira, IS and Amorim, CL and Wu, R and Ho, YW and Fang, JK and Castro, PML and Gonçalves, D},
title = {Exploring the biodegradation of PET in mangrove soil and its intermediates by enriched bacterial consortia.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-23},
doi = {10.1080/09593330.2025.2521762},
pmid = {40629992},
issn = {1479-487X},
abstract = {The biodegradation of Polyethylene terephthalate (PET) is important due to the environmental impact of plastic waste. This study investigates the degradation of PET films in soil microcosms, with and without mangrove plants, and with mangrove plants bioaugmented with a bacterial consortium (Bacillus sp.- GPB12 and Enterococcus sp.- WTP31B-5) while following the evolution of soil microcosm microbiome. The ability of bacterial consortia retrieved from soil microcosms of each tested condition to degrade PET intermediates - bis(2-hydroxyethyl) terephthalate (BHET), terephthalic acid (TPA), and monoethylene glycol (MEG) was also assessed. In the microcosms' assays with mangrove plants, variations in functional groups and surface morphology detected by FTIR and SEM analysis indicated PET degradation. Soil microcosms microbiome evolved differently according to the conditions imposed, with dominance of phylum Proteobacteria in all final microcosms. After 270 days, bacterial consortia retrieved from all soil microcosms revealed to be able to completely degrade TPA within three days. MEG degradation reached ca. 84% using the consortium retrieved from the microcosm with bioaugmented mangrove plants. BHETdegradation was ca. 96% with the consortium obtained from the microcosm with non-bioaugmented mangrove plants. These intermediates are key molecules in PET degradation pathways; thus, their degradation is an indicator of biodegradation potential. To the best of authors' knowledge, this is the first report on biodegradation of PET, BHET, TPA, and MEG by microbial community from mangrove soil, providing insights into key taxa involved in PET degradation. These findings can pave a way to develop bioremediation strategies and more efficient waste management solutions.},
}

@article {pmid40629974,
year = {2025},
author = {Haenel, A and Grzybowski, T and Skonieczna, K},
title = {Oral microbiome dynamics in Postmortem Interval estimation: research standards and guidelines.},
journal = {Archiwum medycyny sadowej i kryminologii},
volume = {75},
number = {1},
pages = {48-55},
doi = {10.4467/16891716AMSIK.25.004.21539},
pmid = {40629974},
issn = {1689-1716},
mesh = {Humans ; *Postmortem Changes ; *Mouth/microbiology ; *Microbiota ; Forensic Medicine ; },
abstract = {Determination of the postmortem interval (PMI) is a crucial aspect of forensic investigations as it verifies an alibi or narrows down suspects. Nevertheless, PMI estimation remains one of the most challenging problems in forensic science. Currently used methods are influenced by various biotic and abiotic factors affecting decomposition. Thus, determining the time of death largely depends on the skills and experience of the forensic experts. Consequently, currently used procedures are prone to inaccuracies. Lately, gut microbiome analysis has proven useful in determining the time of death. Furthermore, emerging evidence indicates that profiling the oral microbiome may also provide valuable insights into PMI estimation. In this review, we examine published reports on oral microbiome and highlight the methodological limitations that diminish their scientific value. Therefore, we summarize the research standards and guidelines for oral microbiome studies to enhance the accuracy and reproducibility of PMI studies. Consequently, standardization of this type of research could lead to the development of innovative approaches that may be implemented into routine forensic genetics practice.},
}

Humans
*Postmortem Changes
*Mouth/microbiology
*Microbiota
Forensic Medicine

@article {pmid40629894,
year = {2025},
author = {Dong, Y and Yan, G and Zhang, Y and Zhou, Y and Shang, J},
title = {Gut microbiota as a predictive tool for outcomes in IgA nephropathy.},
journal = {Renal failure},
volume = {47},
number = {1},
pages = {2514184},
doi = {10.1080/0886022X.2025.2514184},
pmid = {40629894},
issn = {1525-6049},
mesh = {Humans ; *Glomerulonephritis, IGA/microbiology/drug therapy/therapy/pathology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Adult ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Middle Aged ; *Dysbiosis/microbiology ; Treatment Outcome ; Disease Progression ; },
abstract = {Immunoglobulin A nephropathy (IgAN) is characterized by the deposition of glycosylation-deficient IgA1 in the glomeruli and has been linked to the gut-kidney axis. This study aimed to determine if baseline differences in gut microbiota could predict therapeutic responses in IgAN patients. We analyzed fecal microbiomes of 55 biopsy-confirmed IgAN patients and followed them for over 6 months. Patients were classified as responders (n = 39) or nonresponders (n = 16) based on remission status. Fecal microbiomes were profiled using 16S rRNA sequencing, revealing significant microbiota differences. Nonresponders had increased Proteobacteria and Firmicutes, with notable enrichment of opportunistic bacteria like Escherichia-Shigella and Pseudomonas. A predictive classifier based on 24 amplicon sequence variants, with Escherichia-Shigella and Pseudomonas as key contributors, showed high accuracy in identifying nonresponders (AUC 0.9103, p < 0.0001). These findings highlight the role of microbial dysbiosis in IgAN progression and treatment response, suggesting that gut microbiota analysis could guide personalized therapy for IgAN. Future studies with larger cohorts are needed to validate these results and explore microbiome-based treatments.},
}

Humans
*Glomerulonephritis, IGA/microbiology/drug therapy/therapy/pathology
*Gastrointestinal Microbiome/genetics
Male
Female
Adult
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Middle Aged
*Dysbiosis/microbiology
Treatment Outcome
Disease Progression

@article {pmid40629699,
year = {2025},
author = {Yuan, Y and Qian, XC and Chen, SM and Zhang, LL and Chen, TM and Ding, C and Liu, WZ and Chen, F and Wang, AJ},
title = {Alternating Current-Driven Bioredox Cycling Achieves in Situ Deep Mineralization of Nitroaromatic Pollutants in Sediments.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c11329},
pmid = {40629699},
issn = {1520-5851},
abstract = {Nitroaromatic compound (NAC)-contaminated sediments pose threats to aquatic ecosystems. The challenges of low mass transfer in sediments and the recalcitrance of NACs to degradation limit the effectiveness of conventional bioremediation techniques. This study demonstrates the potential of alternating current (AC)-driven bioredox cycling to overcome these barriers by coupling in situ reduction-oxidation processes. We report the successful application of AC stimulation in achieving the mineralization of nitrobenzene (NB) while elucidating its role in modulating bioredox dynamics, electron transfer, and electromicrobiome function. Sine-wave AC stimulation achieved an 87.7% reduction of NB and 90.3% mineralization of its intermediates. The AC stimulation promoted robust biofilm formation, enhanced bidirectional electrocatalytic activity, and increased microbial biomass. It also enriched a diverse microbial consortium capable of reducing NB, oxidizing aromatic intermediates, and facilitating electron transfer, as indicated by the upregulation of key enzymatic genes through multiomics analyses. Carbon metabolites from catechol meta-cleavage further supported nitro-reduction and sustained microbial viability. Compared to DC processes, AC-driven bioredox cycling reduced energy consumption by 16.8% in the remediation of NB-contaminated sediments. This approach offers a sustainable, low-carbon solution for efficient in situ biomineralization of NACs in sediments.},
}

@article {pmid40629635,
year = {2025},
author = {Zeng, B and Ren, X and Cheng, Y and Wang, C and Li, J and Jiang, L and Zhang, S and Chen, S and Yu, D and Lin, J},
title = {Correlation analysis between vaginal microecology and high-risk human papillomavirus (HR-HPV)-positive cervical squamous intraepithelial lesions (SIL).},
journal = {Medicine},
volume = {104},
number = {27},
pages = {e42914},
doi = {10.1097/MD.0000000000042914},
pmid = {40629635},
issn = {1536-5964},
mesh = {Humans ; Female ; Adult ; *Papillomavirus Infections/virology/complications/epidemiology ; *Vagina/microbiology/virology ; Middle Aged ; Risk Factors ; *Squamous Intraepithelial Lesions of the Cervix/virology/microbiology/pathology ; *Squamous Intraepithelial Lesions/virology/pathology/microbiology ; *Uterine Cervical Neoplasms/virology/pathology ; Papillomaviridae/isolation & purification ; *Uterine Cervical Dysplasia/virology ; Human Papillomavirus Viruses ; },
abstract = {This study is aimed to investigate the correlation between vaginal microecology and high-risk human papillomavirus (HR-HPV)-positive cervical squamous intraepithelial lesions (SIL) using the regression analysis. Patients (n = 372) with HR-HPV-positive from January 2020 to June 2022 were recruited after preliminary confirmation by colposcopy, HPV test, and typing, as well as loop electrosurgical excision procedure. Based on the pathological results, the recruited subjects were divided into 3 groups, that is, negative for intraepithelial lesion or malignancy, low-grade SIL, and high-grade SIL (HSIL). Finally, the clinical factors, virological data, and vaginal microecological changes of the 3 experimental groups were analyzed. Age was identified as a significant risk factor for HSIL, with an OR of 1.048 (95% CI: 1.006-1.094 and P = .026). Various HR-HPV types (HPV16, HPV18, and HPV52) were closely associated with HSIL, with multiple infections significantly increasing the risk (odds ratio, OR: 5.810, P = .04). The changes in the vaginal microecology were strongly associated with HSIL, including elevated pH (>4.5), reduced hydrogen peroxide levels, and increased bacterial vaginosis (BV) prevalence. BV demonstrated a sensitivity of 66.10% and a specificity of 70.31% for predicting HSIL. Furthermore, decreased Lactobacillus levels (OR: 3.20, P < .001) showed their protective role, while elevated sialidase activity (OR: 5.610, P = .002) emerged as a significant risk factor. Accordingly, the key independent predictors for low-grade SIL and HSIL included age, infection type, pH, microbiome density, BV, and sialidase activity. The mixed infection of HPV16, HPV18, HPV52, and HPV resulting in cervical SILs could be closely related to the vaginal microecology.},
}

Humans
Female
Adult
*Papillomavirus Infections/virology/complications/epidemiology
*Vagina/microbiology/virology
Middle Aged
Risk Factors
*Squamous Intraepithelial Lesions of the Cervix/virology/microbiology/pathology
*Squamous Intraepithelial Lesions/virology/pathology/microbiology
*Uterine Cervical Neoplasms/virology/pathology
Papillomaviridae/isolation & purification
*Uterine Cervical Dysplasia/virology
Human Papillomavirus Viruses

@article {pmid40629482,
year = {2025},
author = {Tretiak, S and Mendes Maia, T and Ducatelle, R and Cherlet, M and Rijsselaere, T and Van Immerseel, F and Impens, F and Antonissen, G},
title = {Proteomic profiling of dysbiosis-challenged broilers reveals potential blood biomarkers for intestinal health.},
journal = {Veterinary research},
volume = {56},
number = {1},
pages = {143},
pmid = {40629482},
issn = {1297-9716},
support = {Baekeland Mandate HBC.2020.2274//VLAIO/ ; BOF/STA/202209/011//Ghent University Concerted Research Action grant/ ; BOF21/GOA/033//Ghent University Concerted Research Action grant/ ; },
mesh = {Animals ; *Chickens/blood ; Biomarkers/blood ; *Dysbiosis/veterinary/microbiology/blood ; Proteomics ; *Gastrointestinal Microbiome ; *Poultry Diseases/microbiology/blood ; *Intestines/microbiology ; *Proteome ; },
abstract = {The intestinal microbiome forms a dynamic ecosystem whose balanced composition and functioning are essential for maintaining overall gut health and well-being in living organisms. In broilers, dysbiosis disrupts the microbiota-host balance, often without obvious clinical symptoms but with intestinal inflammation, and leads to impaired animal performance. This study aimed to identify host blood-based protein biomarkers that indicate intestinal inflammation and intestinal barrier dysfunction. Using mass spectrometry-based proteomics, blood plasma samples from broilers derived from an in vivo dysbiosis model were analyzed and compared to healthy controls. Microscopic histologic changes in the gut (shortened villi, increased crypt depth) were observed in the duodenal and jejunal tissue of 25-days old challenged birds. Elevated levels of permeability markers faecal ovotransferrin and serum iohexol additionally indicated increased intestinal leakage in the challenged group. The blood plasma proteome analysis enabled quantification of 388 proteins, 25 of which were significantly different between the tested groups. The challenge was marked by activation of immune and signaling pathways, and response to bacteria, while proteins related to cellular physiology, cell-cell communication, and extracellular matrix (ECM) processes were suppressed. Protein-protein interaction analysis revealed two clusters of downregulated proteins involved in ECM organization and cell adhesion. Intestinal dysbiosis in broilers demonstrated that the host prioritizes immune defense over structural maintenance. The activation of immune processes and suppression of ECM pathways highlight potential biomarkers and therapeutic targets. Data are available via ProteomeXchange with identifier PXD056546.},
}

Animals
*Chickens/blood
Biomarkers/blood
*Dysbiosis/veterinary/microbiology/blood
Proteomics
*Gastrointestinal Microbiome
*Poultry Diseases/microbiology/blood
*Intestines/microbiology
*Proteome

@article {pmid40629442,
year = {2025},
author = {Matson, AP and Unterhauser, K and Rezaul, K and Lesmes, S and Zhou, Y and Michelow, IC and Hussain, N and Driscoll, MD},
title = {Source-tracking Klebsiella outbreaks in premature infants using a novel amplicon fingerprinting method.},
journal = {Antimicrobial resistance and infection control},
volume = {14},
number = {1},
pages = {83},
pmid = {40629442},
issn = {2047-2994},
mesh = {Humans ; Infant, Premature ; *Klebsiella Infections/epidemiology/microbiology ; Infant, Newborn ; Intensive Care Units, Neonatal ; *Klebsiella/genetics/classification/isolation & purification ; *Disease Outbreaks ; Feces/microbiology ; Female ; *Cross Infection/microbiology/epidemiology ; Male ; Milk, Human/microbiology ; Sepsis/microbiology/epidemiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Even with state-of-the-art infection control practices, premature infants can develop life-threatening infections in the neonatal intensive care unit (NICU). The precise sources of most NICU-associated infections frequently remain unknown and, therefore, are difficult to address. In this study, we used a novel microbiome sequencing approach to source-track lethal sepsis-causing Klebsiella, opportunistic pathogens, and commensal bacterial strains colonizing the gut of hospitalized premature infants.

METHODS: An exploratory-methods, case series was at performed Connecticut Children's Medical Center NICU in 2021. Long-read 16-23 S rRNA gene sequencing was used to analyze fecal samples, mother's milk, and clinical bacterial isolates derived from a cluster of Klebsiella-infected, and concurrently hospitalized non-infected, premature infants who were simultaneously enrolled in a neonatal microbiome study. Distinct groups of amplicons comprising a unique fingerprint pattern for a given strain were compared among the samples to ascertain relatedness.

RESULTS: We confirmed 100% amplicon identity between lethal Klebsiella quasipneumoniae from milk, gut, blood and trachea during sepsis in twins, while differentiating other infecting and colonizing Klebsiella strains in concurrently hospitalized premature infants. The method also successfully discriminated between multiple Klebsiella strains within the gut microbiota of a non-infected infant. Additionally, we showed that human milk is the source of many early intestinal colonizers, including Klebsiella, Enterococcus, Veillonella, and Bifidobacterium strains.

CONCLUSIONS: Amplicon fingerprinting can be utilized as a high-throughput high-resolution test to assist in the investigation of nosocomial outbreaks. Additional applications such as routine monitoring of various reservoirs for potential pathogens could inform infection prevention and control strategies in the NICU.},
}

Humans
Infant, Premature
*Klebsiella Infections/epidemiology/microbiology
Infant, Newborn
Intensive Care Units, Neonatal
*Klebsiella/genetics/classification/isolation & purification
*Disease Outbreaks
Feces/microbiology
Female
*Cross Infection/microbiology/epidemiology
Male
Milk, Human/microbiology
Sepsis/microbiology/epidemiology
RNA, Ribosomal, 16S/genetics

@article {pmid40629427,
year = {2025},
author = {Bell, AG and Vaughan, ER and Kasprzyk-Hordern, B and Cable, J and Temperton, B and Tyler, CR},
title = {Impacts of environmentally relevant concentrations of antibiotic cocktails on the skin microbiome of Eurasian carp (Cyprinus carpio).},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {73},
pmid = {40629427},
issn = {2524-4671},
support = {NE/R011524/1//Natural Environment Research Council/ ; NE/R011524/1//Natural Environment Research Council/ ; CGR/SD6387//NERC Environmental Bioinformatics Centre/ ; },
abstract = {BACKGROUND: The skin surfaces of fish harbour diverse assemblages of microbes (microbiomes) that play critical roles in host health and disruption of these microbiomes can lead to disease conditions. Antibiotics, widely used in medicine for human and animal health treatments, are increasingly found in waterways and this is a growing concern due to their potential to alter the balance of microbial ecosystems and drive antimicrobial resistance (AMR). The effects of antibiotics on skin microbiomes in fish, however, have been little explored. This study examines how exposure to environmental levels of antibiotics affects the skin microbiomes of Eurasian carp (Cyprinus carpio).

