@article {pmid40667988,
year = {2025},
author = {Gless, BH and Sereika-Bejder, BS and Jensen, I and Bojer, MS and Tsiko, K and Schmied, SH and Vitolo, L and Toledo-Silva, B and De Vliegher, S and Ingmer, H and Olsen, CA},
title = {Mapping of quorum sensing interaction network of commensal and pathogenic staphylococci.},
journal = {mBio},
volume = {},
number = {},
pages = {e0096725},
doi = {10.1128/mbio.00967-25},
pmid = {40667988},
issn = {2150-7511},
abstract = {Staphylococci utilize secreted autoinducing peptides (AIPs) to regulate group behavior through a process called quorum sensing (QS). For pathogenic staphylococci, such as Staphylococcus aureus, QS regulates the expression of major virulence factors, and QS inhibition has been proposed as an alternative to antibiotics for the treatment of infections with methicillin-resistant S. aureus (MRSA). Here, we surveyed the interaction map between QS systems of the pathogens S. aureus, Staphylococcus epidermidis, and Staphylococcus lugdunensis and all the currently known staphylococcal AIPs, covering 21 different species. We identified six of these ribosomally synthesized and post-translationally modified peptides (RiPPs) in this study and compiled the full collection of AIPs by chemical synthesis. The resulting mapping provided 280 QS interactions that were divided into human- and animal-associated staphylococci, showing substantial differences in inhibitory potencies between the groups. AIPs of the bovine-associated species Staphylococcus simulans displayed potential as QS inhibitors toward the investigated strains and were therefore chosen as a starting point for a structure-activity relationship study. This study provides insights into the requirements for QS interference, yielding the most potent inhibitors reported to date for S. epidermidis and S. lugdunensis. Furthermore, we tested an S. simulans AIP as an anti-virulence agent in an assay to assess the risk of acquired suppression of the inhibitory effect, and we established an assay set-up to successfully monitor agr deactivation of virulent MRSA by the QS inhibitor. Finally, a peptide was shown to attenuate skin infection caused by MRSA in a mouse model. Our results reveal a complex network of staphylococcal interactions and provide further impetus for the investigation of QS modulation in the targeting of antibiotic-resistant pathogens.IMPORTANCEBacteria from the Staphylococcus genus produce macrocyclic peptides, called autoinducing peptides (AIPs), used in inter-cell communication with their kin. Differences in AIP sequence and length produced by different staphylococcal species can result in communication interference, altering the physiology of co-inhabiting staphylococci in complex microbiotas. Opportunistic pathogens like Staphylococcus aureus regulate the expression of toxins using this peptide-mediated communication, and its inhibition has, therefore, been proposed as a strategy to target infections caused by methicillin-resistant S. aureus (MRSA). The systematic mapping of AIP activities, structure-activity relationship studies, and evaluation of resistance development provided in this paper, therefore, serve as a resource for the future discovery of inhibitory peptides for the investigation of bacterial communication.},
}

@article {pmid40667611,
year = {2025},
author = {Choi, I and Kim, KA and Kim, SC and Park, D and Nam, KT and Cha, JH and Baek, S and Cha, J and Jo, HY and Jung, M and Zeng, MY and Matei, I and Bullman, S and Ahn, JB and Han, YD and Kim, HS and Lee, I},
title = {Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2528428},
doi = {10.1080/19490976.2025.2528428},
pmid = {40667611},
issn = {1949-0984},
mesh = {*Colorectal Neoplasms/microbiology/immunology/pathology ; Animals ; *Immunoglobulin A, Secretory/immunology/metabolism/genetics ; Humans ; Mice ; *Fusobacterium nucleatum/immunology/physiology ; *Fusobacterium Infections/immunology/microbiology/complications ; Prognosis ; Gastrointestinal Microbiome ; Tumor Microenvironment ; Female ; Male ; Tumor-Associated Macrophages/immunology ; Mice, Inbred C57BL ; Disease Models, Animal ; Plasma Cells/immunology ; },
abstract = {Fusobacterium nucleatum (Fn) is commonly enriched in colorectal cancer (CRC) and associated with poor outcomes, though its mechanisms remain unclear. Our study investigated how Fn affects the tumor microenvironment through single-cell transcriptomic analyses of 42 CRC patient tissues, comparing Fn-positive and Fn-negative tumors. We discovered that Fn impairs IgA plasma cell development and secretory IgA (sIgA) production by disrupting communication with tumor-associated macrophages. Additional experiments in germ-free mice, together with our re-analysis of a publicly available single-cell RNA-seq data set from a CRC mouse model with an intact gut microbiome-both models having been orally gavaged with Fn-jointly validated the causal role of Fn in impairing sIgA induction. We identified a dysregulated IgA maturation (IGAM) module in Fn-positive patients, indicating compromised mucosal immunity and increased bacterial infiltration. This IGAM signature effectively stratified Fn-positive patients, suggesting potential for targeted therapeutic approaches. Our findings reveal that Fn disrupts sIgA production, increasing tumor microbial burden and worsening prognosis through chronic inflammation in Fn-positive CRC.},
}

*Colorectal Neoplasms/microbiology/immunology/pathology
Animals
*Immunoglobulin A, Secretory/immunology/metabolism/genetics
Humans
Mice
*Fusobacterium nucleatum/immunology/physiology
*Fusobacterium Infections/immunology/microbiology/complications
Prognosis
Gastrointestinal Microbiome
Tumor Microenvironment
Female
Male
Tumor-Associated Macrophages/immunology
Mice, Inbred C57BL
Disease Models, Animal
Plasma Cells/immunology

@article {pmid40667520,
year = {2025},
author = {Miyamae, N and Ogai, K and Kunimitsu, M and Okamoto, S and Fujiwara, M and Nagai, M and Okuwa, M and Oe, M},
title = {Changes in the Skin Microbiome of a Patient with Head and Neck Cancer with Severe Radiodermatitis: A Case Report.},
journal = {Case reports in oncology},
volume = {18},
number = {1},
pages = {958-964},
pmid = {40667520},
issn = {1662-6575},
abstract = {INTRODUCTION: Identifying the skin microbiome associated with severe radiodermatitis could lead to the development of preventive care strategies and early healing interventions, which are currently lacking. In this study, we investigated changes in the skin microbiome of a patient with head and neck cancer who developed severe radiodermatitis from the initiation of radiation therapy to the resolution of dermatitis.

CASE PRESENTATION: An 82-year-old male underwent chemoradiotherapy with cisplatin (69.96 Gy/33 fractions) for recurrent laryngeal cancer after a total laryngectomy. At baseline, Cutibacterium accounted for 64.3% of the skin microbiome and Staphylococcus for 23.2%. During the occurrence of moist desquamation associated with severe radiodermatitis, Cutibacterium decreased sharply to 0.2%, whereas Staphylococcus increased to 91.0%. Species-level analysis revealed that Staphylococcus aureus was dominant at 50.6%, whereas Staphylococcus hominis and Staphylococcus epidermidis were identified at 0.4% and 1.7%, respectively.

CONCLUSION: These findings demonstrated that changes in the skin microbiome occur during the progression of severe radiodermatitis. The reduction in Cutibacterium and overgrowth of Staphylococcus, particularly Staphylococcus aureus, suggest their involvement in the development of severe radiodermatitis in patients with head and neck cancer.},
}

@article {pmid40667443,
year = {2025},
author = {Wei, J and Ding, W and Song, K and Zhang, Y and Luo, Q and Qi, C},
title = {Next-generation probiotics and engineered BEVs for precision therapeutics in osteoporosis.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1581971},
pmid = {40667443},
issn = {2296-861X},
abstract = {Osteoporosis, characterized by reduced bone density and increased fracture risk, faces limitations with conventional therapies due to adverse effects and poor gut microbiota modulation. Emerging strategies leveraging probiotics and bacterial extracellular vesicles (BEVs) offer novel therapeutic potential by targeting the gut-bone axis. Engineered probiotics and next-generation formulations enhance osteoprotection via immunomodulation, metabolite production (e.g., SCFAs), and neuroendocrine regulation. BEVs, as biocompatible nanocarriers, enable targeted delivery of osteogenic factors while circumventing colonization challenges. Synthetic biology advances facilitate precision engineering of probiotics and BEVs, improving therapeutic efficacy and scalability. This review highlights pre-clinical and clinical progress, challenges in standardization and safety, and future directions for microbiome-based interventions to revolutionize osteoporosis management. Integrating engineered probiotics with BEV technology promises transformative approaches for bone health restoration.},
}

@article {pmid40667442,
year = {2025},
author = {Zhang, X and Chen, K and Lan, H and Chen, H and Chen, H and Yang, P and He, N and Hung, W and Zeng, Z and Liu, C},
title = {Effect of Bifidobacterium longum subsp. infantis YLGB-1496 on common diseases in pediatrics: a randomized, blinded, placebo-controlled trial.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1585504},
pmid = {40667442},
issn = {2296-861X},
abstract = {INTRODUCTION: Respiratory, gastrointestinal, and allergic diseases can significantly impact both the physical and mental health of children, affecting their overall quality of life. This study aimed to evaluate the preventive effects and safety of Bifidobacterium longum subsp. infantis YLGB-1496 in relation to respiratory, gastrointestinal, and allergic diseases in children.