RESULTS: A 2-week exposure of Eurasian carp to cocktails of five antibiotics (ciprofloxacin, clarithromycin, sulfamethoxazole, trimethoprim, and tetracycline) at concentrations found in the environment resulted in significant skin bacterial community compositional shifts. Applying 16S rRNA amplicon sequencing, we found enrichment of the genus Arcicella (Proteobacteria) and depletion of Sphaerotilus (Bacteroidetes) with limited recovery even after maintaining the fish for a further two weeks in clean (antibiotic-free) water. In the low-antibiotic concentration exposure group, the tank water microbiome assemblages resembled those of the fish skin suggesting similar responses to the antibiotic treatments. Metagenomic analysis observed no increase in antibiotic resistance genes or changes in metabolic pathway abundance, possibly due to the relatively short duration of antibiotic exposure.

CONCLUSION: This study highlights that even low-level exposure to chemical mixtures can alter fish skin microbiome compositions, with limited recovery observed after cessation of exposure. These findings warrant further assessments of the long-term effects and functional consequences of these altered microbiomes on fish health, particularly in environments increasingly affected by anthropogenic chemical pollution.},
}

@article {pmid40611897,
year = {2025},
author = {Fletcher, JR and Hunter, RC},
title = {Cross-feeding interactions between Fusobacterium nucleatum and the glycan forager Segatella oris.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40611897},
issn = {2692-8205},
abstract = {Fusobacterium nucleatum is a common member of the oral microbiota frequently associated with extraoral infections and diverse polymicrobial environments, including chronic airway diseases and colorectal tumors. Yet, its interactions with co-colonizing microbiota remain poorly defined. Here, we investigate cross-feeding interspecies dynamics between F. nucleatum and Segatella oris, a glycan-foraging anaerobe enriched in airways and gastrointestinal tumors. Using broth cultures, cell-free supernatants, and co-culture on primary human airway epithelial cells, we identify bidirectional interactions that shape nutrient acquisition, biofilm formation, gene expression, and host responses. While mucin or S. oris supernatants modestly enhanced F. nucleatum growth, both conditions triggered transcriptional remodeling, including induction of the nan operon for sialic acid catabolism, suggesting reliance on glycan degradation by S. oris. Conversely, S. oris exhibited differential expression of multiple polysaccharide utilization loci (PULs) when exposed to F. nucleatum or its metabolites. Biofilm formation by F. nucleatum was strongly inhibited by S. oris, indicative of antagonistic interactions. Dual and triple RNA-seq revealed that epithelial responses were predominately shaped by F. nucleatum, with enrichment of inflammatory and cancer-associated pathways; however, co-colonization with S. oris modulated the magnitude and specificity of host gene expression. These findings demonstrate that glycan-mediated cross-feeding and microbial interactions shape the physiology and pathogenic potential of F. nucleatum in mucosal environments. This work underscores the importance of modeling polymicrobial communities under host-relevant conditions to better understand pathobiont behavior at the epithelial interface.},
}

@article {pmid40451181,
year = {2025},
author = {Okumura, T and Hiraiwa, H and Yanagisawa, S and Murohara, T},
title = {The Gut-Heart Axis in Heart Failure: Emerging Evidence and Therapeutic Implications.},
journal = {Cardiology},
volume = {},
number = {},
pages = {1-3},
doi = {10.1159/000546542},
pmid = {40451181},
issn = {1421-9751},
}

@article {pmid40629403,
year = {2025},
author = {Somodi, C and Dora, D and Horváth, M and Szegvari, G and Lohinai, Z},
title = {Gut microbiome changes and cancer immunotherapy outcomes associated with dietary interventions: a systematic review of preclinical and clinical evidence.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {756},
pmid = {40629403},
issn = {1479-5876},
support = {#146775//Nemzeti Kutatási, Fejlesztési és Innovaciós Alap/ ; #142287//Nemzeti Kutatási, Fejlesztési és Innovaciós Alap/ ; Bolyai Research Scholarship//Magyar Tudományos Akadémia/ ; },
abstract = {INTRODUCTION: Cancer patient's survival has gradually improved due to immune checkpoint inhibitors (ICIs). Several studies showed a possible association between the intestinal microbiome and ICI efficacy. Strategies for modifying the composition of the gut microbiome encompass various dietary interventions, which may have distinct impacts on the outcomes of ICI-treated patients. In our systematic review, we explored how dietary habits correlate with therapeutic responses in cancer patients and cancer mouse models undergoing immunotherapy.

METHODS: A systematic review was conducted using search terms: "cancer", "immunotherapy", "diet", and "microbiome", from Medline, Web of Science, Scopus, and Cochrane Library databases. The outcomes in the clinical studies were overall response rate (ORR), overall survival (OS), or progression-free survival (PFS) in human studies. In mouse studies, change in tumor size was the endpoint. The comparator attributions were questionnaire-based dietary interventions.

RESULTS: Nineteen articles met the inclusion criteria and were included in the review (6 prospective cohort studies, 1 cross-sectional observational study, and 12 mouse studies). A consistent association was observed between high (vs. low) fiber consumption and improved therapeutic response with a pooled odds ratio of 5.79 when including all human prospective cohort studies. In mice, limited availability of methionine, cysteine, and low intake of leucine and glutamine was linked to reduced tumor progression. Combining ICIs with intermittent fasting or a fasting-mimicking diet significantly decreased tumor volume in mouse melanoma models. In humans, a higher relative abundance of short-chain fatty acid (SCFA) and lactic acid-producing bacteria-particularly Faecalibacterium prausnitzii and Akkermansia muciniphila-correlated with objective response rates (ORR). Similar microbiome alterations were observed in mouse models. Increased fiber intake enhanced ICI efficacy in mice by modulating the gut microbiome, primarily via elevated SCFA production-an effect also reflected in human studies.

CONCLUSION: Intermittent fasting, high fiber, and low sugar consumption are significantly associated with better ICI outcomes. The studies revealed alterations in microbiota composition linked to diet, and these findings were confirmed in animal models, regarding the production of SCFAs and lactic acid, as well as an increase in Bacteroidota/Bacillota ratio and microbial diversity.},
}

@article {pmid40629382,
year = {2025},
author = {Song, JX and Scales, BS and Nguyen, M and Westberg, E and Witalis, B and Urban-Malinga, B and Oberbeckmann, S},
title = {Close encounters on a micro scale: microplastic sorption of polycyclic aromatic hydrocarbons and their potential effects on associated biofilm communities.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {84},
pmid = {40629382},
issn = {2524-6372},
support = {BONUS (Art 185), 03F0775A//European Union and the German Federal Ministry of Education and Research/ ; BONUS (Art 185), 03F0775A//European Union and the German Federal Ministry of Education and Research/ ; BONUS (Art 185), 03F0775A//European Union and the German Federal Ministry of Education and Research/ ; Vinnova, 2017-00001//Swedish Governmental Agency for Innovation Systems/ ; Vinnova, 2017-00001//Swedish Governmental Agency for Innovation Systems/ ; BONUS-BB/MICROPOLL/06/2017//National Centre for Research and Development, Poland (NCBR)/ ; BONUS-BB/MICROPOLL/06/2017//National Centre for Research and Development, Poland (NCBR)/ ; },
abstract = {BACKGROUND: Within systems as dynamic as the aquatic environment, it is crucial to address the impacts of an ever-growing network of emerging pollutants at their intersection. With previous research having demonstrated the capacity of microplastics (MPs) to sorb persistent organic pollutants, we ask in our study how different plastic polymers that are found throughout aquatic systems interact with polycyclic aromatic hydrocarbons (PAHs) and how this intersection of pollutants might impact the bacterial communities that form on MP surfaces. We performed an in situ incubation experiment at different sites along the Baltic Sea coast and through a PAH and 16S amplicon analysis, we investigated the sorption patterns of different substrates and their potential impacts on associated biofilm communities.

RESULTS: PAH sorption patterns of polyethylene (PE), polystyrene (PS), and aquaria stone were found to be dictated predominantly by substrate type and secondly by incubation site. While PE showed a general positive trend of sorption, stone rather leached PAHs into the environment, whereas the PAH levels of PS remained relatively unchanged following incubation. These sorption patterns correlated significantly with the composition of biofilm communities observed on all three substrate types after a 6-week incubation period. Strong correlations between specific PAHs and bacterial taxa indicate a direct relationship between these factors. Elevated levels of specific 3- and 4-ring PAHs on PE and PS coincided with higher proportions of specific taxa reportedly capable of hydrocarbon utilisation as well as a reduced diversity among biofilm communities.

CONCLUSION: The findings in our study highlight the importance of investigating contaminants such as MPs holistically, including any associated substances, to fully understand how they impact surrounding ecological systems as they traverse the different compartments of the aquatic ecosystem.},
}

@article {pmid40629225,
year = {2025},
author = {Florek, K and Komorowska, K and Ptak, J and Jarocki, M and Gontarczyk, J and Mania, R and Boluk, A and Żurawska-Płaksej, E and Łaczmański, Ł and Sokolski, M},
title = {Gut microbiota's role in heart failure.},
journal = {Heart failure reviews},
volume = {},
number = {},
pages = {},
pmid = {40629225},
issn = {1573-7322},
abstract = {The pathogenesis of heart failure (HF) is complex, and from an immunological perspective, the "gut-heart axis" plays a pivotal role in its development. The composition of gut microbiota differs significantly between HF patients and healthy individuals, with variations observed across different nations, HF etiologies, and stages defined by the New York Heart Association (NYHA) classification. Moreover, gut-derived metabolites such as short-chain fatty acids (SCFAs), trimethylamine N-oxide (TMAO), bile acids, and lipopolysaccharides (LPS) influence HF progression through specific mechanisms and signaling pathways. Notably, medications recommended in cardiovascular diseases and advanced interventions applied in HF, such as heart transplantation requiring immunosuppressive therapy or the implantation of mechanical circulatory support devices, are associated with significant alterations in gut microbiota composition. However, these mechanisms are still not well-established. This review aims to summarize current data on the impact of the gut microbiome on HF progression and treatment, encompassing both standard medical treatment and advanced therapies of HF.},
}

@article {pmid40629040,
year = {2025},
author = {Ju, CW and Lyu, R and Li, H and Wei, J and Parra Vitela, AJ and Dougherty, U and Kwesi, A and Luna, A and Zhu, X and Shen, S and Liu, Y and Wang, L and Cui, X and Xu, Y and Jiang, B and Ji, Y and Xia, P and West-Szymanski, DC and Sun, C and Zhong, Y and Ye, C and Moran, A and Lehmann, C and Pamer, E and Zhang, W and Bissonnette, M and Zhang, LS and He, C},
title = {Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40629040},
issn = {1546-1696},
abstract = {Circulating cell-free RNA (cfRNA) in plasma represents a promising avenue for cancer detection. We report low-input multiple methylation sequencing, a method for profiling modification patterns in cfRNA, enabling the detection of diverse transfer RNAs and small noncoding RNAs derived from both the human genome and the microbiome. RNA modification patterns in microbiome-derived cfRNA accurately reflect host microbiota activity and hold potential for the early detection of colorectal cancer.},
}

@article {pmid40629022,
year = {2025},
author = {Teo, JJY and Ho, EXP and Ng, AHQ and How, SHC and Chng, KR and Ateş, YC and Fau'di, MT and Aung, KT and Nagarajan, N},
title = {Citywide metagenomic surveillance of food centres reveals local microbial signatures and antibiotic resistance gene enrichment.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {63},
pmid = {40629022},
issn = {2731-8745},
abstract = {The distribution of microorganisms in built environments with high human traffic, such as food centres, can potentially have a significant impact on public health, particularly in the context of increasing worldwide incidence of food and fomite-related outbreaks. In many major Asian cities, public food centres are central to daily food consumption, yet there is a lack of baseline knowledge about their environmental microbiomes. We performed a city-wide metagenomic survey of food-centre microbiomes in Singapore, covering 16 centres and 240 samples, to map the abundances of microbial (bacteria, archaea, fungi, viruses) and non-microbial DNA across two timepoints. Food-centre microbiomes were found to be enriched in food-related DNA signatures compared to other environments, such as hospitals and offices, with specific food-microbe associations (e.g., Enterobacteriaceae and fish) and food DNA providing a partial explanation for the microbial profiles observed (44% of variation explained). Machine learning analysis identified a small set of microbial species (n = 22) that serve as highly accurate (>80%) location-specific signatures for various food centres, some of which persist even after 3 years. Profiling of antibiotic resistance genes (ARGs) and pathogens identified a surprising enrichment of ARGs in food centres relative to other non-healthcare environments (>2.5×), and an order of magnitude enrichment of key pathogenic species (e.g., Klebsiella pneumoniae, Enterobacter spp) even compared to hospital environments. These results highlight the contribution of diverse biotic and abiotic factors in shaping the unique microbiome profiles of different food-centre environments, and the potential for using metagenomic surveillance to understand the risk for infections and antibiotic resistance gene transmission.},
}

@article {pmid40628921,
year = {2025},
author = {Maskawa, R and Takayasu, L and Takayasu, H and Watanabe, K and Takemine, S and Kakimoto, T and Takeshita, K and Narushima, S and Suda, W and Takayasu, M},
title = {High-resolution fecal pharmacokinetic modeling in mice with orally administered antibiotics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24441},
pmid = {40628921},
issn = {2045-2322},
support = {24KJ1073//Japan Society for the Promotion of Science/ ; JPMJCR22N3//Japan Science and Technology Agency/ ; JPMJCR22N3//Japan Science and Technology Agency/ ; JPMJCR22N3//Japan Science and Technology Agency/ ; 23ae0121046//Japan Agency for Medical Research and Development/ ; },
mesh = {Animals ; *Anti-Bacterial Agents/pharmacokinetics/administration & dosage ; *Feces/chemistry ; Administration, Oral ; Mice ; *Vancomycin/pharmacokinetics/administration & dosage ; Mice, Inbred C57BL ; *Models, Biological ; Male ; Gastrointestinal Motility/drug effects ; Gastrointestinal Microbiome/drug effects ; },
abstract = {High-resolution fecal pharmacokinetics are crucial for optimizing therapeutic design and evaluating gastrointestinal motility. However, empirical studies with detailed fecal concentration over time data remain limited. This study aims to characterize fecal pharmacokinetics through high-frequency sampling and parallelized fecal concentration quantification, establishing a simple pharmacokinetics model with physiologically interpretable parameters. We quantified vancomycin concentrations in fecal samples collected at a minimum interval of 4 hours from C57BL/6N mice following a single oral administration of either a low (1 mg/mL) or high (20 mg/mL) dose. Fecal concentrations gradually increased and exhibited an exponential decay, leading to the development of a compartmental model with an absorption phase. This simple model accurately fit the experimental data and provided physiological explanations for intra- and inter-individual pharmacokinetics variability. The results suggest that inter-individual differences in pharmacokinetics are attributable to fecal elimination capacity, which may be influenced by drug dosage via changes in gastrointestinal motility. Since the model predicts antibiotic concentrations within the gastrointestinal tract, it can be applied to fundamental studies investigating the effects of antibiotics on the gut microbiome and gastrointestinal motility.},
}

Animals
*Anti-Bacterial Agents/pharmacokinetics/administration & dosage
*Feces/chemistry
Administration, Oral
Mice
*Vancomycin/pharmacokinetics/administration & dosage
Mice, Inbred C57BL
*Models, Biological
Male
Gastrointestinal Motility/drug effects
Gastrointestinal Microbiome/drug effects

@article {pmid40628728,
year = {2025},
author = {Arp, G and Jiang, AK and Dufault-Thompson, K and Levy, S and Zhong, A and Wassan, JT and Grant, MR and Li, Y and Hall, B and Jiang, X},
title = {Identification of gut bacteria reductases that biotransform steroid hormones.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6285},
pmid = {40628728},
issn = {2041-1723},
mesh = {*Gastrointestinal Microbiome/physiology/genetics ; Humans ; Phylogeny ; Male ; Female ; *Oxidoreductases/metabolism/genetics ; *Bacteria/enzymology/genetics/classification ; *Steroids/metabolism ; Biotransformation ; Pregnenolone/metabolism ; *Bacterial Proteins/metabolism/genetics ; },
abstract = {The metabolism of steroid hormones by the gut microbiome is increasingly recognized as a key factor in human health; however, the specific enzymes mediating these transformations remain largely unidentified. In this study, we identify Δ[4]-3-ketosteroid 5β-reductase, 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase, and Δ[6]-3-ketosteroid reductase enzyme families encoded by common human gut bacteria. Through phylogenetic reconstruction and mutagenesis, we show that 5β-reductase evolved to specialize in converting both natural and synthetic 3-ketosteroid hormones into their 5β-reduced derivatives, while Δ[6]-3-ketosteroid reductase adapted to produce Δ[6]-reduced derivatives. We also find that the novel 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase is fused with 5β-reductase in multiple species, streamlining the conversion of pregnenolone, a 3β-hydroxy-5-ene and steroid hormone precursor, into epipregnanolone. Through metagenomic analysis, we reveal that these enzymes are prevalent in healthy populations and enriched in females compared to males. These findings lay the groundwork for mechanistic investigations into how microbial steroid metabolism modulates host hormonal physiology.},
}