METHODS: Eligible healthy children were randomly assigned to either an intervention group (IG, n = 50), which received the probiotic, or a control group (CG, n = 50), which received a placebo, for a duration of 3 months. The primary outcome was the morbidity of upper respiratory tract infections (URTIs). Gut microbiota profiles were assessed via fecal 16S rRNA sequencing. Fecal immune biomarkers, including cytokines, immunoglobulins, and short-chain fatty acids (SCFAs), were measured to evaluate immune and metabolic responses.

RESULTS: The morbidity of URTIs over the 3-month intervention and follow-up period was significantly lower in the IG than in the CG. The incidence of upper respiratory tract infections (URTIs) over the 3-month intervention and follow-up period was significantly lower in the IG than in the CG, based on intention-to-treat (ITT) analysis [34.0% (17/50) vs. 58.0% (29/50), χ[2] = 5.797, p = 0.016]. Per protocol (PP) analyses yielded similar results [36.2% (17/47) vs. 60.4% (29/48), χ[2] = 5.59, p = 0.018]. YLGB-1496 supplementation significantly increased the relative abundance of Bifidobacterium bifidum, Bifidobacterium kashiwanohense PV2, and Bifidobacterium longum, while reducing Bacteroides thetaiotaomicron levels in the IG compared to the CG (p < 0.05). Additionally, YLGB-1496 reduced fecal levels of pro-inflammatory factors (IL-1β and IFNγ) levels, and increased levels of immunoglobulin (IgA, IgG, and IgM) and SCFAs (including butyric acid and total SCFAs).

CONCLUSION: Daily administration of YLGB-1496 at a dosage of 1.5 × 10[10] CFU for 3 months significantly reduced the episodes of cough, fever, dry stool (defined as Bristol stool scale type 1-3), and eczematous changes of the skin. It also decreased the morbidity of URTIs, bronchopneumonia, and eczema, while beneficially modulating gut microbiome composition and immune function without any adverse effects.

CLINICAL TRIAL REGISTRATION: https://www.isrctn.com/ISRCTN12824613, identifier: ISRCTN12824613.},
}

@article {pmid40667355,
year = {2025},
author = {Amarnani, A and Rivera, CF and Cornwell, M and Weinstein, T and Gottesman, SRS and Loomis, C and Azad, Z and Lee, A and Prasad, J and Barnes, B and Yi, M and Ullah, N and Gisch, N and Ruggles, K and Ramkhelawon, B and Silverman, GJ},
title = {Pathogenic strains of a gut commensal drive systemic platelet activation and thromboinflammation in lupus nephritis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.20.641288},
pmid = {40667355},
issn = {2692-8205},
abstract = {Imbalances in the gut microbiome have been linked to increased intestinal permeability and disease flares in systemic lupus erythematosus (SLE). Our study revealed that patients with flares of lupus nephritis (LN) and intestinal expansions of the anaerobic commensal, Ruminococcus gnavus (RG), displayed whole blood transcriptome profiles indicative of platelet, neutrophil, and myeloid cell activation, a profile reminiscent of sepsis. Serum analysis confirmed elevated serum levels of Platelet Factor 4 and neutrophil extracellular traps, which significantly correlated with levels of IgG-antibody to a novel lipoglycan (LG) produced by pathogenic RG strains, which was also documented in an independent LN cohort. To test for causality, in vivo mouse models further demonstrated that gut colonization with LG-producing RG strains, as well as a single intraperitoneal challenge with an LG preparation, caused platelet activation and megakaryocytosis in bone marrow and spleen. Mice colonized with RG strains that produce LG developed cellular infiltration of the kidneys by neutrophils and monocytes. Hence, RG expansions during renal flares may identify a specific LN flare endotype driven by thromboinflammatory mechanisms. Antibodies that arise from immune exposure to the RG lipoglycan may serve as a surrogate biomarker, helping to elucidate the impact of the relationship between gut microbiota communities and clinical outcomes in patients afflicted by LN. [208].},
}

@article {pmid40667290,
year = {2025},
author = {Rutkowski, N and Yang, B and Gray-Gaillard, E and Ruta, A and Mejías, JC and Patatanian, M and Cherry, C and Stivers, KB and Ramanujam, S and Price, NL and Housseau, F and Pardoll, DM and Sears, CL and Elisseeff, JH},
title = {Antibiotic-induced microbiota depletion impairs the pro-regenerative response to a biological scaffold in mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.23.661121},
pmid = {40667290},
issn = {2692-8205},
abstract = {UNLABELLED: Therapeutic biological scaffolds promote tissue repair primarily through the induction of type 2 immunity. However, systemic immunological factors-including aging, sex, and previous infections-can modulate this response. The gut microbiota is a well-established modulator of immune function across organ systems, yet its influence on type 2-mediated repair remains underexplored. Here, we establish a bidirectional relationship between the gut microbiota and biological scaffold-mediated tissue repair. Utilizing a conventionalized germ-free mouse, we demonstrate that scaffold implantation induces compositional and functional changes in the gut microbiome, particularly affecting amino acid biosynthesis. Additionally, in a model of antibiotic-induced microbiota depletion (AIMD), we show that dysbiosis disrupts key immune regulators of type 2 immunity, including reductions in eosinophils, pro-regenerative macrophages, and IL-4-producing CD4 [+] T cells. At 6 weeks post-scaffold implantation, we observed a significant decrease in myocytes with centrally located nuclei alongside an upregulation in pro-fibrotic gene expression with antibiotic treatment. These findings provide insights into the influence of the gut microbiota on type 2-mediated tissue repair.

SIGNIFICANCE STATEMENT: Antibiotics are routinely administered perioperatively to prevent infection during surgeries and biomaterial implantation. Here, we demonstrate that antibiotic-induced microbiota depletion disrupts the type 2 immune response critical for biomaterial-mediated tissue repair. Our findings highlight the gut microbiota as a determinant of constructive healing and a potential contributor to inter-individual variability in responses to biologic scaffolds.},
}

@article {pmid40667084,
year = {2025},
author = {Mohssen, M and Zayed, AA and Kigerl, KA and Du, J and Smith, GJ and Schwab, JM and Sullivan, MB and Popovich, PG},
title = {Precision Prediction of Microbial Ecosystem Impact on Host Metabolism Using Genome-Resolved Metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.27.661827},
pmid = {40667084},
issn = {2692-8205},
abstract = {Microbes drive ecosystem function through their physical interactions and metabolic transformations. However, since microbiomes are ecologically and metabolically interconnected, it is challenging to predict emergent ecosystem responses once the microbiome is disturbed. While it is widely acknowledged that mammalian gut dysbiosis influences host metabolism, mechanistic links that predict these effects are understudied. This study employs a genome-resolved eco-systems biology approach, using a high-resolution 'spinal cord-gut axis' model system and dataset, to predict how dysbiotic gut metabolism impacts overall mammalian health. By scaling and combining temporally resolved network analytics and consensus statistical methods, key microbial species were identified that predict overall host physiology and presumably control the gut ecosystem. In silico validation by pathway-centric functional analyses and comparative genomics revealed that key bacteria, sometimes exclusively, encode functions linking microbial and host metabolisms. Notably, spinal-mediated disturbances in the ecosystem shifted gut microbial nitrogen metabolism from urease-to amino acid-dependent pathways, with patterns that varied by host sex and bacterial species. Overall, this research challenges the traditional paradigm that only the host maintains whole-body nitrogen balance and instead invokes the microbiome as an environmentally-sensitive regulatory organ that can dictate health or disease by influencing mammalian whole-body elemental balance.},
}

@article {pmid40666980,
year = {2025},
author = {Markey, L and Qu, EB and Mendall, C and Finzel, A and Materna, A and Lieberman, TD},
title = {Microbiome diversity of low biomass skin sites is captured by metagenomics but not 16S amplicon sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.24.661265},
pmid = {40666980},
issn = {2692-8205},
abstract = {UNLABELLED: Established workflows for microbiome analysis work well for high microbial biomass samples, like stool, but often fail to accurately define microbial communities when applied to low microbial biomass samples. Here, we systemically compare microbiome analysis methods -16S rRNA sequencing, shallow metagenomics, and qPCR PMP™ panels-as well as extraction methods across skin swab samples and mock community dilutions. While extraction method minimally impacted results, with no significant signal for method-specific contamination or bias, we observed critical differences in inferred composition across analysis methods for low biomass samples. Metagenomic sequencing and qPCR revealed concordant, diverse microbial communities on low biomass leg skin samples, whereas 16S amplicon sequencing exhibited extreme bias toward the most abundant taxon. Both qPCR and metagenomics showed that female genital tract bacteria dominated the leg skin microbiome in about half of female subjects. Metagenomics also enabled sub-species analysis, which demonstrated that individuals have consistent within-species diversity across high-biomass forehead and low-biomass leg skin sites. This work illustrates that shallow metagenomics provides the necessary sensitivity and taxonomic resolution to characterize species and strain-level diversity in extremely low biomass samples, opening possibilities for microbiome discovery in previously unexplored niches.