*Gastrointestinal Microbiome/physiology/genetics
Humans
Phylogeny
Male
Female
*Oxidoreductases/metabolism/genetics
*Bacteria/enzymology/genetics/classification
*Steroids/metabolism
Biotransformation
Pregnenolone/metabolism
*Bacterial Proteins/metabolism/genetics

@article {pmid40628719,
year = {2025},
author = {Gencel, M and Cofino, GM and Hui, C and Sahaf, Z and Gauthier, L and Matta, C and Gagné-Leroux, D and Tsang, DKL and Philpott, DP and Ramathan, S and Menendez, A and Bershtein, S and Serohijos, AWR},
title = {Quantifying the intra- and inter-species community interactions in microbiomes by dynamic covariance mapping.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6314},
pmid = {40628719},
issn = {2041-1723},
support = {PG-408523//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; RGPIN-2016-06566//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; CRC-2022-00138//Canada Research Chairs (Chaires de recherche du Canada)/ ; 89967//National Research Foundation (NRF)/ ; },
mesh = {Animals ; *Escherichia coli/genetics/physiology/drug effects ; Mice ; *Gastrointestinal Microbiome/drug effects/genetics ; *Microbial Interactions ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; Mice, Inbred C57BL ; },
abstract = {A microbiome's composition, stability, and response to perturbations are governed by its community interaction matrix, typically quantified through pairwise competition. However, in natural environments, microbes encounter multispecies interactions, complex conditions, and unculturable members. Moreover, evolutionary and ecological processes occur on overlapping timescales, making intra-species clonal diversity a critical but poorly understood factor influencing community interactions. Here, we present Dynamic Covariance Mapping (DCM), a general approach to infer microbiome interaction matrices from abundance time-series data. By combining DCM with high-resolution chromosomal barcoding, we quantify inter- and intra-species interactions during E. coli colonization in the mouse gut under three contexts: germ-free, antibiotic-perturbed, and innate microbiota. We identify distinct temporal phases in susceptible communities: (1) destabilization upon E. coli invasion, (2) partial recolonization of native bacteria, and (3) a quasi-steady state where E. coli sub-lineages coexist with resident microbes. These phases are shaped by specific interactions between E. coli clones and community members, emphasizing the dynamic and lineage-specific nature of microbial networks. Our results reveal how ecological and evolutionary dynamics jointly shape microbiome structure over time. The DCM framework provides a scalable method to dissect complex community interactions and is broadly applicable to bacterial ecosystems both in vitro and in situ.},
}

Animals
*Escherichia coli/genetics/physiology/drug effects
Mice
*Gastrointestinal Microbiome/drug effects/genetics
*Microbial Interactions
*Microbiota
Anti-Bacterial Agents/pharmacology
Mice, Inbred C57BL

@article {pmid40628650,
year = {2025},
author = {Crawford, CJ and Reintjes, G and Solanki, V and Ricardo, MG and Harder, J and Amann, R and Hehemann, JH and Seeberger, PH},
title = {Activity-Based Tracking of Glycan Turnover in Microbiomes.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.5c07546},
pmid = {40628650},
issn = {1520-5126},
abstract = {Glycans shape microbiomes in the ocean and the gut, driving key steps in the global carbon cycle and human health. Yet, our ability to track microbial glycan turnover across microbiomes is limited, as identifying active degraders without prior genomic knowledge remains a key challenge. Here, we introduce an activity-based fluorescence resonance energy transfer (FRET) probe that enables direct visualization and quantification of glycan metabolism in complex microbial communities. As a proof of concept, we investigated α-mannan degradation, a prominent polysaccharide in algal blooms. Using automated glycan assembly, we synthesized a mannan hexasaccharide bearing a fluorescein-rhodamine FRET pair. The probe was validated using a recombinantly expressed endo-α-mannanase (GH76) from Salegentibacter sp. Hel_I_6. It was shown to function in cell lysates, pure cultures, and complex microbiomes (via plate assays and microscopy). This probe enabled spatiotemporal visualization of in situ α-mannan turnover in a marine microbiome. Glycan FRET probes are versatile tools for tracking glycan degradation across biological scales from single enzymes to microbiomes.},
}

@article {pmid40628517,
year = {2025},
author = {Yang, Y and Zhang, X and Chen, T},
title = {Research progress in the role of gut microbiota in ethanol metabolism.},
journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences},
volume = {50},
number = {3},
pages = {501-510},
doi = {10.11817/j.issn.1672-7347.2025.240537},
pmid = {40628517},
issn = {1672-7347},
support = {202211004855//the Scientific Research Project of Health Commission of Hunan Province/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; *Ethanol/metabolism ; Humans ; Fatty Acids, Volatile/metabolism ; Liver Diseases, Alcoholic/microbiology/metabolism ; Animals ; Alcohol Drinking/metabolism ; },
abstract = {In recent years, gut microbiota has been increasingly recognized as a key player in ethanol metabolism and the development of related diseases. On one hand, ethanol intake directly affects the gut, leading to significant alterations in microbial diversity and composition. On the other hand, gut microbiota influences ethanol-induced damage to various organs, especially the liver, through multiple metabolic byproducts (such as short-chain fatty acids like butyrate, propionate, and acetate), modulation of immune responses, alteration of intestinal barrier function, and regulation of ethanol-metabolizing enzymes. Given the close association between gut microbiota and ethanol metabolism, the gut microbiome presents a promising therapeutic target for alcohol-related liver diseases. This review summarizes recent advances in understanding how gut microbiota affects ethanol metabolism, aiming to elucidate its role in the onset and progression of ethanol-related diseases and to provide a theoretical basis and novel targets for microbiota-based interventions.},
}

*Gastrointestinal Microbiome/physiology
*Ethanol/metabolism
Humans
Fatty Acids, Volatile/metabolism
Liver Diseases, Alcoholic/microbiology/metabolism
Animals
Alcohol Drinking/metabolism

@article {pmid40628430,
year = {2025},
author = {Kapicıi, İ and Erken Güngör, Ö and Yildirim, K and Atas, C and Yilmaz Coban, A},
title = {Impact of Z-spring appliance and clear aligner therapy on oral microorganisms in children: A clinical trial.},
journal = {Saudi medical journal},
volume = {46},
number = {7},
pages = {825-830},
doi = {10.15537/smj.2025.46.7.20250264},
pmid = {40628430},
issn = {1658-3175},
mesh = {Humans ; Child ; Male ; Female ; Streptococcus mutans/isolation & purification ; Candida albicans/isolation & purification ; *Dental Plaque/microbiology ; Streptococcus mitis/isolation & purification ; Streptococcus salivarius/isolation & purification ; *Mouth/microbiology ; },
abstract = {OBJECTIVES: To evaluate the effect of Z-spring appliance and clear aligners, used in anterior crossbite treatment, on dental plaque colonization in children.

METHODS: A 2-arm randomized controlled trial included 30 patients aged 7-12 years with anterior crossbite. Participants were divided into 2 groups: clear aligner (group A, n=15) and Z-spring appliance (group B, n=15). Dental plaque samples were collected at treatment initiation and completion, inoculated onto selective media, and analyzed for colony counts (cfu/ml) of Streptococcus mutans (S. mutans), Streptococcus mitis (S. mitis), Streptococcus salivarius (S. salivarius), and Candida albicans (C. albicans).

RESULTS: In group A, S. mutans counts significantly increased (p=0.006), while C. albicans counts decreased (p=0.039). In group B, S. mutans counts significantly decreased (p=0.002). No significant changes were observed in S. salivarius or S. mitis counts in either group.

CONCLUSION: Short-term clear aligner use in children increases S. mutans colonization, suggesting a potential risk for dental caries with prolonged treatment. Early preventive measures are crucial to mitigate this risk and ensure better oral health outcomes.ClinicalTrials.gov Reg. No. ID: NCT06858033.},
}

Humans
Child
Male
Female
Streptococcus mutans/isolation & purification
Candida albicans/isolation & purification
*Dental Plaque/microbiology
Streptococcus mitis/isolation & purification
Streptococcus salivarius/isolation & purification
*Mouth/microbiology

@article {pmid40628420,
year = {2025},
author = {Pervaiz, U and Nabeel, P and Zhao, R and Zhao, Z and Zhang, Y and Wang, D},
title = {Global Research Trends on the Links Between the Oral Microbiome and Cancer From 2014 to 2024: A Visualization Analysis.},
journal = {Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jop.70000},
pmid = {40628420},
issn = {1600-0714},
support = {82203630//National Natural Science Foundation of China/ ; 81902364//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: In recent years, noteworthy connections have been discovered between human wellness and microbiota. This study aims to outline the hotspots and trends in the links between the oral microbiome and cancer over the past 10 years from a bibliometric perspective.

METHODS: Reports on original research and literature reviews on the relationship between the oral microbiome and cancer from 2014 to 2024 were retrieved from the Web of Science Core Collection and PubMed databases. CiteSpace and VOSviewer were utilized to display the research patterns.

RESULTS: A bibliometric analysis was conducted on 4638 relevant publications, of which 3450 research articles and 1188 reviews were examined. China and the United States have contributed greatly to the research on the relationship between the oral microbiota and cancer, most of which were published in Frontiers in Microbiology, Frontiers in Cellular and Infection Microbiology, and International Journal of Molecular Sciences. The Chinese Academy of Sciences (107), Sichuan University (81), and Zhejiang University (79) are the most productive institutions. Zhou Xuedong, Hao Zhang, and Christian C. Abnet are the most recognized authors. Keyword co-occurrence revealed that the terms microbiome, oral microbiota, oral cancer, inflammatory diseases, probiotics, and dysbiosis are research hotspots in the past 10 years.

CONCLUSIONS: The knowledge map provides a helpful visual representation of the main relevant topics in research conducted in the last 10 years on the relationship between the oral microbiome and cancer. The findings imply that oral squamous cell carcinoma, F. nucleatum, biomarkers, dysbiosis, and cancer treatment therapies have become popular topics in recent years.},
}

@article {pmid40628054,
year = {2025},
author = {Yu, S and Yoshikuni, Y},
title = {Biotechnological advances in algae-based foods: applications in nutrition and microbiome health.},
journal = {Current opinion in biotechnology},
volume = {94},
number = {},
pages = {103335},
doi = {10.1016/j.copbio.2025.103335},
pmid = {40628054},
issn = {1879-0429},
abstract = {Algae are a sustainable, nutrient-rich resource with growing potential in food biotechnology. Their ability to thrive in diverse environments makes them a promising alternative to conventional crops. Rich in proteins, essential fatty acids, and bioactive compounds, algae support the development of functional foods, including plant-based meat and seafood alternatives. Advances in synthetic biology and fermentation have enhanced algal nutrient profiles and enabled novel applications. Algae-derived polysaccharides, such as alginate, fucoidan, laminarin, and porphyran, exhibit prebiotic effects by modulating the gut microbiota and promoting SCFA production. Enzymatic hydrolysis efficiently produces bioactive oligosaccharides, while engineered microbial systems support scalable production. Algae also enable synbiotic food development by serving as both prebiotic substrates and probiotic carriers.},
}

@article {pmid40627887,
year = {2025},
author = {Kong, M and Wang, M and Liang, S and Chen, H and Zhang, S and Zheng, M and Zhang, C},
title = {Relationship between antibiotic resistance genes and microbiome in the Arctic marine sediments.},
journal = {Marine environmental research},
volume = {210},
number = {},
pages = {107345},
doi = {10.1016/j.marenvres.2025.107345},
pmid = {40627887},
issn = {1879-0291},
abstract = {The global dissemination of antibiotic resistance genes (ARGs) presents a significant threat to public health and ecosystems. The Arctic has been contaminated with ARGs due to the global spread of ARGs. However, the remote nature of the Arctic need a comprehensive characterization of the diversity and distribution of ARGs. In this study, ARGs and bacterial communities in marine sediments from the Arctic were analyzed using qPCR and 16s rRNA gene sequencing. The results indicated that the abundance of ARGs was correlated with the location of the sediments. The absolute abundance of target ARGs exhibited higher values in BJ2 and BJ3. Microbial community composition showed low similarity, with significant structural differences across samples. Proteobacteria was the dominant phylum in all sediment samples, with a large number of highly abundant unclassified genera present. Additionally, the Mantel test and correlation analyses revealed a significant relationship between the abundance of ARGs and bacterial communities. Acidobacteriota was identified as a potential host for sul1 and blaTEM. In summary, this study provides insights into the relationship between antibiotic resistance genes and microbiome in Arctic marine sediments and serves as an important reference for global ARGs management strategies.},
}

@article {pmid40627637,
year = {2025},
author = {Ramírez-Larrota, JS and Juyoux, P and Guerra, P and Eckhard, U and Gomis-Rüth, FX},
title = {Biochemical and structural characterization of the human gut microbiome metallopeptidase IgAse provides insight into its unique specificity for the Fab' region of IgA1 and IgA2.},
journal = {PLoS pathogens},
volume = {21},
number = {7},
pages = {e1013292},
doi = {10.1371/journal.ppat.1013292},
pmid = {40627637},
issn = {1553-7374},
mesh = {Humans ; *Immunoglobulin A/metabolism/chemistry ; *Immunoglobulin Fab Fragments/metabolism/chemistry ; *Gastrointestinal Microbiome ; *Metalloproteases/metabolism/chemistry ; Crystallography, X-Ray ; Models, Molecular ; *Bacterial Proteins/metabolism/chemistry ; },
abstract = {Human immunoglobulin A (IgA), comprising the isotypes IgA1 and IgA2, protects ~400 m2 of mucosal surfaces against microbial infections but can also lead to aberrant IgA deposits that cause disease. Certain bacteria have evolved peptidases that cleave the hinge between the Fab and Fc fragments of IgA, undermining its immune function. These peptidases specifically target IgA1, but not IgA2, which predominates in the gut and possesses a structurally distinct hinge region. The only known IgA2-specific peptidase is IgAse from the gut microbiome member Thomasclavelia ramosa, which also targets IgA1 but no other proteins. IgAse is a ~ 140-kDa, seven-domain, membrane-bound metallopeptidase (MP). Differential scanning fluorimetry, small-angle X-ray scattering, AI-based structural predictions, mass spectrometry, and high-resolution crystallography and cryo-electron microscopy of multidomain fragments of IgAse revealed a novel 313-residue catalytic domain (CD) from the igalysin family within the metzincin MP clan. The CD is flanked by an N-terminal globular C-type lectin-like domain and a wrapping domain (WD), followed by four all-β domains. Functional studies involving a comprehensive set of constructs (wild-type and mutant), authentic and recombinant IgA fragments, and inhibitors demonstrated that the minimal functional assembly requires the CD and WD, along with the Fab and hinge region (Fab'). Modelling studies suggested that the Fab heavy-chain constant domain interacts with the N-terminal subdomain of the CD, positioning the hinge peptide for cleavage-a mechanism confirmed by mutational analysis. These findings open avenues for therapeutic strategies to inhibit the only known IgA1/IgA2 peptidase and to develop it for dissolving pathologic IgA deposits.},
}

Humans
*Immunoglobulin A/metabolism/chemistry
*Immunoglobulin Fab Fragments/metabolism/chemistry
*Gastrointestinal Microbiome
*Metalloproteases/metabolism/chemistry
Crystallography, X-Ray
Models, Molecular
*Bacterial Proteins/metabolism/chemistry

@article {pmid40627541,
year = {2025},
author = {Hisatomi, A and Yoshida, T and Hasunuma, T and Ohkuma, M and Sakamoto, M},
title = {Difficult-to-culture micro-organisms specifically isolated using the liquid-liquid co-culture method - towards the identification of bacterial species and metabolites supporting their growth.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {7},
pages = {},
doi = {10.1099/mic.0.001581},
pmid = {40627541},
issn = {1465-2080},
mesh = {Coculture Techniques/methods ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/isolation & purification/genetics/classification/metabolism/growth & development ; Animals ; Phylogeny ; DNA, Bacterial/genetics ; Culture Media/chemistry ; },
abstract = {In this study, the liquid-liquid co-culture method was applied using faecal samples and specific bacterial species as growth-supporting bacteria. We aimed to isolate new, difficult-to-culture bacterial species using metabolites produced by supportive bacteria to promote the growth of small bacteria selected using filter treatment. This study aimed to identify the supporting bacteria and their metabolites that promote the growth of these isolates. Analysis of the 16S rRNA gene sequences of the isolates obtained by co-culture revealed that they were Waltera spp., Roseburia spp. and Phascolarctobacterium faecium. Roseburia spp. and Waltera spp. were isolated from several faecal samples, suggesting that they were specifically isolated using this culture method. We focused on Waltera spp. isolated from several faecal samples with unique shapes, from long to short or thin cells. The growth of Waltera spp. was not promoted by co-culture on the agar medium, suggesting that growth was only promoted by liquid-liquid co-culture. The growth of the selected small-sized Waltera spp. was promoted by co-culture, whereas the growth of the unfiltered long-cell Waltera sp. strain was suppressed by co-culture. The selected small Waltera spp. did not grow when the supporting bacterial supernatant was added, suggesting that the supporting bacteria and Waltera spp. had a symbiotic relationship through the continuous exchange of metabolites. Co-cultured supporting bacteria (diluted faecal samples) with selected small-sized Waltera spp. were predominantly Bacteroides thetaiotaomicron and Escherichia coli, compared with monoculture diluted faecal samples. We further confirmed the growth of filtered Waltera spp. by co-culturing them with B. thetaiotaomicron and E. coli. Additionally, when B. thetaiotaomicron and E. coli were co-cultured with the selected small Waltera spp., some nutrients and metabolites were reduced. Decreased metabolites were added to the medium, and selected small-sized Waltera spp. were cultured, but Waltera spp. did not grow. Therefore, it was again strongly suggested that continuous co-culturing with the supporting bacteria was important for the growth of Waltera spp. The liquid-liquid co-culture method used in this study can be used to isolate new and unique bacterial species from any environment, not just the gut microbiome. Furthermore, this co-culture method helped identify supporting bacteria and understand metabolite variations.},
}

Coculture Techniques/methods
Feces/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/isolation & purification/genetics/classification/metabolism/growth & development
Animals
Phylogeny
DNA, Bacterial/genetics
Culture Media/chemistry

@article {pmid40627410,
year = {2025},
author = {Erskine, E and Skinner, N and Holden, N},
title = {The contribution of irrigation water and growth substrate for microbial flux in a vertical farm.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf093},
pmid = {40627410},
issn = {1472-765X},
abstract = {Controlled environmental agriculture (CEA) is an emerging technology with increasing adoption for commercial applications. However, its impact on the plant microbiome is not entirely clear. The assumption is that controlled conditions reduce the risk of introduction and spread of pathogens, human or plant. Here, we assessed the microbial flux through a commercially-relevant CEA plant growth tower from culture-dependent and independent approaches. This allowed the relationship between two of the main entry points for microbes to be determined, the circulating water system and plant growth substrates, on two crop species systems, kale and lettuce. There was a clear distinction between the taxonomic compositions of bacteria in the water-associated and coir-associated compartments. Overall, water did not contribute the most abundant members of the microbiota on plants. Rainwater, used as a top-up source of water, was not the major source of sequenced microbes in either the circulating water system or in coir compartments. The main points of expansion of cultural microbes were in the irrigation tray system and the physical presence and growth of the crop plants. The effect of UV-C, typically used to treat water, and the LED lighting system were quantified for proxy pathogen strains.},
}

@article {pmid40627403,
year = {2025},
author = {Xue, Y and Huang, M and Zhang, J and Navin, S and Tao, Y and Zeng, G},
title = {Sex-Specific Postmortem Microbiome Dynamics in Mice: Implications for Death Definitions.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf070},
pmid = {40627403},
issn = {1574-6968},
abstract = {Gut microbes form a complex and dynamic symbiotic relationship with their host. However, the microbial response during the early stages following host death remains largely uncharacterized. In this study, we employed a mouse model to systematically characterize the postmortem response of the intestinal microbiota, and analyzed the dynamic changes in microbial composition during the early stages after death in both male and female mice (at 0, 0.5, 2, 6, 12, and 24 hours postmortem). Our findings reveal that sex-dimorphic shifts in microbiome composition occur as early as 2 hours postmortem. Male mice exhibited increased functional redundancy and delayed community restructuring, whereas female mice displayed earlier community shifts. These sex-specific patterns were accompanied by differences in metabolic pathway activity and biomarker taxa. Notably, the observed retention of regulatory capacity by intestinal microbes after host death offers a novel perspective on the conceptualization of death itself. We propose the term "ecological death" to describe the irreversible collapse of the host-associated microbial ecosystem following death, marking a critical transition in the functional and structural integrity of the intestinal microbiota.},
}

@article {pmid40627346,
year = {2025},
author = {Geer, M and Riwes, M},
title = {Throwing the microbiome out with the bathwater.},
journal = {Blood advances},
volume = {9},
number = {13},
pages = {3368-3369},
doi = {10.1182/bloodadvances.2025016205},
pmid = {40627346},
issn = {2473-9537},
}

@article {pmid40627052,
year = {2025},
author = {Zhou, X and Shen, X},
title = {Probiotics Modulate the Ruminal Microbiome and Metabolite Availability to Enhance Rumen Barrier Function and Growth Performance in Goats Fed a High-Concentrate Diet.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40627052},
issn = {1867-1314},
support = {42171060//National Natural Science Foundation of China/ ; CARS-38//Modern Agricultural Industry Technology System in China/ ; 2021DB014//Innovation Development Supporting Plan Project of Key Industries in Southern Xinjiang/ ; },
abstract = {The purpose of this study was to evaluate the effects of probiotics supplementation on goats fed a high-concentrate diet in terms of growth performance, rumen fermentation, microbiome and metabolite, and barrier function. Twelve 5-month-old goats (22.74 ± 0.31 kg) were randomly assigned to two groups. The control group (CON) was given a basal diet, whereas the experimental group (PRB) was provided with a diet supplemented with 2 g/kg of a probiotics for 60 days. The results indicated that the final weight (FW) and average daily gain (ADG) were significantly increased in the PRB group compared to the CON group (p < 0.05). Rumen fluid in the PRB group showed significantly elevated levels of butyrate, ammonia nitrogen, propionate, acetate, and total volatile fatty acids, with a significantly reduced acetate/propionate (p < 0.05). Additionally, the PRB group demonstrated significant increases in rumen papilla width and density of gastric papillae (p < 0.05). The mRNA relative expression of tight junction proteins Claudin-4, Claudin-1, Occludin, and ZO-1 in the rumen epithelium was significantly upregulated (p < 0.05). Furthermore, the mRNA relative expression of the anti-inflammatory factor IL-10 was significantly elevated, whereas the pro-inflammatory factors IL-1β and TNF-α were significantly reduced (p < 0.05). 16S rDNA sequencing revealed enrichment of beneficial microbes, such as Lachnospiraceae_NK4A136_group, Christensenellaceae_R-7_group, Monoglobus, Parabacteroides, Bacteroides, and Roseburia, which promoted fiber degradation and volatile fatty acid production. Elevated metabolites, including 2-lysophosphatidylcholin, PC(18:0/0:0), tryptophol, 5-hydroxy-6-methoxyindole glucuronide, and mevalonic acid, contribute to epithelial repair, barrier function, and fermentation. Additionally, 4-nitrocatechol was associated with improved rumen papillae structure and anti-inflammatory effects. In conclusion, probiotics supplementation enhanced rumen fermentation, microbial composition, and barrier function while alleviating inflammation, ultimately improving growth performance and rumen health in goats on a high-concentrate diet.},
}

@article {pmid40626932,
year = {2025},
author = {Talwar, C and Guria, A and Hoffman, K and Biest, S and Jimenez, P and Kommagani, R},
title = {A role for gut mycobiome and altered fungal-bacterial interactions in women with endometriosis.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioaf148},
pmid = {40626932},
issn = {1529-7268},
abstract = {Endometriosis is a gynecological pathology prevalent in reproductive age women in which the inner uterine wall (endometrium) grows outside as ectopic lesions. The inflammation resulting from these growing implants closely associates with disease severity, causing chronic pain and infertility. Emerging studies have found altered bacterial communities in endometriosis and a causal role for gut bacteria in endometriosis. However, the role of the gut mycobiome i.e., the fungal component of the microbiome in endometriosis is a current knowledge gap that needs to be addressed. In this study, utilizing the stool samples from women with endometriosis, we found that the gut fungal communities are altered in women with endometriosis. By integrating the bacterial microbiota and studying the co-occurring relationships between fungi and bacteria, we identify the altered fungal-bacterial community interactions in endometriosis. In addition, we studied the microbial interactions with the host and identified the bacterial taxa as 'microbiome-associated host genetic variants' in endometriosis. By determining their interactions with fungi, we highlight the fungal taxa as underlying regulators of the disease. Experimentally, we demonstrate that the progression of endometriosis in mice is significantly impeded by the depletion of fungi, revealing a role for the gut mycobiome in endometriosis. Our results highlight the positive- and negative- co-abundance relationships shared between bacteria-fungi, bacteria-bacteria and microbes-host in the disease pathogenesis. These findings promise to stimulate future experimental research on the bacterial-fungal interactions that must be contemplated when designing microbiome-based therapeutic strategies using antifungal agents.},
}

@article {pmid40626910,
year = {2025},
author = {Kust, A and Zorz, J and Paniker, CC and Bouma-Gregson, K and Krishnappa, N and Liu, W and Banfield, JF and Diamond, S},
title = {Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf142},
pmid = {40626910},
issn = {1751-7370},
abstract = {Cyanobacteria are integral to biogeochemical cycles, influence climate processes, and hold promise for commercial applications. In natural habitats, they form complex consortia with other microorganisms, where interspecies interactions shape their ecological roles. Although in vitro studies of these consortia have significantly advanced our understanding, they often lack the biological replication needed for robust statistical analysis of shared microbiome features and functions. Moreover, the microbiomes of many model cyanobacterial strains, which are central to our understanding of cyanobacterial biology, remain poorly characterized. Here, we expanded on existing in vitro approaches by co-culturing five well-characterized model cyanobacterial strains with microorganisms filtered from three distinct freshwater sources, generating 108 stable consortia. Metagenomic analyses revealed that, despite host and inoculum diversity, these consortia converged on a similar set of non-cyanobacterial taxa, forming a 25-species core microbiome. The large number of stable consortia in this study enabled statistical validation of both previously observed and newly identified core microbiome functionalities in micronutrient biosynthesis, metabolite transport, and anoxygenic photosynthesis. Furthermore, core species showed significant enrichment of plasmids, and functions encoded on plasmids suggested plasmid-mediated roles in symbiotic interactions. Overall, our findings uncover the potential microbiomes recruited by key model cyanobacteria, demonstrate that laboratory-enriched consortia retain many taxonomic and functional traits observed more broadly in phototroph-heterotroph assemblages, and show that model cyanobacteria can serve as robust hosts for uncovering functional roles underlying cyanobacterial community dynamics.},
}

@article {pmid40626776,
year = {2025},
author = {Spanoghe, L and Domain, G and Posastiuc, F and Hettiarachchi, A and Panattoni, A and Theuns, S and Van Immerseel, F and Opsomer, G and Van Soom, A and Banchi, P},
title = {Toward standardized methods in canine vaginal microbiome research: evaluation of storage, host DNA depletion, and database selection.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0058325},
doi = {10.1128/spectrum.00583-25},
pmid = {40626776},
issn = {2165-0497},
abstract = {UNLABELLED: Standardized methods for investigating the canine vaginal microbiome are not available yet. Data using next-generation sequencing (NGS) are still limited, and methodologies lack consistency. In theory, microbiome results can be significantly affected by factors like sampling technique, storage, DNA extraction methods, and reference databases, which can all introduce bias. To address these concerns, we compared two storage methods for the sample (no medium vs. medium), examined the effect of host DNA depletion, and tested two reference databases (Emu vs. SILVA) using samples from six bitches, totaling 26 samples. Host depletion showed no significant impact on bacterial composition, nor did the storage conditions. However, when comparing reference databases, we found significant differences in beta diversity, emphasizing the importance of database choice when comparing studies. The proposed protocol paves the way for future studies on the canine vaginal microbiome, setting the basis for more precise and comprehensive microbiome profiling in this field.

IMPORTANCE: Understanding the vaginal microbiome in dogs could lead to new insights into reproductive health and fertility, but progress is limited by the lack of clear guidelines on how samples should be collected, stored, and analyzed. This study helps clarify which steps in the process truly matter and which have little impact, offering practical guidance for researchers entering this field. By highlighting where inconsistencies can influence outcomes and which methodological choices affect results, we take an important step toward more reliable and comparable research. These findings support future scientific studies and hold potential to improve veterinary care over time.},
}

@article {pmid40626762,
year = {2025},
author = {Kula, A and Kolar, O and Gilewicz, K and Qureshi, Z and Singh, A and Wolfe, AJ and Putonti, C},
title = {Complete genome sequence of Staphylococcus haemolyticus UMB6531B, isolated from a perineal swab.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0037125},
doi = {10.1128/mra.00371-25},
pmid = {40626762},
issn = {2576-098X},
abstract = {Staphylococcus haemolyticus UMB6531B was isolated from a perineal swab of a female with overactive bladder symptoms and sequenced to better characterize opportunistic pathogens of the female urogenital tract. Here, we present the complete genome sequence, which includes the chromosome as well as two complete plasmid sequences.},
}

@article {pmid40626735,
year = {2025},
author = {Kellom, M and Berg, M and Chen, I-MA and Chu, K and Clum, A and Huntemann, M and Ivanova, NN and Kyrpides, NC and Mukherjee, S and Reddy, TBK and Roux, S and Seshadri, R and Szabo, G and Varghese, NJ and Woyke, T and Eloe-Fadrosh, EA},
title = {Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0174424},
doi = {10.1128/msystems.01744-24},
pmid = {40626735},
issn = {2379-5077},
abstract = {UNLABELLED: Microbiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to analyze genomic content in the context of natural environments, establishing concepts of microbial ecological trends. Here, we developed a data discovery tool-a tetranucleotide-informed metagenome stability diagram-that is publicly available in the integrated microbial genomes and microbiomes (IMG/M) platform for metagenome ecosystem analyses. We analyzed the tetranucleotide frequencies from quality-filtered and unassembled sequence data of over 12,000 metagenomes to assess ecosystem-specific microbial community composition and function. We found that tetranucleotide frequencies can differentiate communities across various natural environments and that specific functional and metabolic trends can be observed in this structuring. Our tool places metagenomes sampled from diverse environments into clusters and along gradients of tetranucleotide frequency similarity, suggesting microbiome community compositions specific to gradient conditions. Within the resulting metagenome clusters, we identify protein-coding gene identifiers that are most differentiated between ecosystem classifications. We plan for annual updates to the metagenome stability diagram in IMG/M with new data, allowing for refinement of the ecosystem classifications delineated here. This framework has the potential to inform future studies on microbiome engineering, bioremediation, and the prediction of microbial community responses to environmental change.