IMPORTANCE: Despite the importance of the skin microbiome in health and disease, there have been far fewer studies characterizing the microbiome of skin compared to that of the gut. In part, this is because microbiome methods were initially developed for bacteria-rich samples like stool and these methods perform poorly on bacteria-poor samples like skin swabs. The perceived difficulty of getting reliable data from such low biomass sites has limited the scope and types of analyses performed. Here we demonstrate that shotgun, whole-genome, metagenomic sequencing recovers the full input from even very dilute control community samples, and reveals a highly diverse population even on very low biomass skin sites. We describe a streamlined sample processing and analysis pipeline which can be applied broadly to characterize low biomass microbiome samples and reveal new host-microbiome interactions.},
}

@article {pmid40666978,
year = {2025},
author = {Chatman, CC and Majumder, EL},
title = {Acute exposure to groundwater contaminants mixture of nitrate, atrazine and imidacloprid impacts growth kinetics of poultry cecal microbiomes and significantly decreases Caco-2 cell viability.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.15.659797},
pmid = {40666978},
issn = {2692-8205},
abstract = {UNLABELLED: Atmospheric deposition, and agricultural runoff or erosion events have substantially contributed to groundwater pollution throughout the USA. This can become troublesome in states like Wisconsin where 68% of the population rely on groundwater for their drinking water source. As such, exposome research must account for the complexity and frequency of environmental exposures. This study aimed to elucidate chemical-biological interactions and adverse outcome pathways associated with an environmentally relevant mixture of agricultural chemicals detected in Wisconsin groundwater via in vitro and in silico methodologies. Using in vitro models, we determined that a ternary mixture of environmentally relevant concentrations of nitrate, atrazine and imidacloprid resulted in an overt decline in growth rate to the poultry cecal microbiome compared to each chemical singularly. Further, there was a decrease in Caco-2 cell viability in various two-chemical combinations. In silico methods analyzed contaminants detected in Wisconsin groundwater wells from across the state and prioritized two groundwater wells as potential for health concerns. Prioritized chemicals in these groundwater wells were linked to nine gene targets and several adverse outcome pathways. In all, the results demonstrated that there is chemical-biological interaction between these model organisms agricultural and chemical mixtures at real world exposure concentrations.

HIGHLIGHTS: in silico methods were able to predict potential adverse effects for communities utilizing these groundwater wells 8 out of 9 chemicals prioritized with in silico tools were herbicides A ternary mixture of nitrate, imidacloprid and atrazine resulted in a decline in growth rate for poultry cecal microbiomeCaco-2 cells significantly impacted by two-chemical combinations but not ternary mixtures.},
}

@article {pmid40666935,
year = {2025},
author = {Sheikh, A and Scano, C and Xu, J and Ojo, T and Conforti, JM and Haberman, KL and King, B and Martinez, AS and Pujol, M and Watkins, J and Lotter, J and Lin, EL and Zechmann, B and Sevcik, A and Sayes, C and Gallagher, ES and Lang, SP and Mell, J and Ehrlich, GD and Taube, JH and Greathouse, KL},
title = {Outer membrane vesicles from Bacteroides fragilis contain coding and non-coding small RNA species that modulate inflammatory signaling in intestinal epithelial cells.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.25.661399},
pmid = {40666935},
issn = {2692-8205},
abstract = {Alterations to the community structure and function of the microbiome are associated with changes to host physiology, including immune responses. However, the contribution of microbe-derived RNAs carried by outer membrane vesicles (OMVs) to host immune responses remain unclear. This study investigated the role of OMVs and OMV-associated small RNA (sRNA) species from pathogenic and commensal Bacteroides fragilis (ETBF and NTBF respectively) in eliciting different immune responses from intestinal epithelial cells. To distinguish the differences in the sRNA profiles of the two strains and their OMVs, RNA-seq, qRT-PCR, and northern blotting were conducted to identify enrichment of discrete sRNA species in OMVs, which were also differentially expressed between the two strains. Specifically, both coding and non-coding RNAs were enriched in OMVs from NTBF and ETBF, with BF9343_RS22680 and BF9343_RS17870 being significantly enriched in ETBF OMVs compared to NTBF. To understand the effects of OMVs on pattern recognition receptors, reporter cells of Toll-like receptor (TLR) activation were treated with OMVs, demonstrating activation of TLRs 2, 3, and 7. Treatment of Caco-2 and HT29-MTX cells with OMVs demonstrated increased expression of IL-8. Surprisingly, we discovered that degradation of RNase-accessible RNAs within ETBF OMVs, but not NTBF OMVs, resulted in vesicles with enhanced capacity to stimulate IL-8 expression, indicating that these extravesicular RNAs exert an immunosuppressive effect. This suggests a dual role for OMV-associated RNAs in modulating host immune responses, with implications for both bacterial pathogenesis and therapeutic applications. Graphical Abstract.},
}

@article {pmid40666868,
year = {2025},
author = {Yang, Y and Wang, T and Huang, D and Wang, XW and Weiss, ST and Korzenik, J and Liu, YY},
title = {Deep Learning Transforms Phage-Host Interaction Discovery from Metagenomic Data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.26.656232},
pmid = {40666868},
issn = {2692-8205},
abstract = {Microbial communities are essential for sustaining ecosystem functions in diverse environments, including the human gut. Phages interact dynamically with their prokaryotic hosts and play a crucial role in shaping the structure and function of microbial communities. Previous approaches for inferring phage-host interactions (PHIs) from metagenomic data are constrained by low sensitivity and the inability to accurately capture ecological relationships. To overcome these limitations, we developed PHILM (P hage- H ost Interaction L earning from M etagenomic profiles), a deep learning framework that predicts PHIs directly from the taxonomic profiles of metagenomic data. We validated PHILM on both synthetic datasets generated by ecological models and real-world data, finding that it consistently outperformed the co-abundance-based approach for inferring PHIs. When applied to a large-scale metagenomic dataset comprising 7,016 stool samples from healthy individuals, PHILM identified 90% more genus-level PHIs than the traditional assembly-based approach. In a longitudinal dataset tracking PHI dynamics, PHILM's latent representations recapitulated microbial succession patterns originally described using taxonomic abundances. Furthermore, we demonstrated that PHILM's latent representations served as more discriminative features than taxonomic abundance-based features for disease classifications. In summary, PHILM represents a novel computational framework for predicting phage-host interactions from metagenomic data, offering valuable insights for both microbiome science and translational medicine.},
}

@article {pmid40666844,
year = {2025},
author = {Alves, G and Ogurtsov, AY and Yu, YK},
title = {Biological Function Assignment Across Taxonomic Levels in Mass-Spectrometry-Based Metaproteomics via a Modified Expectation Maximization Algorithm.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.12.659309},
pmid = {40666844},
issn = {2692-8205},
abstract = {A major challenge in mass-spectrometry-based metaproteomics is accurately identifying and quantifying biological functions across the full taxonomic lineage of microorganisms. This issue stems from what we refer to as the "shared confidently identified peptide problem". To address this issue, most metaproteomics tools rely on the lowest common ancestor (LCA) algorithm to assign biological functions, which often leads to incomplete biological function assignments across the full taxonomic lineage of identified microorganisms. To overcome this limitation, we implemented an expectation-maximization (EM) algorithm, along with a biological function database, within MiCId workflow. Using synthetic datasets, our study demonstrates that the enhanced MiCId workflow achieves better control over false discoveries and improved accuracy in microorganism identification and biomass estimation compared to Unipept and MetaGOmics. Additionally, the updated MiCId offers improved accuracy and better control of false discoveries in biological function identification compared to Unipept, along with reliable computation of function abundances across the full taxonomic lineage of identified microorganisms. Reanalyzing human oral and gut microbiome datasets using the enhanced MiCId workflow, we show that the results are consistent with those reported in the original publications, which were analyzed using the Galaxy-P platform with MEGAN5 and the MetaPro-IQ approach with Unipept, respectively.},
}

@article {pmid40666811,
year = {2025},
author = {Li, X and Chen, J and Xu, C and Li, Y and Li, K},
title = {Galla chinensis alleviated liver damage induced by acetaminophen by regulating intestinal microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1589946},
pmid = {40666811},
issn = {1664-302X},
abstract = {INTRODUCTION: Drug-induced liver injury is a common condition of therapeutics and requires solutions other than drugs. Dietary supplements and herbal products have beneficial potential against liver failure and are often associated with changes in intestinal flora. This study was designed to investigate Galla chinensis (GC) potential in alleviating drug-induced liver injury.