IMPORTANCE: Microbes adapt to diverse environments influenced by factors like temperature, acidity, and nutrient availability. We developed a new tool to analyze and visualize the genetic makeup of over 12,000 microbial communities, revealing patterns linked to specific functions and metabolic processes. This tool groups similar microbial communities and identifies characteristic genes within environments. By continually updating this tool, we aim to advance our understanding of microbial ecology, enabling applications like microbial engineering, bioremediation, and predicting responses to environmental change.},
}

@article {pmid40626727,
year = {2025},
author = {Serrador, D and Campbell, JR and Getz, LJ and Cheung, D and Shefraw, G and Kaul, R and Navarre, WW},
title = {Practical media formulations for rapid growth of Lactobacillus iners and other vaginal bacteria.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0018325},
doi = {10.1128/aem.00183-25},
pmid = {40626727},
issn = {1098-5336},
abstract = {The composition of the vaginal microbiome is closely tied to host health. Bacterial vaginosis (BV), caused by the overgrowth of specific anaerobes (e.g., Gardnerella vaginalis), is associated with negative health outcomes. A vaginal microbiome dominated by Lactobacillus species is thought to protect against BV. However, the role of Lactobacillus iners is controversial, with evidence suggesting that some strains may not protect against BV while others do. To better characterize L. iners strains, their interactions with vaginal bacteria and human cells need to be investigated in vitro, but this has been impeded by the lack of liquid media that supports rapid L. iners growth. We have developed three liquid media formulations for L. iners growth: Serrador's Lactobacillus-adapted Iscove's medium (SLIM), which supports robust L. iners growth; a vaginally adapted version of SLIM (SLIM-V); and a chemically defined version (SLIM-CD). SLIM and SLIM-V improve L. iners growth compared to previously published formulations and also support the growth of other vaginal bacteria, including Lactobacillus crispatus, Lactobacillus jensenii, Lactobacillus gasseri, and Gardnerella vaginalis. SLIM-CD leads to slower growth but may be useful for characterizing L. iners nutrient requirements or metabolite production. Importantly, SLIM and SLIM-V also support the growth of human vaginal epithelial cells, providing a foundation for future co-culture studies. Here, we present the formulations of SLIM, SLIM-V, and SLIM-CD and compare the growth of bacterial strains and human cells in these media.IMPORTANCELactobacillus iners is one of the most prevalent members of the vaginal microbiome, but whether it promotes health or leads to bacterial vaginosis is not well understood. We have developed media formulations that lead to improved L. iners growth and support growth of other vaginal bacteria and human vaginal cells. This will allow for investigation of how L. iners interacts with vaginal bacteria and the host, improving our understanding of its role in the vaginal microbiome.},
}

@article {pmid40626548,
year = {2025},
author = {Kalairaj, MS and George, I and George, SM and Farfán, SE and Lee, YJ and Rivera-Tarazona, LK and Wang, S and Abdelrahman, MK and Tasmim, S and Dana, A and Zimmern, PE and Subashchandrabose, S and Ware, TH},
title = {Controlled Release of Microorganisms from Engineered Living Materials.},
journal = {ACS applied materials & interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.5c11155},
pmid = {40626548},
issn = {1944-8252},
abstract = {Probiotics offer therapeutic benefits by modulating the local microbiome, the host immune response, and the proliferation of pathogens. Probiotics have the potential to treat complex diseases, but their persistence or colonization is required at the target site for effective treatment. Although probiotic persistence can be achieved by repeated delivery, no biomaterial that releases clinically relevant doses of metabolically active probiotics in a sustained manner has been previously described. Here, we encapsulate stiff probiotic microorganisms within relatively less stiff hydrogels and show a generic mechanism where these microorganisms proliferate and induce hydrogel fracture, resulting in microbial release. Importantly, this fracture-based mechanism leads to microorganism release with zero-order release kinetics. Using this mechanism, small (∼1 μL) engineered living materials (ELMs) release >10[8] colony-forming-units (CFUs) of Escherichia coli in 2 h. This release is sustained for at least 100 days. Cell release can be varied by more than 3 orders of magnitude by varying initial cell loading and modulating the mechanical properties of the encapsulating matrix. As the governing mechanism of microbial release is entirely mechanical, we demonstrate the controlled release of model Gram-negative, Gram-positive, and fungal probiotics from multiple hydrogel matrices.},
}

@article {pmid40626408,
year = {2025},
author = {Kim, JA and Choi, JY and Lee, SH and Choi, CY},
title = {Effects of Hyposalinity on Osmoregulation, Oxidative Stress, and Microbial Disruption in Chromis notata (Temminck & Schlegel, 1843).},
journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.70009},
pmid = {40626408},
issn = {2471-5646},
support = {//This study was supported by a grant from the National Institute of Fisheries Science (R2025036), and by a grant from the Korea Institute of Marine Science & Technology Promotion (KIMST), funded by the Ministry of Oceans and Fisheries (20220559)./ ; },
abstract = {Climate change causes substantial alterations in marine environments, including salinity reduction due to glacial melting, increased rainfall, and freshwater influx, which impose stress on marine organisms. Hypoosmotic stress leads to increased production of reactive oxygen species, thereby disrupting physiological processes, such as osmoregulation, oxidative responses, and gut microbial stability, in marine fish. Here, we investigated the responses of Chromis notata, a stenohaline damselfish, exposed to hyposaline conditions (27 and 20 psu), to better understand the effects of hyposalinity on osmoregulation, oxidative stress, and gut microbiota. Plasma osmolality was measured alongside Na[+]/K[+]-ATPase (NKA) activity in gill tissue to assess osmoregulatory changes. The plasma levels of hydrogen peroxide (H2O2) and lipid peroxidation (LPO) levels were measured as oxidative stress markers. Furthermore, 16S rRNA sequencing and RNA sequencing were conducted to analyze gut microbial diversity and transcriptomic responses, respectively. Plasma osmolality and NKA activity markedly decreased, whereas H2O2 and LPO levels remarkably increased under low-salinity conditions. The gut microbiome in the low-salinity groups exhibited decreased α-diversity and increased abundance of Proteobacteria, including pathogenic genera, whereas Lactobacillus abundance was reduced. Upregulated genes were associated with immune and inflammatory responses, including complement activation, and salt transmembrane transporter activity, whereas downregulated genes were linked to the lateral plasma membrane and mitochondrial membrane. These findings suggest that hyposaline induces oxidative stress and disrupts gut microbiome stability in C. notata, thereby triggering complex physiological and molecular responses. These findings provide insights into the challenges encountered by marine fish in coastal and oceanic ecosystems due to climate change.},
}

@article {pmid40626364,
year = {2025},
author = {Sequoia, JA and Haddock, NL and Gay, PM and Barkal, LJ and Narasimhan, P and Martinez, N and Winn, VD and Bollyky, PL},
title = {Identification of bacteriophage DNA in human umbilical cord blood.},
journal = {JCI insight},
volume = {10},
number = {13},
pages = {},
doi = {10.1172/jci.insight.183123},
pmid = {40626364},
issn = {2379-3708},
mesh = {Humans ; *Fetal Blood/virology ; Female ; Pregnancy ; *DNA, Viral/blood/genetics/isolation & purification ; *Bacteriophages/genetics/isolation & purification ; Adult ; Infant, Newborn ; Pre-Eclampsia/virology/blood ; Cell-Free Nucleic Acids/blood ; Chorioamnionitis/virology/blood ; Premature Birth/virology/blood ; },
abstract = {Bacteriophages, viruses that parasitize bacteria, are abundant in the human microbiome and may influence human health, in part, through their interactions with bacterial hosts. Whether endogenous bacteriophages or their products are vertically transmitted from mother to fetus during human pregnancy is not known. Here, we searched for bacteriophage sequences from five bacteriophage databases (474,031 total sequences) in cell-free DNA (cfDNA) of paired maternal and umbilical cord blood samples from two independent cohorts. First, we sequenced cfDNA from 10 pairs of maternal and cord blood samples, including four pairs affected by preeclampsia. We validated our findings in a previously published dataset of 62 paired maternal and cord blood samples, including 43 pairs from preterm or chorioamnionitis-affected deliveries. We identified 94 and 596 bacteriophage sequences in maternal and cord blood cfDNA samples from the first and second cohort, respectively. We identified 58 phage sequences across maternal-infant dyads and 581 phage sequences that were unique to a single sample. We did not identify any phage sequences consistently associated with preeclampsia, preterm, or chorioamnionitis-affected samples. This study demonstrated the presence of bacteriophage DNA in human cord blood at birth, providing evidence that the human fetus is exposed to bacteriophage DNA in utero.},
}

Humans
*Fetal Blood/virology
Female
Pregnancy
*DNA, Viral/blood/genetics/isolation & purification
*Bacteriophages/genetics/isolation & purification
Adult
Infant, Newborn
Pre-Eclampsia/virology/blood
Cell-Free Nucleic Acids/blood
Chorioamnionitis/virology/blood
Premature Birth/virology/blood

@article {pmid40626169,
year = {2025},
author = {Boidin-Wichlacz, C and Maresca, M and Correia, I and Lequin, O and Point, V and Casanova, M and Reinbold, A and Iranzo, O and Huws, SA and Brodin, P and Oyama, LB and Tasiemski, A and Canaan, S and Cavalier, JF},
title = {Potency of all-D amino acid antimicrobial peptides derived from the bovine rumen microbiome on tuberculous and non-tuberculous mycobacteria.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100395},
pmid = {40626169},
issn = {2666-5174},
abstract = {Despite the availability of antibiotics, tuberculosis (TB), caused by Mycobacterium tuberculosis, was once again declared the world's leading cause of death from a single infectious agent in 2023. Furthermore, the rising prevalence of drug-resistant strains of M. tuberculosis, coupled with the limitations of existing therapeutics, underscores the urgent need for new antimicrobial agents that act through different mechanisms, thereby providing novel therapeutic options. From this perspective, antimicrobial peptides (AMPs) derived from the bovine rumen microbiome have shown promise against many resistant pathogens and may therefore offer a promising alternative against TB. Here, we evaluated the efficacy of AMPs from bovine rumen microbiome, namely the Lynronne 1, 2 & 3 and P15s as well as their all-D amino acid enantiomers, against non-tuberculous (M. abscessus, M. marinum and M. smegmatis) and tuberculous (M. bovis BCG, M. tuberculosis) mycobacteria. In particular, their antimycobacterial activity was assessed against extracellularly and intracellularly replicating M. tuberculosis H37Rv pathogenic strain. Their innocuity was further studied by determining their respective cytotoxicity against human cell lines and hemolytic activity on human erythrocytes. Finally, their mechanism of action was investigated by a membrane permeabilization assay and a lipid insertion assay via surface pressure measurement. Although all-D enantiomers showed increased cytotoxicity to human cell lines, they still offer a good therapeutic window with improved activity compared to their L-form counterparts, especially Lynronne 2D all and P15sD all which emerged as the best growth inhibitors of all mycobacteria. Remarkably, the all-D enantiomers also demonstrated activity against intramacrophagic replicating M. tuberculosis H37Rv, with very limited toxicity towards human cells and no hemolytic activity at their respective minimum inhibitory concentration. Membrane permeabilization and monolayer lipid insertion assays suggested that these peptides mostly act by insertion into the mycobacterial membrane resulting in a rapid membranolytic effect. These findings highlight the potential of the all-D enantiomers of Lynronne peptides, as attractive candidates for the development of new anti-TB drugs. Their effective antibacterial properties combined with low toxicity underscore Lynronne 2D all and P15sD all as building blocks for the development of promising alternatives to conventional antibiotics in the treatment of mycobacterial infections, particularly against M. tuberculosis.},
}

@article {pmid40626037,
year = {2025},
author = {Fang, J and Wu, Y and Wang, H and Zhang, J and You, L},
title = {Oral Health and Diabetic Cardiomyopathy: Mechanisms, Biomarkers, and Early Screening Approaches.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {8689-8704},
pmid = {40626037},
issn = {1178-7031},
abstract = {Diabetic Cardiomyopathy (DCM) is a common cardiovascular complication in patients with diabetes. In recent years, the association between oral health and diabetic heart disease has gained increasing attention. This perspective reviews the potential mechanisms of oral diseases in diabetic heart disease, oral indicators for early screening of diabetic heart disease, and proposes future research directions. The potential mechanisms of oral diseases in diabetic heart disease primarily involve abnormal activation of inflammatory responses, dysregulation of the oral microbiome, and immune system disorders. In the context of early screening for diabetic heart disease, oral health indices, salivary biomarkers, and the oral microbiome serve as critical oral indicators with significant clinical value for early diagnosis. Future research should promote interdisciplinary diagnosis and collaboration, develop non-invasive early screening technologies, integrate multimodal and multi-omics oral data, leverage large-scale multicenter clinical data to comprehensively evaluate the association between oral health indicators and diabetic cardiomyopathy, and simultaneously train and validate precise artificial intelligence models. This perspective integrates existing research findings on the role of oral health in diabetic heart disease, highlights current research limitations, and emphasizes the need for further studies to clarify causal relationships and facilitate widespread clinical application.},
}

@article {pmid40625836,
year = {2025},
author = {Kosińska-Kaczyńska, K and Krawczyk, D and Bednorz, M and Chaberek, K and Czapska, A and Zgliczyńska, M and Goryca, K and Piątkowska, M and Bałabas, A and Czarnowski, P and Żeber-Lubecka, N},
title = {Maternal and placental microbiome and immune crosstalk in pregnancies with small-for-gestational-age fetuses - a pilot case-control study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1596588},
pmid = {40625836},
issn = {2235-2988},
mesh = {Humans ; Female ; Pregnancy ; *Placenta/microbiology/immunology ; Pilot Projects ; *Infant, Small for Gestational Age ; Case-Control Studies ; Adult ; Cytokines/blood ; Infant, Newborn ; *Gastrointestinal Microbiome ; Feces/microbiology/chemistry ; *Microbiota ; *Fetal Growth Retardation/immunology/microbiology ; Bacteria/classification/isolation & purification/genetics ; },
abstract = {INTRODUCTION: Pregnancies complicated by fetal growth restriction are associated with specific bacterial abundances and elevation of proinflammatory cytokines. The aim of the study was to simultaneously analyze the relation between the gut and placenta microbiome and cytokine profile in pregnant women with fetuses appropriate (AGA) and small for gestational age (SGA).

MATERIAL AND METHODS: Women with singleton pregnancies at or beyond 32 weeks of gestation were recruited. 11 delivered SGA newborns (study group) and 11 AGA newborns (control group). Samples of maternal venous blood, stool and placenta were collected perinatally.

RESULTS: In SGA group lower Chao index in placental samples collected from maternal side, while higher Chao index in placental samples collected from fetal side were observed. Taxonomic analysis identified four significantly less abundant genera in samples collected from maternal side. No taxa remained significant after correction in samples from fetal side, but several taxa showed trends of differing abundance. Veillonella showed a trend toward higher abundance in stool samples in SGA group, while other taxa were significant only at a lower threshold. Metabolite analysis revealed that hexanoic acid was significantly elevated compound in the stool of women from the SGA group. Proteobacteria unclassified and Halomonadaceae correlated with stool metabolites, while IL-6 and TNF-α correlated with specific bacterial groups.

CONCLUSIONS: Specific changes in the gut microbiome and metabolome as well as placenta microbiome of women with SGA have been observed, with additional associations with inflammatory cytokine levels, suggesting a potential role of these factors in SGA development and highlighting the need for further research.},
}

Humans
Female
Pregnancy
*Placenta/microbiology/immunology
Pilot Projects
*Infant, Small for Gestational Age
Case-Control Studies
Adult
Cytokines/blood
Infant, Newborn
*Gastrointestinal Microbiome
Feces/microbiology/chemistry
*Microbiota
*Fetal Growth Retardation/immunology/microbiology
Bacteria/classification/isolation & purification/genetics

@article {pmid40625835,
year = {2025},
author = {Cumbo, F and Niccolai, E},
title = {Editorial: Microbiota in tumors: is it a new hope for treatment?.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1628182},
doi = {10.3389/fcimb.2025.1628182},
pmid = {40625835},
issn = {2235-2988},
}

@article {pmid40625831,
year = {2025},
author = {Han, Y and Ding, PH},
title = {Advancing periodontitis microbiome research: integrating design, analysis, and technology.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616250},
pmid = {40625831},
issn = {2235-2988},
mesh = {Humans ; *Periodontitis/microbiology ; *Microbiota ; Biofilms/growth & development ; Gingiva/microbiology ; Bacteria/genetics/classification ; },
abstract = {Periodontitis, a chronic inflammatory disease affecting 20%-50% of adults worldwide, is driven by polymicrobial synergy and dysbiosis. Despite numerous studies on the oral microbiota in periodontitis, significant heterogeneity exists between findings, posing challenges for treatment strategies. To understand the sources of this variability and establish standardized protocols, we reviewed the literature to identify potential factors contributing to these discrepancies. We found most studies focus on microbial communities in periodontal pockets, with fewer investigating microbial composition within gingival tissue. Research indicates that bacterial communities in gingival tissue exist as biofilms, potentially serving as reservoirs for persistent infection. Therefore, further exploration of the microbiome within periodontal tissues is needed, which may offer new insights for treatment strategies. Metatranscriptomics provides valuable insights into gene expression patterns of the oral microbiota, enabling the exploration of microbial activity at a functional level. Previous studies revealed that most upregulated virulence factors in periodontitis originate from species not traditionally considered major periodontal pathogens. However, current studies have not fully identified or revealed the functional changes in key symbiotic microbes in periodontitis. We reviewed the analytical paradigms of metatranscriptomics and found that current analysis is largely limited to assessing functional changes in known periodontal pathogens, highlighting the need for a functional-driven approach. Beyond the limitations of current analytical paradigms, the metatranscriptomics also has inherent constraints. We suggested integrating emerging high-throughput microbial sequencing technologies with functional-driven analytical strategies to provide a more comprehensive and higher-resolution insight for microbiome reconstruction in periodontitis.},
}

Humans
*Periodontitis/microbiology
*Microbiota
Biofilms/growth & development
Gingiva/microbiology
Bacteria/genetics/classification