METHODS: The treatment group and model group were administered 0.5 mL of GC oil daily for 14 days, followed by induction of acute drug-induced liver injury using Acetaminophen (APAP) on the 15th day via intraperitoneal injection. Serum biochemical analysis and intestinal bacteria 16S rRNA sequencing were conducted to explore the anti-drug liver injury activity of GC.

RESULTS: The results showed that GC treatment alleviated the increased liver organ index caused by APAP. Furthermore, serum biochemical analysis revealed that GC therapy reduced alanine transaminase (ALT) and aspartate transaminase (AST) levels, indicating a protective effect against APAP-induced liver injury. Additionally, GC demonstrated the ability to regulate the diversity and composition of intestinal microbes and help increase the prevalence of beneficial microbes such as Faecalibaculum and Odoribacter while reducing the prevalence of pathogenic bacteria, including Corynebacterium, Rikenella, Bacillus, Phocaeicola, and Alloprevotella.

DISCUSSION: Our findings indicate that GC plays a significant role in mitigating drug-induced liver injury by improving gut microbiome composition, reducing plasma ALT and AST levels, and inhibiting oxidative stress and inflammatory responses. The study further demands investigations to make pharmaceutical products to be used as nutraceuticals against drug-induced toxicities.},
}

@article {pmid40666810,
year = {2025},
author = {He, B and Zhang, P and Bai, X and Li, W and Zou, S},
title = {Compartment-specific dynamics of soil microbiota along a Pinus armandii plantation chronosequence in karst mountain ecosystems.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1626892},
pmid = {40666810},
issn = {1664-302X},
abstract = {Soil microbiomes play pivotal roles in mediating plant diversity maintenance by regulating multifunctional ecosystem services during plant development. However, how different stand age of plants influence soil microbial communities in various soil compartments remains poorly understood. Through Illumina-based 16S rRNA and ITS amplicon sequencing, we systematically investigated the successional trajectories of soil microbiome in Pinus armandii plantations spanning various developmental phases. Key findings revealed that stand age exerted a stronger influence on microbial restructuring than soil compartment, significantly altering community composition in both soil types. Alpha diversity (Shannon and Chao1 indices) exhibited a U-shaped trajectory with stand age, except for fungal Chao1 in bulk soil. While dominant bacterial and fungal phyla remained relatively stable, community composition displayed significant stage-dependent variations. Co-occurrence network analysis demonstrated lower fungal network complexity compared to bacterial networks, with rhizosphere soils harboring more intricate interactions compared to bulk soils. Community assembly mechanisms diverged: deterministic processes dominated bacterial assembly, whereas stochasticity governed fungal communities. Soil properties exerted significant influences on microbial composition and diversity: bacterial composition correlated strongly with pH and stoichiometric ratios (C/N, C/P, N/P), while fungal composition showed stronger associations with TN, TP, and AN. Our results demonstrate that P. armandii plantations maintain core phylum-level microbial populations while developing stage-specific diversity patterns. Crucially, bacteria and fungi exhibit divergent responses to stand development, highlighting their divergent ecological strategies in adapting to nutrient-limited karst ecosystems.},
}

@article {pmid40666793,
year = {2025},
author = {Riedmüller, J and Monteiro, A and Männer, K and Saliu, EM and Vahjen, W and Zentek, J},
title = {Effects of different doses and preparations of zinc oxide in weanling piglets on performance, intestinal microbiota and microbial metabolites.},
journal = {Translational animal science},
volume = {9},
number = {},
pages = {txaf073},
pmid = {40666793},
issn = {2573-2102},
abstract = {For years, high zinc levels (up to 3000 mg/kg feed) have been used to aid piglets during the weaning phase. However, studies revealed drawbacks like antimicrobial resistance and environmental impact. Since 2022, the EU limits zinc inclusion levels to 150 mg total zinc per kg. Therefore, alternative strategies for replacing high levels of zinc are of great interest. This study compares a potentiated zinc oxide source (HiZox[®]) and feed grade zinc oxide at various levels on piglet performance, fecal consistency and fecal microbiome. The trial involved a total of 1,440 healthy weaned piglets (DanBred × Duroc; 50% barrows, 50% gilts; initial BW 10.1 ± 1.46 kg) over the 28-day duration of the experimental period. Piglets were randomly assigned to 12 treatment groups, each consisting of 12 pens, with 10 piglets per pen. The trial comprised two periods: the starter period (days 1 to 14) focused on comparing the two zinc products, while all animals received a diet supplemented with 150 mg/kg of potentiated ZnO in the grower period (days 15 to 28). Treatment groups receiving feed grade ZnO were denoted as Z150, Z300, Z600, Z900, Z1500, and Z3000, while corresponding groups with the potentiated ZnO product were labeled H150, H300, H600, H900, H1500, and H3000, respectively. Body weight (BW) and feed intake (FI) were measured for every pen at days 1, 14 and 28. Fecal samples were collected on the same days. During the starter phase (days 1 to 14), potentiated ZnO significantly improved average daily gain (ADG) compared to feed-grade ZnO (P ≤ 0.001), with the highest values observed at 3000 mg/kg (H3000: 247 g/d vs. Z3000: 233 g/d). Feed intake (FI) was also higher in potentiated ZnO groups (P ≤ 0.001), and feed conversion ratio (FCR) was more efficient (e.g., H3000: 1.2 vs. Z3000: 1.24; P = 0.001). In the grower phase residual effects from the starter phase persisted: animals previously fed potentiated ZnO had improved FCR (P = 0.003). Fecal microbiota analysis revealed that higher zinc levels reduced Lactobacillus abundance (P ≤ 0.001) and increased the presence of genera typical of adult pigs, such as Clostridium sensu stricto 1 and Terrisporobacter (P < 0.01). In conclusion, based on the observed shift in fecal microbiota composition characterized by a reduction in lactobacilli and an increase in proteobacteria due to heightened dietary zinc levels, it is advised to adjust zinc supplementation to 150 mg/kg after the initial 2 wk post-weaning.},
}

@article {pmid40666732,
year = {2025},
author = {Cantas, L and Goll, R and Fenton, CG and Paulssen, RH and Sørum, H},
title = {Impact of fecal microbiota transplantation in dogs.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1505226},
pmid = {40666732},
issn = {2297-1769},
abstract = {BACKGROUND: The digestive tract hosts a variety of microorganisms. These microorganisms "micro-organs" play multiple crucial roles in physiological, immunological, and metabolic processes in the body. The manipulation and transplantation of "micro-organs" have lately gained increasing interest in human medicine with promising clinical outcomes, whereas much less is known in veterinary practice.

OBJECTIVES: The goals of this pilot study were to evaluate the safety and impact of Fecal Microbiota Transplantation (FMT) for dogs suffering from non-infectious digestive disorders.

ANIMALS: Seven client-owned adult dogs with idiopathic persistent diarrhea (>3 weeks) and very poor skin-coat conditions received the intervention (FMT) and were evaluated in a private veterinary clinic.

METHODS: Transplants have been taken from healthy donors and were administered rectally to recipients. Objective clinical examinations with analyses of blood and feces samples on day 0 (pre-FMT) and days 14-28 (post-FMT) were performed. Besides the conventional blood hematology and biochemistry analyses, 16S rRNA sequencing analysis was used in fecal samples.

RESULTS: No FMT-related complications occurred. Five of seven (71%) patients demonstrated improved fecal parameters associated with better overall clinical outcome, whereas four of the five (80%) recovered recipients showed molecular correlation with the donor gut microbiota after rectal FMT. There were insignificant changes shown for the conventionally analyzed blood samples. The serum cobalamin levels showed a tendency to increase in recovered recipients.

CONCLUSION: FMT was easy to apply and displayed certain health benefits in this study. Our findings reveal the important role of a "re-gained" gut microbiome balance in the overall health of dogs. Further research is needed to identify the dynamics and interplay between the different bacterial phyla that may have an impact on the stimuli of host immunologic and metabolic responses.},
}

@article {pmid40666332,
year = {2025},
author = {Golan, Y and Nyquist, SK and Liu, Z and Ennis, D and Zhao, J and Blair, E and Khan, AR and Prahl, M and Gaw, SL and Yassour, M and Engelhardt, BE and Flaherman, VJ and Ahituv, N},
title = {Genomic characterization of normal and aberrant human milk production.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.22.25329156},
pmid = {40666332},
abstract = {Breastfeeding is essential for reducing infant morbidity and mortality, yet exclusive breastfeeding rates remain low, often due to insufficient milk supply. The molecular causes of low milk production are not well understood. Fresh milk samples from 30 lactating individuals, classified by milk production levels across postpartum stages, were analyzed using genomic and microbiome techniques. Bulk RNA sequencing of milk fat globules (MFG), milk cells, and breast tissue revealed that MFG-derived RNA closely mirrors luminal milk cells. Transcriptomic and single-cell RNA analyses identified changes in gene expression and cellular composition, highlighting key genes (GLP1R, PLIN4, KLF10) and cell-type differences between low and high producers. Infant microbiome diversity was influenced by feeding type but not maternal milk supply. This study provides a comprehensive human milk transcriptomic catalog and highlights that MFG could serve as a useful biomarker for milk transcriptome analysis, offering insights into the genetic factors influencing milk production.},
}

@article {pmid40666331,
year = {2025},
author = {Quinn-Bohmann, N and Gibbons, SM},
title = {Metabolic modeling reveals determinants of synbiotic efficacy in a human intervention trial.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.24.25330246},
pmid = {40666331},
abstract = {Synbiotic interventions show variable effects across individuals, likely driven by ecological interactions with the endogenous microbiota and the host diet. Rationally predicting individual-specific success or failure of probiotic and prebiotic interventions remains an outstanding challenge. In this study, we leverage microbial community-scale metabolic models (MCMMs) to predict probiotic engraftment and shifts in microbiota-mediated short-chain fatty acid (SCFA) production in response to a synbiotic intervention. Using data from a placebo-controlled synbiotic intervention trial, involving a cocktail of five probiotic strains and the prebiotic inulin, we validate model engraftment predictions with quantitative PCR (qPCR), demonstrating that MCMMs accurately predict probiotic engraftment outcomes in the treatment group with over 85% accuracy. Engraftment varied by species, with Akkermansia muciniphila and Bifidobacterium infantis displaying higher engraftment rates than Clostridium beijerinckii, Anaerobutyricum hallii , and Clostridium butyricum . Furthermore, MCMMs predicted significant increases in butyrate and propionate production following synbiotic treatment. MCMM-predicted changes in propionate production in the treatment group were negatively associated with changes in C-reactive protein (CRP), a blood marker of systemic inflammation, from baseline to 12 weeks after the synbiotic intervention. Finally, we explore MCMM-predicted responses to a wider range of synbiotic combinations in a larger observational cohort, suggesting that personalized prebiotic selection can augment probiotic efficacy. These findings highlight the potential of metabolic modeling to inform precision microbiome therapeutics.},
}

@article {pmid40665938,
year = {2025},
author = {Chen, Q and Wang, F and Ma, G and Liu, C and Zhu, T and Wang, K and Wang, H},
title = {Microbial agents suppress jujube black spot disease and enhance jujube quality by regulating soil physicochemical and microbial properties.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70062},
pmid = {40665938},
issn = {1526-4998},
support = {//Central Guidance of Local Science and Technology Development Special Foundation of Shandong Province (YDZX2021088)/ ; //Open Project of Research Center of Pesticide Environmental Toxicology, Shandong Agricultural University (HJDL202407)/ ; //Shandong Provincial Key Research and Development Program (2024TSGC0619)/ ; },
abstract = {BACKGROUND: Jujube black spot disease, caused by the soil-borne pathogenic fungus Alternaria alternata, threatens the sustainability of the jujube industry by adversely affecting yield. However, it is unclear whether microbial agents can increase yield by improving soil, inhibiting jujube black spots, and regulating microbial communities.

RESULTS: Bacillus velezensis strain SDTB038 had significant inhibitory effects on A. alternata, and sound field control effects (the control effects after two applications were 39.71% and 41.97%). SDTB038 had good saline-alkali tolerance and grew well in Potato Dextrose Broth medium containing 1%-7% NaCl or over pH range of 4-10. Upon application of B-1, multiple soil parameters were significantly improved, including levels of soil organic matter, total nitrogen and available potassium, and the activities of soil urease, alkaline phosphatase, catalase and sucrase. In a Tai'an jujube orchard, soil organic matter reached 16.54 g/kg, soil organic carbon 28.51 g/kg, and total nitrogen content 1.93 g/kg, consistent with the data trend in the Kashi area. Furthermore, applying B-1 resulted in a more complex interaction network among soil microorganisms. B-1 promoted the enrichment of beneficial microorganisms such as Bacillus spp. and Sphingomonas spp., while significantly reducing Alternaria spp. and Fusarium spp. levels. This increased jujube yield and overall quality (single fruit weight increased by 1.22-1.72 times).

CONCLUSION: This study fills a gap in current research on the application of microbial agents to prevent and control of jujube diseases, and has important theoretical and practical significance. © 2025 Society of Chemical Industry.},
}

@article {pmid40665935,
year = {2025},
author = {Bak, MTJ and Olivera, PA and Hernandez-Rocha, C and Borowski, K and Turpin, W and Leibovitzh, H and Milgrom, R and Stempak, J and Silverberg, M and Lee, SH},
title = {Isolated Anastomotic Ulcers Are Associated with a Higher Long-Term Risk for Postoperative Recurrence and a Differential Mucosa-Associated Microbiome Composition in Patients with Crohn's Disease Following Ileocolic Resection.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf147},
pmid = {40665935},
issn = {1536-4844},
support = {/DK/NIDDK NIH HHS/United States ; 5U01DK062423/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: The clinical relevance and underlying mechanism of isolated anastomotic ulcers (IAUs) following ileocolic resection (ICR) in patients with Crohn's disease (CD) are poorly understood. This study aimed to assess the postoperative recurrence (POR) risk and the mucosa-associated microbiome composition in CD patients with or without IAUs among those with a healthy neo-terminal ileum (TI).

METHODS: CD patients who underwent ICR and without any ulcerations in the neo-TI (SES-CD ≤2) at first postoperative ileocolonoscopy were identified from an ongoing prospective multicenter study. The primary study outcome was time to POR measured from the first postoperative ileocolonoscopy. Cox proportional hazard models were used to assess the association of IAUs with time to POR. The mucosa-associated microbiome at first ileocolonoscopy was assessed by sequencing the 16S rRNA gene using biopsies taken from both sides of the anastomosis.

RESULTS: Sixty patients were included, of whom 27 patients had IAUs (45.0%) at first ileocolonoscopy. Median time to first postoperative ileocolonoscopy was 6.5 months (interquartile range [IQR] 5.3-8.1). During a median follow-up duration of 3.0 years (IQR 1.4-5.5) after first postoperative ileocolonoscopy, POR was observed in 53.3%. After adjustment for clinical risk factors, IAUs were independently associated with POR (adjusted hazard ratios 5.4; 95% CI 2.4-12.4; P < .001). At the ileal and colonic side of the anastomosis, a significantly higher abundance of Klebsiella was associated with IAUs (q < 0.05).

CONCLUSIONS: IAUs in CD patients with otherwise healthy neo-TI at first postoperative ileocolonoscopy are associated with long-term POR. In addition, a differential mucosa-associated microbiome composition was observed in patients with IAUs, specifically the proteobacteria Klebsiella, suggesting that putative taxa are related to these lesions. Further validation studies in larger cohorts, along with mechanistic studies, are still required.},
}

@article {pmid40665871,
year = {2025},
author = {Bucking, C and Terblanche, JS and Regan, MD},
title = {The ins and outs of integrative digestive biology.},
journal = {The Journal of experimental biology},
volume = {228},
number = {14},
pages = {},
doi = {10.1242/jeb.250770},
pmid = {40665871},
issn = {1477-9145},
support = {RGPIN-2021-03606//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2021-03109//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; *Digestive System Physiological Phenomena ; *Gastrointestinal Tract/physiology ; },
abstract = {The digestive system facilitates exchanges between animals and their environments. It not only converts resources into energy and growth but also shapes ecosystem processes through waste outputs, all while mediating an animal's relationship with complex microbial communities. The Special Issue: The Integrative Biology of the Gut delves into many aspects of this expansive relationship. Further, this Commentary collects the special issue papers under themes to highlight and explore the physiology of the digestive system and the plasticity that enables its acclimatization to dietary and environmental changes. The themes that have been identified portray the gastrointestinal (GI) tract as an integrative moderator of physiology, and show that when this system is explored using novel techniques or by asking innovative questions, one can reveal phenomena with applications well beyond digestive biology. Further, we discuss how embracing multidisciplinary approaches - including systems biology, evolutionary comparisons and environmental considerations - will allow us to use the unique physiology of the GI tract to form critical insights into evolved organismal biology, microbial symbioses and ecological stewardship. Ultimately, the pivotal role of the GI tract in connecting internal physiology with external ecological dynamics across taxa exemplifies its value as a model system.},
}

Animals
*Digestive System Physiological Phenomena
*Gastrointestinal Tract/physiology