@article {pmid40625829,
year = {2025},
author = {Paredes Salgado, EM and Guevara, FE and Muentes, C and Flores, FJ and Magdama, F},
title = {Identifying bacterial and fungal communities associated with Fusarium-wilt symptomatic and non-symptomatic 'Gros Michel' banana plants in Ecuador.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1572860},
pmid = {40625829},
issn = {2235-2988},
mesh = {*Musa/microbiology ; *Plant Diseases/microbiology ; *Fusarium ; *Bacteria/classification/genetics/isolation & purification ; Ecuador ; RNA, Ribosomal, 16S/genetics ; *Fungi/classification/genetics/isolation & purification ; Rhizosphere ; Soil Microbiology ; *Microbiota ; Phylogeny ; High-Throughput Nucleotide Sequencing ; *Mycobiome ; DNA, Bacterial/genetics ; Rhizome/microbiology ; Biodiversity ; },
abstract = {Fusarium wilt of banana (FWB), caused by Fusarium oxysporum f. sp. cubense (Foc), remains a critical threat to banana production worldwide. Despite the persistence of the disease in fields planted with susceptible cultivars such as 'Gros Michel', little is known about the microbial interactions influencing symptom development. In this study, we assessed the bacterial and fungal communities associated to symptomatic and non-symptomatic 'Gros Michel' bananas plants sampled in Ecuador banana fields affected by Foc race 1. We aimed to compare their diversity, composition, and to identify potential microbial taxa that could be active in disease suppression. Samples were collected from the pseudostem, rhizome, and rhizosphere, and analyzed through high-throughput sequencing of the 16S rRNA and ITS2 regions to characterize bacterial and fungal communities, respectively. Results revealed that non-symptomatic plants harbored significantly higher bacterial diversity, particularly in pseudostem and rhizome tissues, compared to symptomatic plants. Genera including, Bacillus, Enterobacter, Paenibacillus, Pectobacterium, Herbaspirillum and Pseudomonas were enriched in non-symptomatic tissues, suggesting a potential role in disease suppression. In contrast, symptomatic plants showed an increased abundance of genera such as Klebsiella and Kosakonia. Fungal community shifts were less pronounced, indicating that bacterial dynamics may play a more critical role in disease development. These findings shed light on the key microbial taxa associated with FWB-affected banana plants and the potential role of their microbiome to plant health and disease suppression.},
}

*Musa/microbiology
*Plant Diseases/microbiology
*Fusarium
*Bacteria/classification/genetics/isolation & purification
Ecuador
RNA, Ribosomal, 16S/genetics
*Fungi/classification/genetics/isolation & purification
Rhizosphere
Soil Microbiology
*Microbiota
Phylogeny
High-Throughput Nucleotide Sequencing
*Mycobiome
DNA, Bacterial/genetics
Rhizome/microbiology
Biodiversity

@article {pmid40625736,
year = {2025},
author = {Chen, J and Wang, J and Fang, W and Wu, Y and Li, H and Xu, H and Zhu, Y and Cheng, Y and Yu, Z and Peng, Y},
title = {BRICS sequential therapeutic regimen as first-Line treatment for PD-L1-negative metastatic non-small cell lung cancer patients harboring EGFR/ALK wild-type status: a retrospective study.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1618110},
pmid = {40625736},
issn = {1664-3224},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/genetics/mortality ; Male ; Middle Aged ; Female ; Retrospective Studies ; *Lung Neoplasms/therapy/genetics/mortality/pathology ; Aged ; ErbB Receptors/genetics ; B7-H1 Antigen/metabolism ; Anaplastic Lymphoma Kinase/genetics ; Immune Checkpoint Inhibitors/therapeutic use ; *Radiosurgery/adverse effects/methods ; Adult ; Treatment Outcome ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/adverse effects ; Combined Modality Therapy ; },
abstract = {BACKGROUND: Patients with PD-L1-negative, EGFR/ALK wild-type metastatic non-small cell lung cancer (NSCLC) exhibit limited responses to immune checkpoint inhibitors (ICIs). This study evaluates the BRICS regimen-a sequential approach combining stereotactic body radiotherapy (SBRT), probiotics, PD-1 inhibitors, and low-dose chemotherapy-to overcome immunotherapy resistance.

METHODS: This retrospective study included 23 patients treated between 2018 to 2024. Eligibility criteria: confirmed PD-L1-negative NSCLC, no actionable mutations, and measurable lesions. The BRICS regimen comprised SBRT (24 Gy in 3 fractions) to a single lesion, oral probiotics (6 g/day), low-dose chemotherapy, and PD-1 inhibitors administered every 21 days for six cycles. Outcomes included objective response rate (ORR), disease control rate (DCR), progression-free survival (PFS), overall survival (OS), and safety.

RESULTS: Median age was 62 years; 82.6% were male. ORR and DCR were both 95.7%. Median PFS was 16 months (95% CI: 9.11-22.89), and median OS was 32.7 months (95% CI: 11.53-53.87). In subgroup analysis based on prior treatment status, median PFS and OS were numerically longer in treatment-naïve patients compared to previously treated patients (mPFS: 20.0 vs. 13.6 months; mOS: 48.0 vs. 18.0 months), though without statistical significance (P > 0.05). Poor ECOG performance status predicted poorer PFS (HR=9.908, p=0.013) and OS (HR=26.406, p=0.008). Adverse events were predominantly grade 1 to 2 (fatigue:13.2%, rash:8.7%), with no grade ≥3 toxicities.

CONCLUSIONS: The BRICS regimen demonstrated promising efficacy and safety in PD-L1-negative NSCLC, potentially overcoming resistance through multimodal immunomodulation. clinical benefit was observed regardless of treatment line, with a trend toward improved outcomes when administered as first-line therapy. Prospective trials are warranted to validate these findings and explore mechanisms underlying radiotherapy-microbiome-chemotherapy synergy.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/therapy/genetics/mortality
Male
Middle Aged
Female
Retrospective Studies
*Lung Neoplasms/therapy/genetics/mortality/pathology
Aged
ErbB Receptors/genetics
B7-H1 Antigen/metabolism
Anaplastic Lymphoma Kinase/genetics
Immune Checkpoint Inhibitors/therapeutic use
*Radiosurgery/adverse effects/methods
Adult
Treatment Outcome
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use/adverse effects
Combined Modality Therapy

@article {pmid40625706,
year = {2025},
author = {Mei, W and Chen, C and Gao, X and Zhang, W and Hu, Z and Qu, M and Wan, G and Xu, L},
title = {Niacin mitigates heat stress-induced reduction in performance of Taihe black-boned silky fowl through modulation of gut microorganisms and short-chain fatty acids.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1592101},
pmid = {40625706},
issn = {2297-1769},
abstract = {This study aimed to evaluate the dose-dependent effects of nicotinic acid (NA) on growth performance, cecal short-chain fatty acid (SCFA) profiles, and gut microbiome composition in Taihe black-boned silky fowl (TBsf) under heat stress (HS) conditions. In the experiment, 150 healthy male TBsf were selected and randomly assigned to five treatment groups, with 30 individuals per group. The HS groups were fed a basal diet supplemented with 0, 200, 400, and 800 mg/kg of NA, respectively. HS significantly elevated body temperature and serum heat shock protein 70 (HSP70) concentration compared with the control group (thermal neutral, TN) (p < 0.05), while reducing the growth performance and apparent digestibility of crude protein in TBsf (p < 0.05). The addition of 800 mg/kg NA to the diet significantly reduced body temperature. Compared with the HS group, the incorporation of 200-800 mg/kg NA significantly decreased serum HSP70 levels, significantly increased the average daily gain (ADG) of TBsf, and significantly decreased the feed-to-gain ratio (F/G) (p < 0.05). Cecal microbial analysis showed that, compared with the TN group, the abundance of Merdimonas, Proteobacteria, and Galbibacter significantly increased (p < 0.05), while the abundance of Bacteroides, Prevotella, and Parasutterella significantly declined (p < 0.05). Furthermore, the NA-supplemented group exhibited a significant rise in the enrichment of Olivibacter and Flintibacter (p < 0.05) and a marked reduction in the enrichment of Proteobacteria (p < 0.05). Additionally, the addition of NA significantly elevated the levels of acetic acid, butyrate, and propionic acid in the cecum (p < 0.05). In conclusion, dietary NA supplementation mitigated the adverse effects of HS on TBsf, primarily by enriching beneficial microbiota such as Bacteroides and Flintibacter, and promoting the production of SCFAs like butyric acid and acetic acid.},
}

@article {pmid40625619,
year = {2025},
author = {Kim, B and Oh, S and Yang, S and Ahn, J and Jung, K and Lee, JC and Hwang, JH and Shin, CM and Lee, HJ and Lee, HS and Kim, J and Park, KU},
title = {Distinct microbiome composition and reduced interactions in patients with pancreatic cancer.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1555479},
pmid = {40625619},
issn = {1664-302X},
abstract = {INTRODUCTION: The results of microbiome composition in patients with malignancy have been inconsistent across studies and are affected by various factors. This study aimed to identify microbiome composition of saliva, feces, and blood in patients with pancreatic cancer.

RESULTS: Overall, 31 patients with pancreatic cancer and 24 healthy controls were sex- and age-matched. Microbiome analysis of saliva, fecal, and blood samples was conducted using 16S rRNA amplicon sequencing. Baseline characteristics were comparable between patients and controls. Saliva showed insignificant difference in alpha diversity (p = 0.42), whereas feces and blood exhibited a significant difference in Shannon's index (feces: 6.19 vs. 6.52, p = 0.013; blood: 8.00 vs. 7.49, p < 0.001) between patients and controls. Beta diversity analysis revealed significant differences between saliva, fecal, and blood samples (p = 0.014, 0.001, and 0.001, respectively). Distinct microbiome compositions were identified in patients, with higher abundance of Lactobacillus, Enterobacter, and Prevotella in saliva, fecal, and blood samples, respectively. Based on microbial network analysis, patients with pancreatic cancer showed lower clustering coefficient (71% vs. 99%) and higher average path length (1.67 vs. 0.68) than healthy controls, suggesting a more compact network and stronger microbial interactions in healthy controls.

CONCLUSION: This study identified a distinctive microbiome in patients with pancreatic cancer, indicating the presence of Lactobacillus, Enterobacter, and Prevotella. A less condensed and robust microbial interaction network was observed in blood samples of patients with pancreatic cancer. These findings provide a basis for research on the connection between the microbiome and pancreatic cancer.},
}

@article {pmid40625618,
year = {2025},
author = {Hu, Y and Zheng, S and Xu, J and Zhao, Y and Wang, J and Fang, Z and Zhou, L},
title = {Gestational diabetes mellitus alters neonatal gut microbiota and increases infection susceptibility.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1600325},
pmid = {40625618},
issn = {1664-302X},
abstract = {INTRODUCTION: Gestational diabetes mellitus (GDM) affects up to 27.6% of pregnancies in certain regions and is associated with a two- to threefold increased risk of neonatal infections. Although maternal gut microbiota undergoes significant remodeling during pregnancy, the specific mechanisms governing GDM-induced microbial reprogramming in offspring and its implications for susceptibility to infections remain unclear. This study aimed to investigate the impact of GDM on the composition of neonatal gut microbiota, metabolomic profiles, and susceptibility to infections using a translational approach.

METHOD: We recruited pregnant women with and without GDM at the JinHua Municipal Central Hospital in China. Meconium and blood samples were collected from newborns within 24 h of birth. The composition of the gut microbiota was analyzed using 16S rDNA amplicon sequencing, and short-chain fatty acids (SCFAs) were quantified using gas chromatography-mass spectrometry. Serum inflammatory markers, including interleukin-6 (IL-6), C-reactive protein (CRP), lipopolysaccharides (LPS), and procalcitonin (PCT), were measured by enzyme-linked immunosorbent assay. To establish causality, fecal microbiota transplantation (FMT) was conducted in antibiotic-treated mice using pooled samples from healthy and GDM-exposed neonates, followed by assessment of inflammatory markers and intestinal barrier integrity.

RESULTS AND DISCUSSION: GDM significantly reduced the diversity of neonatal gut microbiota and altered its composition, characterized by a depletion of beneficial taxa (Bifidobacterium, Blautia, Faecalibacterium) and an enrichment of potential pathogens (Stenotrophomonas, Chryseobacterium). These alterations were accompanied by significant reductions in fecal SCFAs, particularly acetate (49.30%), butyrate (41.00%), and propionate (17.83%). GDM-exposed neonates exhibited elevated serum inflammatory markers, including IL-6, CRP, LPS, and PCT, which correlated negatively with beneficial bacteria and positively with opportunistic pathogens. FMT experiments demonstrated that mice receiving GDM-associated microbiota developed increased systemic inflammation and compromised intestinal barrier function, as evidenced by the downregulation of tight junction proteins (ZO-1, occludin, claudin-1, mucin1). These findings suggest that GDM-induced alterations in neonatal gut microbiota composition and metabolite production may compromise intestinal barrier function and increase susceptibility to infections, highlighting the potential for microbiome-targeted interventions to mitigate infection risk in GDM-exposed neonates.},
}

@article {pmid40625617,
year = {2025},
author = {Zeng, Q and Feng, X and Hu, Y and Su, S},
title = {The human gut microbiota is associated with host lifestyle: a comprehensive narrative review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1549160},
pmid = {40625617},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiota serves as a critical interface between lifestyle factors and host physiology. Despite extensive research on individual domains including diet, sleep, and exercise, an integrated understanding of their synergistic effects on microbial communities remains incomplete. This knowledge gap limits our ability to develop targeted microbiome-based interventions for metabolic and immune-related disorders.

METHODS: To address this gap, we conducted a comprehensive evaluation of peer-reviewed literature from 2000 to present, identified through systematic searches of PubMed, Web of Science, and Scopus using key terms related to gut microbiota and lifestyle interventions. Our analysis focused on studies incorporating microbiome profiling techniques, controlled lifestyle interventions, and multi-omics data integration. The review prioritized mechanistic insights from both clinical and preclinical investigations while critically assessing methodological approaches across the field.

RESULTS: High-fiber dietary patterns consistently promoted the abundance of beneficial, short-chain fatty acid-producing bacteria, though with notable inter-individual variation. Circadian rhythm disruption was associated with reduced microbial diversity and expansion of pro-inflammatory bacterial taxa, paralleling increases in systemic inflammation markers. Athletic populations demonstrated unique microbial signatures characterized by enhanced metabolic potential, with distinct taxonomic profiles emerging across different sport disciplines.

CONCLUSION: This work synthesizes current evidence into a novel framework for understanding lifestyle-microbiota interactions, while identifying key challenges in study design and data interpretation. We propose standardized methodological approaches for future investigations and outline translational strategies for personalized microbiota modulation. These insights advance the potential for targeted microbial interventions to optimize metabolic and immune health outcomes.},
}

@article {pmid40625616,
year = {2025},
author = {Gilliam, FS},
title = {Linkage of strata of forest vegetation with forest soil microbiomes: a review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1575691},
pmid = {40625616},
issn = {1664-302X},
abstract = {A major dimension of pattern and process in ecological systems is the way in which species interact. In the study of forest communities, the phenomenon of linkage among forest strata (e.g., overstory and herbaceous layer) has been well investigated and arises when forest strata interact in ways that lead to causal connections between them. Whereas trees alter the light regime of forest herb communities, the herb layer can direct survivorship among seedlings of overstory species. Less studied, however, is linkage between forest strata and forest soil microbiomes. This review examines ways in which forest vegetation and soil microbiomes exert reciprocating effects on each other that can lead to linkage, beginning with a brief literature review of several phenomena relevant to how these effects occur. Because of the coincidence of the ubiquity of soil microbes with their almost infinitely small size, their interactions-both above and belowground in nature-with forest vegetation are particularly intimate. Although the most direct link, and certainly one that likely first comes to mind, is through root/microbe interactions, foliar surfaces and internal foliar tissues can support a diverse microbiome. Following the overview of potential mechanisms, examples from two separate forest studies of how linkage was demonstrated will be summarized. In each of these studies, linkage was evident through significant correlations among axis scores generated by canonical correspondence run separately for forest vegetation and soil microbial communities.},
}

@article {pmid40625325,
year = {2025},
author = {Garcias-Bonet, N and Villela, H and García, FC and Duarte, GAS and Delgadillo-Ordoñez, N and Raimundo, I and El-Khaled, YC and Santoro, EP and Bennett-Smith, M and Nieuwenhuis, BO and Curdia, J and Zgliczynski, B and Edwards, C and Sandin, S and Osman, EO and Sicat, R and Przybysz, A and Rosado, AS and Jones, BH and Benzoni, F and Berumen, ML and Salama, K and Park, S and Aranda, M and Duarte, CM and Schmidt-Roach, S and Hauser, CAE and Truscott, T and Suggett, DJ and Voolstra, CR and Carvalho, S and Peixoto, RS},
title = {The Coral Probiotics Village: An Underwater Laboratory to Tackle the Coral Reefs Crisis.},
journal = {Ecology and evolution},
volume = {15},
number = {7},
pages = {e71558},
pmid = {40625325},
issn = {2045-7758},
abstract = {Restoration efforts are urgently needed for the conservation of coral reefs. Among emerging tools, the use of probiotics has shown promise in laboratory settings for improving coral resilience, but their validation under real-world reef conditions remains limited. Here, we present the Coral Probiotics Village (CPV) as a novel and fully operational underwater research laboratory and a testing ground designed to support the in situ testing of microbial-based coral restoration interventions. This manuscript describes the design, establishment, and scientific validation of the CPV, including continuous environmental monitoring, a summary of previously developed pilot trials of probiotic applications, and an integration of sensor networks, AI-assisted reef monitoring, and autonomous technologies. We propose the CPV as a scalable model for integrated coral restoration science and suggest its replication as a tool to accelerate applied reef conservation efforts globally.},
}