@article {pmid40665828,
year = {2025},
author = {Arroyo-Calatayud, M and Haberl, EM and Olivares, L and Collado, MC and Schaubeck, M},
title = {Impact of extensively hydrolyzed infant formula on the probiotic and postbiotic properties of Lactobacillus fermentum in an in vitro co-culture model.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo06330a},
pmid = {40665828},
issn = {2042-650X},
abstract = {Early gut homeostasis is a balance between dietary antigen exposure, gut barrier function, microbiome establishment and orchestration of innate and adaptive immune responses. Imbalances during this early time of development can lead to increased susceptibility to immune reactions like allergy. Especially for infants with a predisposition to allergies and who cannot be exclusively breastfed, there are different human milk substitutes, including hydrolyzed infant formula, which are supposed to prevent allergy-associated mechanisms. The physiologic mechanism beyond the destruction of cow's milk allergenic structures in those formulas are currently not fully understood. Therefore, our aim was to elucidate the impact of hydrolyzed infant formula on intestinal homeostasis and presumed mechanisms behind the beneficial effects. In this study, we used a triple co-culture in vitro model of gut inflammation and homeostasis, including enterocyte-, goblet- and macrophage-like cells in a transwell setup, to assess the effect of extensively hydrolyzed (eHF) infant formula compared to standard cow's milk-based infant formula with intact protein (iPF). These formulas were combined or not with heat-inactivated Limosilactobacillus fermentum CECT 5716 (Lf) to test the effect of probiotic compounds in combination with different types of infant formula (i.e. eHF and iPF) on the intestinal barrier and cytokine production. Under LPS-inflammatory trigger, eHF and eHF + Lf increased mucus production and MUC2 mRNA expression, restored epithelial barrier integrity and increased secretion of regulatory TGFβ, compared to respective controls. These results suggest a beneficial role for eHF, and especially eHF + Lf, in restoring intestinal homeostasis and attenuating pro-inflammatory responses.},
}

@article {pmid40665733,
year = {2025},
author = {Hao, X and Wu, T and Li, X and He, Q and Qin, Y and Zhang, N and Yu, H and Jiang, Y and Gao, F},
title = {Dietary energy improves Holstein heifer conception through rumen microbiota interactionsfers during initial breeding.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.25.0141},
pmid = {40665733},
issn = {2765-0189},
abstract = {OBJECTIVE: This study aimed to elucidate how graded dietary energy levels regulate the hypothalamic-pituitary-gonadal axis in Holstein heifers during initial breeding, with a focus on rumen microbiota-host interactions.

METHODS: Forty-four pubertal heifers (398.96 ± 6.56 kg BW; 12.72 ± 0.02 months) were stratified by body condition score (BCS) and estrous cyclicity, then randomly allocated to control (CON, 8.64 MJ/kg DM NEL) or high-energy (HE, 9.50 MJ/kg DM NEL) diets (n = 22/group). Although practical constraints limited pen replication, we implemented rigorous matching procedures: Pens were matched for surface area (120 m²), feed bunk space (0.8 m/head) and growth performance, serum biochemical/immune/antioxidant markers, reproductive hormones, rumen fermentation parameters, microbiota, and metabolome profiles were analyzed.

RESULTS: Results The HE group exhibited elevated gonadotropins (FSH, LH) and prolactin (PRL), indicating enhanced hypothalamic-pituitary activity. Serum triglycerides increased, while immune markers showed the altered state of immunoregulation characterized by significant increases in IL-2 and IL-6, reductions in IL-4, and decreases in TNF-α and IFN-γ. Antioxidant capacity improved with lower MDA levels. Rumen pH decreased, accompanied by elevated total VFA, bacterial crude protein(BCP), acetic acid, propionic acid, butyric acid, and valeric acid concentrations. Microbial shifts included Treponema and Prevotellaceae_UCG_003 showing positive correlations with PRL and LH, while Ruminococcus was associated with acetyl-CoA precursors through enriched pyruvate metabolism.

CONCLUSION: High-energy diets (9.50 MJ/kg NEL) enhance hypothalamic-pituitary signaling and rumen fermentation efficiency, advancing first-service conception rates by 15% (55% vs. 70%) in pasture-based systems. This strategy optimizes reproductive management in intensive dairy operations through microbiota-driven metabolic modulation.},
}

@article {pmid40665731,
year = {2025},
author = {Zhou, X and Shen, X},
title = {Evaluation of garlic skin as a forage source for goats: Effects on performance, antioxidant capacity , immune function and.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.25.0169},
pmid = {40665731},
issn = {2765-0189},
abstract = {OBJECTIVE: This study aimed to evaluate the effects of garlic skin as a feed ingredient on growth performance, antioxidant capacity, immune function, and rumen health in goats.

METHODS: Twelve male black goats with similar body conditions were randomly assigned to two groups. The control group (CON) was fed a basal diet, while the experimental group (GAS) received a diet supplemented with garlic skin for 60 days.

RESULTS: Results showed that goats' final weight (FW) and average daily gain (ADG) significantly increased in the GAS group compared to the CON group (p < 0.05). The GAS group exhibited enhanced activities of total superoxide dismutase (T-SOD), glutathione peroxidase (GSH-Px), catalase (CAT), and higher total antioxidant capacity (T-AOC) levels, while malondialdehyde (MDA) content significantly decreased (p < 0.05). Immunoglobulin A (IgA) and immunoglobulin G (IgG) levels were significantly elevated, along with increased concentrations of anti-inflammatory cytokines interleukin-4 (IL-4) and interleukin-10 (IL-10), whereas pro-inflammatory cytokines interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) were significantly reduced (p < 0.05). The rumen fluid of GAS group showed significant increases in ammonia nitrogen, acetate, propionate, and total volatile fatty acids, with a reduction in the acetate-to-propionate ratio (p < 0.05). Significant improvements were also observed in rumen papilla height, width, and density (p < 0.05). 16S rDNA analysis revealed enhanced microbial diversity and enrichment of functional bacterial groups, such as Firmicutes and Christensenellaceae_R-7_group, involved in fiber degradation and volatile fatty acid production. Key metabolites, including 5-methylthioribose and glucose 6-phosphate, were positively correlated with growth and antioxidant capacity, while 21-deoxycortisol negatively affected metabolic balance.

CONCLUSION: In conclusion, garlic skin supplementation enhanced antioxidant and immune function, optimized rumen fermentation, improved microbial composition, and promoted goat health and productivity.},
}

@article {pmid40665422,
year = {2025},
author = {Gfeller, V and Schneider, M and Bodenhausen, N and Horton, MW and Wille, L and Oldach, KH and Studer, B and Hartmann, M and Messmer, MM and Hohmann, P},
title = {Crop genotype modulates root rot resistance-associated microbial community composition and abundance of key taxa.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {89},
pmid = {40665422},
issn = {2524-6372},
support = {GRS-082/19//Gebert Rüf Foundation, Schwiez/ ; GRS-082/19//Gebert Rüf Foundation, Schwiez/ ; GRS-082/19//Gebert Rüf Foundation, Schwiez/ ; GRS-082/19//Gebert Rüf Foundation, Schwiez/ ; GRS-082/19//Gebert Rüf Foundation, Schwiez/ ; GRS-082/19//Gebert Rüf Foundation, Schwiez/ ; GRS-082/19//Gebert Rüf Foundation, Schwiez/ ; Root2Res (EU Horizon Europe no. 101060124 and Swiss State Secretariat for Education, Research and Innovation no 23.00050)//European Commission (European Union) and Swiss State Secretariat for Education, Research and Innovation (Switzerland)/ ; Root2Res (EU Horizon Europe no. 101060124 and Swiss State Secretariat for Education, Research and Innovation no 23.00050)//European Commission (European Union) and Swiss State Secretariat for Education, Research and Innovation (Switzerland)/ ; Root2Res (EU Horizon Europe no. 101060124 and Swiss State Secretariat for Education, Research and Innovation no 23.00050)//European Commission (European Union) and Swiss State Secretariat for Education, Research and Innovation (Switzerland)/ ; Root2Res (EU Horizon Europe no. 101060124 and Swiss State Secretariat for Education, Research and Innovation no 23.00050)//European Commission (European Union) and Swiss State Secretariat for Education, Research and Innovation (Switzerland)/ ; LIVESEED (EU Horizon 2020 no. 727230 and Swiss State Secretariat for Education, Research and Innovation no. 17.0009)//European Commission (European Union) and Swiss State Secretariat for Education, Research and Innovation (Switzerland)/ ; RYC2022-037997-I//MICIU/AEI/10.13039/501100011033 and FSE+/ ; },
abstract = {BACKGROUND: Plants are constantly challenged by pathogens, which can cause substantial yield losses. The aggressiveness of and damage by pathogens depends on the host-associated microbiome, which might be shaped by plant genetics to improve resistance. How different crop genotypes modulate their microbiota when challenged by a complex of pathogens is largely unknown. Here, we investigate if and how pea (Pisum sativum L.) genotypes shape their root microbiota upon challenge by soil-borne pathogens and how this relates to a genotype's resistance. Building on the phenotyping efforts of 252 pea genotypes grown in naturally infested soil, we characterized root fungi and bacteria by ITS region and 16 S rRNA gene amplicon sequencing, respectively.

RESULTS: Pea genotype markedly affected both fungal and bacterial community composition, and these genotype-specific microbiota were associated with root rot resistance. For example, genotype resistance was correlated (R[2] = 19%) with root fungal community composition. Further, several key microbes, showing a high relative abundance, heritability, connectedness with other microbes, and correlation with plant resistance, were identified.

CONCLUSIONS: Our findings highlight the importance of crop genotype-specific root microbiota under root rot stress and the potential of the plant to shape its associated microbiota as a second line of defense.},
}

@article {pmid40665363,
year = {2025},
author = {Liu, Y and Hou, J and Qi, Z and Yang, L and Du, Z and Wu, Y and Song, Q and Li, X and Sun, J and Chen, P and Guan, X and Li, L},
title = {Prenatal psychological stress mediates vertical transmission of gut microbiome to the next generation affecting offspring depressive-like behaviors and neurotransmitter.},
journal = {BMC psychology},
volume = {13},
number = {1},
pages = {791},
pmid = {40665363},
issn = {2050-7283},
support = {S202210471038//College Student Innovation and Entrepreneurship Training Program in Henan/ ; 81973596//National Natural Science Foundation of China/ ; 212102310341//Science and Technology Innovation Talents in Universities of Henan Province/ ; 20B360004//Key Scientific Research Foundation of the Higher Education Institutions of Henan Province/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Pregnancy ; Female ; *Stress, Psychological/metabolism/microbiology ; *Prenatal Exposure Delayed Effects/metabolism/microbiology/psychology ; Rats ; *Depression/microbiology/metabolism ; *Neurotransmitter Agents/metabolism ; *Dysbiosis/microbiology/metabolism ; Male ; Disease Models, Animal ; Rats, Sprague-Dawley ; Behavior, Animal ; Prefrontal Cortex/metabolism ; Feces/microbiology ; },
abstract = {OBJECTIVE: Prenatal stress has been proven to be associated with dysbiosis of the gut microbiota. Despite the established phenomenon that psychological stress can be transmitted to offspring and the ability of maternal gut microbiota to colonize the offspring's gut through vertical transmission, the intricate relationships linking cross-generational depression with the microbiome remain poorly understood.

METHODS: We utilized combined fear stress stimuli to establish a pregnancy psychological stress (PPS) rat model, in which offspring exhibited trans-generational depression-like behavior. The relationship between vertical transmission of the gut microbiome, intergenerational effects, and psychological stress in offspring was investigated using microbiology and metabolomics.

RESULTS: We demonstrated that the vertical transmission of co-altered species from PPS dams to their puberty offspring was strongly associated with dysbiosis of the gut microbiota in the offspring. In terms of microbial function, both PPS dams and their offspring exhibited upregulation of glycine, glutamate, and serine metabolism in fecal samples, as revealed by untargeted metabolomics. Additionally, this microbial trans-generational effect was reflected in the prefrontal cortical tissue of PPS offspring, where serine in the pathway and its interconverted glycine was significantly increased. Furthermore, the co-altered species and metabolites of the pathway formed a highly correlated module with disordered inflammatory factors and neurotransmitters in the prefrontal cortex tissue of PPS offspring. This indicates that the microbiome plays a significant role in prefrontal cortex neuroinflammation as well as neurotransmitter disorders in depression-like offspring.

CONCLUSIONS: Our findings highlight the gut microbiome as a plausible mediator of prenatal stress effects on offspring neurodevelopment, though further mechanistic validation is required.},
}

Animals
*Gastrointestinal Microbiome/physiology
Pregnancy
Female
*Stress, Psychological/metabolism/microbiology
*Prenatal Exposure Delayed Effects/metabolism/microbiology/psychology
Rats
*Depression/microbiology/metabolism
*Neurotransmitter Agents/metabolism
*Dysbiosis/microbiology/metabolism
Male
Disease Models, Animal
Rats, Sprague-Dawley
Behavior, Animal
Prefrontal Cortex/metabolism
Feces/microbiology

@article {pmid40665305,
year = {2025},
author = {Zhang, W and Xiang, Y and Ren, H and Liu, Y and Wang, Q and Ran, M and Zhou, W and Tian, L and Zheng, X and Qiao, C and Liu, Y and Yan, M},
title = {The tumor microbiome in cancer progression: mechanisms and therapeutic potential.},
journal = {Molecular cancer},
volume = {24},
number = {1},
pages = {195},
pmid = {40665305},
issn = {1476-4598},
support = {YJSCX2024-78HYD//Postgraduate Research & Practice Innovation Program of Harbin Medical University/ ; No.82472867//National Natural Science Foundation of China/ ; YQ2024H003//The Outstanding Young Scholar Project of the Natural Science Foundation of Heilongjiang Province/ ; },
mesh = {Humans ; *Neoplasms/microbiology/therapy/pathology/etiology/metabolism ; Tumor Microenvironment/immunology ; *Microbiota ; Disease Progression ; Animals ; Signal Transduction ; },
abstract = {The tumor microbiome (TM) comprises diverse microbial communities, such as bacteria, fungi, and viruses. Recent advancements in microbial sequencing technologies have improved our understanding of the distribution and functional roles of microbes in solid tumors. The TM is formed through several mechanisms, such as direct invasion of mucosal barriers, diffusion from adjacent normal tissues, metastasis of tumor cells, and dissemination via blood and lymphatic circulation. Microbes play a critical role in the tumor microenvironment (TME), and the TM has a heterogeneous composition in different types of cancer. This heterogeneity affects tumor development, progression, and response to treatment. The TM modulates tumor cell physiology and immune responses via several signaling pathways, such as WNT/β-catenin, NF-κB, toll-like receptors (TLRs), ERK, and stimulator of interferon genes (STING). Extensive studies have characterized the role of TM in tumor progression, revealing the importance of genetic abnormalities, epigenetic changes, metabolic regulation, invasion and metastasis, and chronic inflammatory responses. The role of TM in cancer treatment, especially in immunotherapy, has received increasing attention, demonstrating significant regulatory potential. This review provides an in-depth overview of the development of TM detection technologies, explores its potential origins and heterogeneity, and elucidates the mechanisms by which TM contributes to tumorigenesis or tumor suppression. Furthermore, this review explored how TM can be used in cancer treatment, offering a comprehensive perspective on targeted and personalized approaches.},
}

Humans
*Neoplasms/microbiology/therapy/pathology/etiology/metabolism
Tumor Microenvironment/immunology
*Microbiota
Disease Progression
Animals
Signal Transduction

@article {pmid40665229,
year = {2025},
author = {Curtis, A and Harrison, F and Kavanagh, K},
title = {Proteomic characterization of Aspergillus fumigatus - host interactions using the ex-vivo pig lung (EVPL) model.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2530675},
doi = {10.1080/21505594.2025.2530675},
pmid = {40665229},
issn = {2150-5608},
mesh = {Animals ; *Aspergillus fumigatus/pathogenicity/physiology/metabolism/genetics ; Swine ; *Lung/microbiology/immunology ; Proteomics ; *Host-Pathogen Interactions ; Disease Models, Animal ; *Proteome/analysis ; },
abstract = {Aspergillus fumigatus is an opportunistic fungal pathogen of the human airway that can cause a variety of chronic infections, typically in the context of pre-existing lung damage. The interaction of A. fumigatus with ex-vivo pig lung (EVPL) samples was characterized at the proteomic level to provide insights into how the fungus may interact with pulmonary tissue in vivo. This model has many advantages, because pigs share 90% immunological homology with humans and display many anatomical similarities. EVPL also retains resident immune cells, has richer cellular complexity compared to in-vitro models, and has a microbiome. Label-free quantitative proteomic analysis identified the metabolism and development of A. fumigatus on the EVPL alveolar sections; at 48 h, there was an increased abundance of proteins associated with carbon metabolism (e.g. malate dehydrogenase (+8.2 fold increase)), and amino acid metabolism and biosynthesis (e.g. 5-methyltetrahydropteroyltriglutamate - homocysteine S-methyltransferase, (+5.04 fold)) at 72 h. Porcine tissue remained responsive to the pathogen with proteins that increased in abundance associated with innate immune recruitment (e.g. protein S100-A8 (+28.5 fold) and protein S100-A9 (calgranulin-B) (+7.25 fold)) at 24 h, while proteins associated with neutrophil degranulation (e.g. elastase, neutrophil (-2.74 fold)) decreased in abundance. At 96 h, the infected tissue demonstrated enhanced abundance of fibrotic markers (e.g. fibrillin 1, collagen type IV alpha 1 chain, and alpha 2 chain, increased by + 16.44, +15.42 and + 11.95 fold, respectively). These results validate the use of this model for studying pathogen-host interactions and highlight how A. fumigatus interacts with pulmonary tissue during colonization.},
}

Animals
*Aspergillus fumigatus/pathogenicity/physiology/metabolism/genetics
Swine
*Lung/microbiology/immunology
Proteomics
*Host-Pathogen Interactions
Disease Models, Animal
*Proteome/analysis