@article {pmid40625320,
year = {2025},
author = {Haque, S and Gamage, HKAH and Kardum Hjort, C and Ponton, F and Encinas-Viso, F and Paulsen, IT and Dudaniec, RY},
title = {Landscape-Wide Metabarcoding Shows Interactions Among the Gut Microbiome and Pollen Diversity in the Invasive Bumblebee, Bombus terrestris.},
journal = {Ecology and evolution},
volume = {15},
number = {7},
pages = {e71717},
pmid = {40625320},
issn = {2045-7758},
abstract = {Gut microbial communities can facilitate traits that are essential for invasive species survival in novel environments. Despite the global plethora of invasive social insect species, the role of the gut microbiome in colonisation success under novel dietary and environmental conditions is little known. The introduction of the European buff-tailed bumblebee, Bombus terrestris, to the island of Tasmania (Australia) ~30 years ago is of ecological concern due to its negative impacts on native vegetation and endemic bees. Here, we investigate how the gut microbiota of B. terrestris workers is affected by corbicular pollen diversity and environmental variation across diverse landscapes in an invaded island system. B. terrestris female workers were sampled from 19 sites across Tasmania, for which environmental data for seven variables were extracted. Using 16S rRNA and ITS2 metabarcoding on gut samples and foraged pollen, respectively, we examine how the gut microbiota of B. terrestris is influenced by pollen diversity, environmental variables and their interactions. Gut bacterial community composition was significantly predicted by site annual precipitation and the percentage of pasture, which each explained 9% of the variation. Gut bacterial diversity was also explained by precipitation and pasture (40% and 30% of the variation, respectively). Furthermore, a positive interaction between annual precipitation and annual temperature significantly predicted site gut bacterial diversity. The interaction effect of pollen diversity and summer wind velocity was also positively related to gut bacterial diversity. Our findings contribute to understanding how interactions between the local environment and pollen diet affect the bee gut microbiome and thus the health and success of invasive pollinators.},
}

@article {pmid40625277,
year = {2025},
author = {Feng, K and He, Q and Peng, X and Yang, X and Du, X and Wei, Z and Wang, S and Zou, X and Zhang, Y and Deng, Y},
title = {Temperature and Biodiversity Regulate the Robustness of Plant-Microbe Networks in Natural Forests at Large Scale.},
journal = {Global change biology},
volume = {31},
number = {7},
pages = {e70335},
doi = {10.1111/gcb.70335},
pmid = {40625277},
issn = {1365-2486},
support = {42207141//National Natural Science Foundation of China/ ; U23A2043//National Natural Science Foundation of China/ ; },
mesh = {*Biodiversity ; *Forests ; *Temperature ; *Plants/microbiology ; *Microbiota ; Soil Microbiology ; },
abstract = {The latitudinal diversity gradient (LDG) is one of the general ecological patterns and has been extensively studied in plant and microbial communities. However, whether plant-microbe networks follow latitudinal trends and the underlying mechanisms driving such patterns remain largely unknown. In this study, we used an ecological survey dataset with simultaneously investigated plant species and microbial data from 26 forests at a continental scale and constructed the plant-microbe networks for each forest across the latitude gradients. We observed clear latitudinal patterns in plant-microbe networks, consistent with the LDG. Specifically, both the richness of networked species and the nestedness of the network architecture declined from tropical to temperate forests. Moreover, the plant-level network robustness decreased with increasing latitude, and positive biodiversity-robustness relationships were observed for plants and microbes. Mean annual temperature (MAT) was the most important factor for the observed latitudinal patterns, especially for plant-microbe network stability, evidenced by the robustness index. Additionally, MAT had a stronger effect on plant robustness than soil pH, primarily through its influence on plant diversity. Overall, this study demonstrated the latitudinal distribution patterns of the plant-microbe networks in natural forests and highlighted the positive relationship between biodiversity and robustness through plant-microbe interaction processes.},
}

*Biodiversity
*Forests
*Temperature
*Plants/microbiology
*Microbiota
Soil Microbiology

@article {pmid40625255,
year = {2025},
author = {Choi, HS and Kim, MS and Yu, MH and You, J and Seon, D and Ko, G and Unno, T and Lee, MY and Kim, YS},
title = {Long-term Effects of Potassium-competitive Acid Blockers and Proton Pump Inhibitors on Gastrin, Gastric Emptying Rate, and Small Intestinal Microbiota in Rats.},
journal = {Journal of neurogastroenterology and motility},
volume = {31},
number = {3},
pages = {384-395},
doi = {10.5056/jnm25024},
pmid = {40625255},
issn = {2093-0879},
abstract = {BACKGROUND/AIMS: Proton pump inhibitors (PPIs) are widely used for gastric acid suppression but are associated with adverse effects such as hypergastrinemia and delayed gastric emptying (GE). Potassium-competitive acid blockers (P-CABs), a new class of acid suppressants, rapidly and sustainably inhibit gastric acid secretion. We compared the long-term effects of different P-CABs and PPIs on gastric pH, serum gastrin levels, GE, and small intestinal microbiota in a rat model.

METHODS: Seventy-two male Sprague-Dawley rats were assigned to receive control, esomeprazole, tegoprazan, or vonoprazan by oral gavage for 1, 2, or 4 weeks. After sacrifice, gastric pH, serum gastrin levels, and GE were measured, and the small intestinal microbiota were analyzed using 16S ribosomal RNA sequencing.

RESULTS: All drug-treated groups exhibited significantly higher gastric pH than the control group. Tegoprazan achieved the highest pH at week 2, surpassing those of esomeprazole and vonoprazan. Serum gastrin levels were significantly elevated in all drug-treated groups but remained stable from weeks 1 to 4, indicating a plateau effect. GE was transiently delayed at week 2 but returned to baseline by week 4 in all drug-treated groups. Long-term administration of both P-CABs and PPI led to reduced microbial diversity and distinct taxonomic shifts with changes in the abundance of Prevotella and Acetatifactor in the small intestine. However, with prolonged administration, these differences in microbiota composition gradually diminished.

CONCLUSIONS: Long-term administration of P-CABs and PPIs altered gastrin levels, GE, and gut microbiota. Therefore, the acid suppression-related adverse effects of P-CABs and PPIs are expected to be similar.},
}

@article {pmid40624668,
year = {2025},
author = {Liu, S and Xu, H and Liu, L and Ma, W and Fan, H and Liu, F and Wei, Z and Hao, J and Zheng, Z and Zhao, L and Yang, B and Wu, Z},
title = {Gut microbiome dysbiosis accelerates osteoarthritis progression by inducing IFP-SM inflammation in "double-hit" mice.},
journal = {Arthritis research & therapy},
volume = {27},
number = {1},
pages = {137},
pmid = {40624668},
issn = {1478-6362},
support = {GZC20240144//Postdoctoral Fellowship Program of China Postdoctoral Science Foundation/ ; 82402893//National Natural Science Foundation of China/ ; 2024-I2M-C&T-B-026//CAMS Special Project of Clinical and Translational Medical Research/ ; 2022YFC2703901//National Key Research and Development Program of China/ ; 2022-PUMCH-D-002//National High Level Hospital Clinical Research Funding/ ; 2021-I2M-1-052 and 2022-I2M-2-001//CAMS Innovation Fund for Medical Sciences/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology/complications ; *Osteoarthritis/microbiology/pathology/metabolism ; Mice ; Disease Progression ; *Inflammation/pathology/microbiology/metabolism ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; },
abstract = {BACKGROUND: This study investigates the complex interplay between gut microbiome dysbiosis and systemic inflammation as a critical risk factor in the pathogenesis of osteoarthritis (OA). Furthermore, it elucidates the role of gut microbiota (GMB) dysbiosis in driving OA progression.

METHODS: A refined "double-hit" murine model was developed to explore this relationship. The first intervention involved inducing gut microbiota dysbiosis through the administration of colistin and Escherichia coli, followed by surgical destabilization of the medial meniscus (DMM) to induce joint instability. The composition of the gut microbiota was analyzed using 16 S rRNA sequencing. Gut permeability was assessed via RT-PCR and immunofluorescence (IF), while mRNA sequencing was employed to examine alterations in gene expression.

RESULTS: Treatment with colistin and E. coli significantly altered the gut microbiota composition, characterized by a marked increase in the absolute abundance of Firmicutes and a concomitant reduction in Bacteroidota and the Bacteroidota/Firmicutes (B/F) ratio. At the genus level, the absolute abundances of Muribaculaceae, Rikenellaceae_RC9_gut_group, and Roseburia were significantly diminished. GMB dysbiosis led to the downregulation of intestinal tight junction proteins, including ZO-1 and Occludin, resulting in increased intestinal permeability. Consequently, serum levels of lipopolysaccharide (LPS) were significantly elevated, indicating LPS translocation from the gut into systemic circulation. Notably, GMB dysbiosis markedly exacerbated OA progression, as evidenced by accelerated cartilage degeneration, increased osteophyte formation, and reduced bone mineral density (BMD). The OARSI scoring system revealed that OA severity in both colistin and E. coli treatment groups was significantly higher than in the control group. Additionally, GMB dysbiosis promoted the expression of inflammation-related genes in the synovium and induced M1 polarization of macrophages, demonstrated by the upregulation of CD86 and an elevated CD86/CD206 ratio. Correlation analyses indicated that Bacteroidota and the B/F ratio were positively associated with intestinal barrier integrity and negatively correlated with OA progression. In contrast, Firmicutes exhibited a positive correlation with inflammation and OA deterioration.

CONCLUSIONS: These findings collectively underscore the critical role of GMB dysbiosis in modulating intestinal permeability, systemic inflammation, and OA pathogenesis. The protective effects of Bacteroidota and the B/F ratio, as well as the detrimental impact of Firmicutes, highlight potential therapeutic targets for mitigating OA progression through GMB modulation.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Dysbiosis/microbiology/complications
*Osteoarthritis/microbiology/pathology/metabolism
Mice
Disease Progression
*Inflammation/pathology/microbiology/metabolism
Male
Mice, Inbred C57BL
Disease Models, Animal

@article {pmid39386636,
year = {2025},
author = {Boyd, AI and Kafer, LA and Escapa, IF and Kambal, A and Tariq, H and Hilsenbeck, SG and Nguyen-Phuc, H and Rajan, A and Lensmire, JM and Patras, KA and Piedra, PA and Blutt, SE and Lemon, KP},
title = {Nasal microbionts differentially colonize and elicit cytokines in human nasal epithelial organoids.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.25.614934},
pmid = {39386636},
issn = {2692-8205},
support = {U19 AI144297/AI/NIAID NIH HHS/United States ; U19 AI116497/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; },
abstract = {UNLABELLED: Nasal colonization by Staphylococcus aureus or Streptococcus pneumoniae is associated with an increased risk of infection by these pathobionts, whereas nasal colonization by Dolosigranulum species is associated with health. H uman n asal epithelial o rganoids (HNOs) physiologically recapitulate human nasal respiratory epithelium with a robust mucociliary blanket. We reproducibly monocolonized HNOs with these three bacteria for up to 48 hours with varying kinetics across species. HNOs tolerated bacterial monocolonization with localization of bacteria to the mucus layer and with minimal cytotoxicity compared to uncolonized HNOs. Human nasal epithelium exhibited both species-specific and general cytokine responses, without induction of type I interferons, consistent with colonization rather than infection. Only live S. aureus colonization robustly induced IL-1 family cytokines, suggestive of inflammasome signaling. D. pigrum and live S. aureus decreased CXCL10, whereas S. pneumoniae increased CXCL11, chemokines involved in antimicrobial responses to both viruses and bacteria. Overall, HNOs are a compelling model system to reveal host-microbe dynamics at the human nasal mucosa.

IMPORTANCE: Human nasal microbiota often includes highly pathogenic members, many of which are antimicrobial resistance threats, e.g., methicillin-resistant Staphylococcus aureus and antibiotic-resistant Streptococcus pneumoniae . Preventing colonization by nasal pathobionts decreases infections and transmission. In contrast, nasal microbiome studies identify candidate beneficial bacteria that might resist pathobiont colonization, e.g., Dolosigranulum pigrum . Discovering how these microbionts colonize the human nasal passages and means to reduce pathobiont colonization is limited by previous models. This creates an urgent need for human-based models that exemplify bacterial nasal colonization. We addressed this need by developing human nasal epithelial organoids (HNOs) as a new model system of bacterial nasal colonization. HNOs accurately represent the mucosal surface of the human nasal passages enabling exploration of bacterial-epithelial interactions, which is crucial since the epithelium instigates the initial innate immune response to bacteria. Here, we identified differential epithelial cytokine responses to these three bacteria setting the stage for future research.},
}

@article {pmid40624665,
year = {2025},
author = {Lin, F and Ma, L and Sheng, Z},
title = {Health disorders in menopausal women: microbiome alterations, associated problems, and possible treatments.},
journal = {Biomedical engineering online},
volume = {24},
number = {1},
pages = {84},
pmid = {40624665},
issn = {1475-925X},
support = {2022KY275//Zhejiang Provincial Medical and Health Science and Technology Project: "Research on the Impact of Hormone Therapy for Menopause on the Vaginal Microbiota of Perimenopausal Women Based on 16S rRNA High-throughput Gene Sequencing Technology/ ; 2022KY275//Zhejiang Provincial Medical and Health Science and Technology Project: "Research on the Impact of Hormone Therapy for Menopause on the Vaginal Microbiota of Perimenopausal Women Based on 16S rRNA High-throughput Gene Sequencing Technology/ ; 2022KY275//Zhejiang Provincial Medical and Health Science and Technology Project: "Research on the Impact of Hormone Therapy for Menopause on the Vaginal Microbiota of Perimenopausal Women Based on 16S rRNA High-throughput Gene Sequencing Technology/ ; },
abstract = {Perimenopause marks a critical transition in women's lives, characterized by declining estrogen levels that trigger profound physiological and psychological changes, impacting quality of life and increasing susceptibility to age-related degenerative diseases. This review systematically examines the intricate relationships among menopause, disease associations, microbiome alterations, and intervention strategies. Estrogen fluctuations disrupt the microbial balance in the vagina, intestine, urethra, and oral cavity, contributing to microecological imbalance and heightened disease risk. Menopause is closely linked to a spectrum of health issues, including reproductive system disorders (e.g., uterine fibroids, ovarian cancer microbiota changes), metabolic syndromes (obesity, type 2 diabetes), cardiovascular diseases (influenced by gut microbiota and dietary patterns), osteoporosis, and mental health disturbances. Current interventions-ranging from dietary modifications (cocoa polyphenols, dietary fiber, soy isoflavones) and menopausal hormone therapy (MHT) to probiotic supplementation, plant extracts (soybean, black cohosh, red clover), and traditional therapies-exhibit distinct advantages and limitations. Technological advancements in microbiome analysis, tissue processing, and cell isolation have revolutionized diagnostic and therapeutic approaches, while immune function, socioeconomic factors, and lifestyle choices significantly modulate health outcomes. Future research should prioritize exploring synergistic intervention strategies, developing personalized health management programs, and unraveling the mechanistic links between the microbiome and menopause-related diseases. This comprehensive synthesis aims to advance evidence-based strategies for improving the health and quality of life of menopausal women.},
}

@article {pmid40624638,
year = {2025},
author = {Yan, X and Lin, X and Wu, J and Zheng, L and Liu, Y and Wu, F and Lin, Y and Lu, Y and Huang, C and Shen, B and Liu, H and Huang, R and Hou, F and Zhou, Q and Song, M and Liu, K and Zhu, F and Li, S and Lin, Y and Wang, W and Li, P and Liao, W and Zhi, F},
title = {Mitigation of chemotherapy-induced gut dysbiosis and diarrhea by supplementation with heat-killed Bacteroides fragilis.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {408},
pmid = {40624638},
issn = {1741-7015},
support = {Y20190159//Study on the Mechanism of FUT7 regulating CD15s+eTreg cells in the Pathogenesis of Ulcerative Colitis/ ; NO.2024B03J1282//Key Technology Project in Guangzhou/ ; NO. 201809010014//Innovation Leading Team Project in Guangzhou/ ; },
abstract = {BACKGROUND: The role of gut microbial dysbiosis in chemotherapy-induced diarrhea (CID) pathogenesis remains unclear in humans. This study investigates gut microbiota alterations in CID patients and evaluates the therapeutic potential of probiotic supplementation.

METHODS: To establish a paired cohort for longitudinal comparison and minimize confounding factors in assessing CID-related microbiota changes, strict inclusion/exclusion criteria were applied to gastrointestinal cancer patients. Fecal samples from eligible participants underwent shotgun metagenomic sequencing to comprehensively profile the gut microbiome composition and function. To evaluate probiotic efficacy and mechanisms, we utilized 6-8-week-old male BALB/c and C57BL/6 mice in established 5-FU- or CPT-11-induced CID models. Probiotic efficacy was assessed using primary (diarrhea severity) and secondary endpoints (body weight change, intestinal permeability). Mechanistic studies were conducted in murine models, complemented by IEC-6 cells and intestinal organoid experiments to elucidate microbiota-host interactions.

RESULTS: Analysis of paired fecal samples (pre- and post-chemotherapy) from 30 gastrointestinal cancer patients (n = 60) revealed chemotherapy-induced reduction of Bacteroides fragilis (B. f) via metagenomics sequencing, with baseline B. f relative abundance negatively correlating with CID severity (r =  - 0.93, p = 3.1e - 12). Building on these clinical observations, in 5-FU/CPT-11-induced CID murine models, oral gavage of heat-killed B. f (hk-B. f) outperformed live bacteria in diarrhea alleviation. Mechanistically, B. f-derived succinate exacerbated diarrhea, while its capsular polysaccharide (PSA) ameliorated mice diarrhea. This discovery explains the discrepant therapeutic effect between hk-B. f and live B. f. Fluorescence tracing confirmed hk-B. f transiently localized to the upper gastrointestinal tract without extraintestinal colonization. hk-B. f preserved epithelial integrity, mitochondrial function, and intestinal organoid development (higher budding count and larger organoid surface area). Moreover, hk-B. f upregulated the expression of BCL2 and downregulated the expression of BAX. Shifting the balance between BCL2 and BAX alleviates intestinal epithelial apoptosis. Caspase-3 inhibition or BCL2 silencing abrogated hk-B. f's anti-apoptotic effects in IEC-6 cells.

CONCLUSIONS: Pathological process of CID can be partially explained by compositional alterations in the gut microbiota. Supplementation with hk-B. f reduces 5-FU-stimulated epithelial injury through mitochondrial apoptotic pathway in CID murine models. These preclinical findings suggest hk-B. f merits further investigation as a potential strategy for improving CID, pending clinical validation.},
}

@article {pmid40624612,
year = {2025},
author = {De, T and Ma, T and Wang, W and An, X and Liu, D and Yin, H and Wang, Q and Zhao, T and Wang, H},
title = {Intestinal microbiota in adults with cholangiocarcinoma identifies the dysregulated Blautia species and bile acid metabolic pathways.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {506},
pmid = {40624612},
issn = {1471-230X},
support = {XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; },
abstract = {BACKGROUND: Cholangiocarcinoma (CCA) represents a significant global health concern. The gut and bile microbiota, which can influence the gut-liver axis and disease progression, have not been thoroughly characterized in CCA patients.

METHODS: We selected two clinical centers at our hospital and collected stool samples from CCA patients and healthy controls (HC). These samples underwent whole-genome metagenomic shotgun sequencing, followed by analysis using both marker gene-based and assembly-based methods. Additionally, KEGG pathway enrichment was performed using the cholangiocarcinoma (CHOL) RNA-seq samples.

RESULTS: Our results revealed distinct dysbiosis of the gut microbiota in our regional CCA patients. The results revealed greater heterogeneity in the gut microbiome of CCA patients compared to HC samples. We found Blautia species to be significantly less abundant in CCA samples, and can distinguish CCA patients from HC. Blautia can also play a role in influencing the modification of secondary bile acids. Additionally, down-regulation of arachidonic acid and linoleic acid metabolism was observed in the tumor tissues of CHOL patients. In summary, the results revealed significant heterogeneity difference in the gut microbiome of CCA patients compared to HC samples, and detected the specifically decreased Blautia species in CCA patients, suggesting that Blautia may influence bile acid metabolic pathways. Further investigation is warranted to explore Blautia as a potential biomarker for CCA.},
}

@article {pmid40624576,
year = {2025},
author = {Liu, H and Su, Y and Ye, C and Zuo, D and Wang, L and Mei, X and Deng, W and Liu, Y and Huang, H and Hao, J and Zhao, J and Wang, D and Zhang, X and Zhu, Y and Liu, J and Yang, M and Zhu, S},
title = {Nucleotides enriched under heat stress recruit beneficial rhizomicrobes to protect plants from heat and root-rot stresses.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {160},
pmid = {40624576},
issn = {2049-2618},
support = {6254033//Beijing Municipal Natural Science Foundation/ ; U23A20202//Natural Science Foundation of China/ ; 2021YFD1601003//National Key Research and Development Program of China/ ; 2021JH002//Major Science and Technology Project of Kunming/ ; 202102AE090042//Major Science and Technology Projects in Yunnan Province/ ; },
abstract = {BACKGROUND: Plants thrive under biotic and abiotic stresses with the help of rhizomicrobiota. Root exudates play a pivotal role in recruiting beneficial microbes that assist plants in surviving environmental challenges, but the mechanisms of plant-microbiome interactions to resist multiple stresses remain elusive. We investigated how heat stress alters the rhizomicrobiomes of Panax notoginseng and how these heat stress-regulated microbes confer enhanced heat tolerance and disease resistance.

RESULTS: We revealed that heat stress at 36 °C caused thermal damage to plants while enhancing heat tolerance and disease resistance for the survival of subsequent plants. Specifically, the beneficial microbes Burkholderia sp. and Saitozyma podzolica were recruited by the heat-stressed P. notoginseng and were confirmed to be responsible for resisting multiple stresses. Heat stress-induced plant roots secrete nucleotides such as purines and pyrimidines to promote the proliferation of these two beneficial microbes rather than root-rot pathogens. The exogenous application of these nucleotides to natural soil also resulted in the enrichment of the same beneficial microbes. Cross-species validation experiments in Capsicum annuum (pepper) and Solanum lycopersicum (tomato) further demonstrated that co-application of nucleotides with beneficial microbes synergistically enhanced heat tolerance.

CONCLUSIONS: Our findings highlight a plant strategy for thriving under multiple adversities and propose a potential pathway by leveraging nucleotide-mediated recruitment of beneficial microbes for enhancing plant resilience against multiple stresses. Video Abstract.},
}

@article {pmid40624564,
year = {2025},
author = {Zhu, J and Jiang, MZ and Chen, X and Li, M and Wang, YL and Liu, C and Liu, SJ and Chen, WH},
title = {Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {161},
pmid = {40624564},
issn = {2049-2618},
support = {2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; 2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; },
abstract = {BACKGROUND: Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, there is a lack of large-scale experiments focusing on bacterial interactions within the human gut microbiome.

METHODS: We investigated the pairwise interactions of 113 bacterial strains isolated from healthy Chinese volunteers, selected for their high abundance and functional representation of the human gut microbiome. Using mGAM agar plates, a rich medium designed to maintain community structure, we established the "PairInteraX" dataset, which includes 3233 pair combinations of culturable human gut bacteria. This dataset was analyzed to identify interaction patterns and the key factors influencing these patterns.

RESULTS: Our analysis revealed that negative interactions were predominant among the bacteria in the PairInteraX dataset. When combined with in vivo gut metagenome datasets, we noted a diminishing mutualism and an increasing competition as microbial abundances increased; consequently, the maintenance of community diversity requires the participation of various types of interactions, especially the negative interactions. We also identified key factors influencing these interaction patterns including metabolic capacity and motility.

CONCLUSIONS: This study provides a comprehensive overview of pairwise bacterial interactions within the human gut microbiome, revealing a dominance of negative interactions. Besides, metabolic capacity and motility were identified as the key factors to influence the pairwise interaction patterns. This large-scale dataset and analysis offer valuable insights for further research on microbial community dynamics and their implications for host health. Video Abstract.},
}

@article {pmid40624562,
year = {2025},
author = {Ferreira, IM and Mantovani, HC and Viquez-Umana, F and Granja-Salcedo, YT and E Silva, LFC and Koontz, A and Holder, V and Pettigrew, JE and Rodrigues, AA and Rodrigues, AN and de Abreu, MJI and de Almeida, STR and Vidigal, PMP and Siqueira, GR and de Resende, FD},
title = {Feeding amylolytic and fibrolytic exogenous enzymes in feedlot diets: effects on ruminal parameters, nitrogen balance and microbial diversity of Nellore cattle.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {96},
pmid = {40624562},
issn = {1674-9782},
support = {2022/00989-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2023/10911-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/50339-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {BACKGROUND: The environmental impact of feedlot operations is a growing concern, as cattle excrete a significant portion of feed nutrients as waste. Exogenous feed enzymes (EFE) have gained interest for their potential to enhance feed efficiency in ruminants by improving nutrient digestion. However, EFE effects on ruminal parameters have shown inconsistencies, with limited research on nitrogen metabolism and rumen microbiome impacts. Moreover, the synergistic effects of combining different EFEs remain unclear. This study aimed to evaluate the effects of individual and combined EFE products in feedlot diets on ruminal fermentation parameters, nitrogen metabolism, and ruminal microbial communities. Ten rumen-cannulated Nellore steers [543 ± 28.6 kg of body weight (BW)] were distributed in a replicated Latin-square design (5 × 5) in individual pens. Treatments included: control (CON, no EFE supplementation), amylase [AML, 0.5 g/kg of diet dry matter (DM)], xylanase (FBL, 0.9 g/kg DM), half dose combination (HD, 0.25 g of AML + 0.45 g of FBL/kg of DM), and full dose combination (FD, 0.5 g of AML + 0.90 g of FBL/kg of DM). The experimental period lasted 19 d and included total urine and feces collection (d 15 to 18) and rumen fluid sampling (d 19) at 0, 4, 8, 12, and 16 h post-feeding for ammonia, volatile fatty acids (VFA), pH and microbiome analysis.

RESULTS: EFE supplemented animals exhibited lower ruminal ammonia concentrations (P = 0.040), and higher acetate proportions (P < 0.001) compared to the control group. EFE supplementation resulted in reduced nitrogen (N) excretion in feces (P = 0.049) and urine (P = 0.036), contributing to improved N retention and efficiency (P = 0.045). Additionally, EFE products induced shifts in various microbial taxa at family and genera levels (P ≤ 0.10), which may be associated with the changes observed in ruminal fermentation.

CONCLUSIONS: Our findings demonstrate that EFE supplementation enhances nitrogen retention, reduces ruminal ammonia, and alters ruminal fermentation profiles and microbial populations in feedlot cattle. While the expected synergism between amylase and xylanase did not significantly impact rumen fermentation parameters, it did induce shifts in the rumen microbiome. These results suggest that EFE supplementation may be a promising strategy for improving nutrient utilization and potentially reducing the environmental impact of feedlot operations.},
}

@article {pmid40624448,
year = {2025},
author = {Mitropoulou, G and Karapantzou, I and Prapa, I and Papanikolaou, D and Charovas, V and Kourkoutas, Y},
title = {Physicochemical, microbial, and microbiome dynamics in winery waste composting.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40624448},
issn = {1614-7499},
support = {ΑΜΘΡ7-0074893//The European Union and National Resources under the Operational Programme "Eastern Macedonia and Thrace" 2014-2020/ ; MIS number: 5076618//The European Union and National Resources under the Operational Programme "Eastern Macedonia and Thrace" 2014-2020/ ; },
abstract = {Compared to more extensively studied composting substrates like food waste or animal manure, winery waste presents unique challenges and opportunities. Its high content of lignin, cellulose, and polyphenolic compounds demands specific microbial consortia for efficient degradation and can potentially inhibit microbial activity if not properly balanced. In the present study, analysis of winery waste composting that combines traditional microbial enumeration with high-resolution microbiome profiling, an approach rarely applied to this type of agro-industrial residue, was implemented. Moreover, a practical proof-of-concept study, for using the composted product as a partial substrate replacement in grapevine cultivation, closing the loop in vineyard waste management, was conducted. Key parameters, such as moisture content, pH, temperature, conductivity, and C/N ratio were monitored, over a 60-day period, along with changes in enzymatic activity and shifts in microbial populations, indicating dynamic microbial activity. At the end of the process, a reduction in the carbon-to-nitrogen (C/N) ratio was observed, pH was stabilized to neutral values, and dehydrogenases activity was notably decreased. Microbiome analysis revealed eight bacterial and six fungal phyla. Acidobacteria, Armatimonadetes, Bacteroidetes, Candidatus Saccharibacteria, Chloroflexi, Cyanobacteria, Planctomycetes were identified. The Ascomycota, Basidiomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, and Mucoromycota fungal phyla were also detected. The compost exhibited no phytotoxicity and supported grapevine growth comparable to commercial substrates. Winery waste microbial composting led to stable biofertilizer production, evidenced by physicochemical stability, lack of phytotoxicity, and effectiveness in promoting grapevine growth suggesting the potential of composting as a sustainable waste management solution in the winemaking industry.},
}

@article {pmid40624404,
year = {2025},
author = {Gao, T and Yun, J and Zheng, Y and Mu, C and Zhao, B},
title = {Time-dependent microbiome dynamics in orthodontic thermoplastic materials: comparing PETG and TPU.},
journal = {Clinical oral investigations},
volume = {29},
number = {8},
pages = {374},
pmid = {40624404},
issn = {1436-3771},
support = {202240182//Shanghai Municipal Health Commission/ ; SHH-2022-YJ-A01//Shanghai Stomatological Hospital/ ; },
abstract = {OBJECTIVES: This study compares the effects of thermoplastic polyurethane (TPU) and polyethylene terephthalate glycol (PETG) aligners on the oral microbiome and salivary pH during orthodontic treatment.

MATERIALS AND METHODS: Ten participants wore TPU and PETG aligners for 24 h. At five time points (1 min, 4, 8, 12, and 24 h), saliva was collected for pH analysis, and microbial samples were taken from both aligner and supragingival plaque surfaces for 16S rRNA sequencing. Statistical analyses included repeated Measures ANOVA for pH, Kruskal-Wallis test for alpha diversity, PERMANOVA for beta diversity, and two-way ANOVA for microbial composition.

RESULTS: In Group PETG, salivary pH significantly decreased from T0 to T4 (p < 0.05). No significant changes in alpha or beta microbiota diversity were observed in either group. Microbial shifts in supragingival plaque microbiomes were detected at T8 in Group PETG, while in Group TPU, these changes became evident between T12 and T24. In aligner microbiomes, Group TPU showed significant reductions in Veillonella, Actinomyces, and Fusobacterium at T24 (p < 0.05). In contrast, Group PETG exhibited significant increases in Streptococcus from T4 to T24 (p < 0.05) and Fusobacterium from T0 to T4 (p < 0.05), followed by a decline from T4 to T24 (p < 0.01).

CONCLUSIONS: PETG aligners caused significant reductions in salivary pH at T4 and triggered pronounced fluctuations at T8 in supragingival plaque microbiomes. TPU aligners caused a delayed decline in salivary pH between T8 and T12 and drove distinct structural shifts during prolonged wear from T12 to T24.

CLINICAL RELEVANCE: Material choice based on microbial impact highlights the need for personalized aligner materials and cleaning cycles.},
}

@article {pmid40624250,
year = {2025},
author = {Fukuda, T and Takagaki, M and Kaimori, J and Motooka, D and Nakamura, S and Kawabata, S and Nakamura, H and Ozaki, T and Nakagawa, R and Matsumura, T and Teranishi, K and Yamazaki, H and Isaka, Y and Kishima, H},
title = {Differences in gut microbiome between autosomal dominant polycystic kidney disease with and without intracranial aneurysms.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24204},
pmid = {40624250},
issn = {2045-2322},
support = {22K09282//Japan Society for the Promotion of Science/ ; 21K09072//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Polycystic Kidney, Autosomal Dominant/microbiology/complications ; *Gastrointestinal Microbiome ; *Intracranial Aneurysm/microbiology/complications ; Female ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Feces/microbiology ; Aged ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder characterized by cyst formation in the kidneys, and is associated with an elevated risk of intracranial aneurysms (IAs). Although a family history is a recognized risk factor for IAs in patients with ADPKD, emerging research suggests that gut microbiome composition may influence IA development. We investigated the relationship between the gut microbiome and the development of IA in patients with ADPKD. We recruited patients with ADPKD with (IA group) and without (non-IA group) IA from Osaka University between October 2021 and December 2023. Fecal samples were analyzed using 16S rRNA sequencing. Data were processed using the QIIME 2 pipeline to determine microbial diversity and composition. We included 60 patients: 26 in the IA and 34 in the non-IA groups. There were significant differences in microbial beta diversity between the groups. The IA group had higher abundances of Eubacterium siraeum group, Oscillibacter, Fournierella, Negativibacillus, Colidextribacter, and Adlercreutzia. The non-IA group had higher abundances of Bifidobacterium, Megamonas, Acidaminococcus, Megasphaera, and Merdibacter. There was a significant association between the gut microbiome composition and the presence of IAs in patients with ADPKD. Specific bacterial taxa were differentially abundant between patients with ADPKD with and without IAs, suggesting a potential role of the gut microbiome in the pathogenesis of IAs in this genetically predisposed population.},
}

Humans
*Polycystic Kidney, Autosomal Dominant/microbiology/complications
*Gastrointestinal Microbiome
*Intracranial Aneurysm/microbiology/complications
Female
Male
Middle Aged
RNA, Ribosomal, 16S/genetics
Adult
Feces/microbiology
Aged
Bacteria/genetics/classification/isolation & purification