@article {pmid40665110,
year = {2025},
author = {Ruiz, A and Sanahuja, I and Torrecillas, S and Gisbert, E},
title = {Anatomical site and environmental exposure differentially shape the microbiota across mucosal tissues in rainbow trout (Oncorhynchus mykiss).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25653},
pmid = {40665110},
issn = {2045-2322},
support = {PRE2019-091259//Ministerio de Ciencia e Innovación/ ; FJC2020-043933-I//Ministerio de Ciencia e Innovación/ ; RYC2021-031414-I//Ministerio de Ciencia e Innovación/ ; PID2023-147976OR-C21//Ministerio de Ciencia e Innovación/ ; },
abstract = {This study investigates the diversity, structure, and composition of the fish microbiota across different mucosal organs by comparing the bacterial communities in the oropharyngeal cavity, posterior intestine, gills, and skin of farmed rainbow trout (Oncorhynchus mykiss), along with water and biofilm samples from the surrounding environment. Four distinct skin regions across the dorsal-ventral and anterior-posterior axes were also compared in fish weighing 390.5 ± 36.8 g. Sample analyses showed that lower values of richness (observed) and diversity (Shannon and Faith indices) were observed in the posterior intestine compared to the gills, skin, and environmental (water and biofilm) samples (P < 0.05). Similarly, the oropharynx showed higher Faith diversity values than the intestine (P = 0.01). Furthermore, bacterial community structures differed significantly across organs based on unweighted and weighted UniFrac distances (P = 0.001 for both), with the posterior intestine showing the greatest divergence from other mucosal sites. Indeed, Pseudomonadota was the most abundant phylum across all sample types, except for the posterior intestine, where Firmicutes, particularly the genus Mycoplasma, showed a clear predominance. The posterior intestine showed facultative anaerobic genera, while the other mucosae and environmental samples were mainly composed of strictly aerobic members, like Flavobacterium and Crocinitomix. The microbial communities across the different skin regions were highly heterogeneous: while the dorsal area showed a consistent microbiota, the ventral region exhibited differences between the anterior and posterior sections in bacterial structure and composition at the genus level (P < 0.05). For instance, Candidatus Piscichlamydia was very abundant in the gills and ventral-anterior skin, but was scarcely detected in the rest of skin areas. Overall, these findings suggest a high differentiation of bacterial communities across fish organs, tailored to the specific physiological and environmental characteristics of each mucosal tissue, with a stronger modulation by the surrounding environment in the external mucosae and a higher influence of host innate factors in inner organs, such as the intestine.},
}

@article {pmid40665053,
year = {2025},
author = {Reicher, L and Shilo, S and Godneva, A and Lutsker, G and Zahavi, L and Shoer, S and Krongauz, D and Rein, M and Kohn, S and Segev, T and Schlesinger, Y and Barak, D and Levine, Z and Keshet, A and Shaulitch, R and Lotan-Pompan, M and Elkan, M and Talmor-Barkan, Y and Aviv, Y and Dadiani, M and Tsodyks, Y and Gal-Yam, EN and Leibovitzh, H and Werner, L and Tzadok, R and Maharshak, N and Koga, S and Glick-Gorman, Y and Stossel, C and Raitses-Gurevich, M and Golan, T and Dhir, R and Reisner, Y and Weinberger, A and Rossman, H and Song, L and Xing, EP and Segal, E},
title = {Deep phenotyping of health-disease continuum in the Human Phenotype Project.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40665053},
issn = {1546-170X},
abstract = {The Human Phenotype Project (HPP) is a large-scale deep-phenotype prospective cohort. To date, approximately 28,000 participants have enrolled, with more than 13,000 completing their initial visit. The project is aimed at identifying novel molecular signatures with diagnostic, prognostic and therapeutic value, and at developing artificial intelligence (AI)-based predictive models for disease onset and progression. The HPP includes longitudinal profiling encompassing medical history, lifestyle and nutrition, anthropometrics, blood tests, continuous glucose and sleep monitoring, imaging and multi-omics data, including genetics, transcriptomics, microbiome (gut, vaginal and oral), metabolomics and immune profiling. Analysis of these data highlights the variation of phenotypes with age and ethnicity and unravels molecular signatures of disease by comparison with matched healthy controls. Leveraging extensive dietary and lifestyle data, we identify associations between lifestyle factors and health outcomes. Finally, we present a multi-modal foundation AI model, trained using self-supervised learning on diet and continuous-glucose-monitoring data, that outperforms existing methods in predicting disease onset. This framework can be extended to integrate other modalities and act as a personalized digital twin. In summary, we present a deeply phenotyped cohort that serves as a platform for advancing biomarker discovery, enabling the development of multi-modal AI models and personalized medicine approaches.},
}

@article {pmid40664985,
year = {2025},
author = {Boutin, S and Laforest-Lapointe, I},
title = {Reproducing plant microbiome research reveals site and time as key drivers of apple tree phyllosphere bacterial communities.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25620},
pmid = {40664985},
issn = {2045-2322},
abstract = {Manipulating plant microbiomes is foreseen as a key biocontrol avenue to tackle the accelerating challenges of global change in agriculture. Several recent studies have identified the spatiotemporal dynamics of phyllosphere microbial communities, stressing the need to understand plant microbiome drivers to design efficient biocontrol interventions. Yet, these works are often performed on small sample counts, rarely provide sufficient information on the relative impact of time or local environment, and are seldom repeated to assess reproducibility. To address these limits, we performed a longitudinal sampling across multiple orchards of contrasting agricultural practices to study the ecological drivers of phyllosphere bacterial communities of apple tree (Malus domestica, Borkh.). We sampled up to eight apple cultivars at six orchards (three conventional, three organic) in the Eastern Townships (Canada) in 2022 and 2023. In contrast with common cross-sectional microbiome studies, our work builds on a two-year sampling design, thus allowing for the evaluation of the reproducibility of previous plant microbiome research. Our results support previous findings indicating that site and time are major drivers of apple tree bacterial community structure, yet their relative influence vary across the two sampling years. In addition, our data showed that leaf and flower bacterial alpha diversity is lower at organic sites compared to conventional sites. Overall, this study provides a comprehensive longitudinal multi-site study design highlighting the value of assessing reproducibility in plant microbiome studies and paving the way for future research in this field.},
}

@article {pmid40664880,
year = {2025},
author = {Smolander, N and Fuchs, B and Helander, M and Puigbò, P and Tamminen, M and Saikkonen, K and Mathew, SA},
title = {Glyphosate and phosphate treatments in soil differentially affect crop microbiomes depending on species, tissue and growth stage.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25502},
pmid = {40664880},
issn = {2045-2322},
support = {355917//Research Council of Finland/ ; 311077//Research Council of Finland/ ; },
mesh = {Glyphosate ; *Glycine/analogs & derivatives/pharmacology ; *Soil Microbiology ; *Microbiota/drug effects ; *Crops, Agricultural/microbiology/growth & development/drug effects ; *Phosphates/pharmacology ; Fertilizers ; *Herbicides/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Soil/chemistry ; Plant Roots/microbiology/drug effects ; Solanum tuberosum/microbiology/growth & development/drug effects ; Bacteria/genetics/drug effects/classification ; Avena/microbiology/growth & development/drug effects ; Plant Leaves/microbiology ; Vicia faba/microbiology/growth & development ; },
abstract = {Glyphosate-based herbicides (GBHs) are widely used for controlling weeds by inhibiting the shikimate pathway. However, the effects of GBH on non-target organisms, such as shikimate pathway-containing microbes, are understudied. Furthermore, the complex interactions between GBH and fertilizers are difficult to predict. Hence, we experimentally investigated the effects of GBH and phosphate fertilizer on the composition of endophytic bacterial communities of potato, faba bean and oat during early and late summer using 16S rRNA gene sequencing, and on plant growth in late summer. GBH treatments significantly affected bacterial communities of early and late summer potato roots and late summer faba bean roots, while phosphate treatments significantly affected bacterial communities of late summer potato leaves, tubers and early summer faba bean leaves. The treatments reduced bacterial diversity in potato and oat and the abundance of putatively beneficial bacteria in potato and faba bean. However, these treatments increased the aboveground biomass of all crops. Thus, agrochemicals had variable effects across crops, tissues and growth stages. While improved crop yield is often prioritized in chemical-intensive farming, the effects of microbiome shifts on crop health need further investigation.},
}

Glyphosate
*Glycine/analogs & derivatives/pharmacology
*Soil Microbiology
*Microbiota/drug effects
*Crops, Agricultural/microbiology/growth & development/drug effects
*Phosphates/pharmacology
Fertilizers
*Herbicides/pharmacology
RNA, Ribosomal, 16S/genetics
*Soil/chemistry
Plant Roots/microbiology/drug effects
Solanum tuberosum/microbiology/growth & development/drug effects
Bacteria/genetics/drug effects/classification
Avena/microbiology/growth & development/drug effects
Plant Leaves/microbiology
Vicia faba/microbiology/growth & development

@article {pmid40664808,
year = {2025},
author = {Lombardo-Hernandez, J and Mansilla-Guardiola, J and Aucello, R and Botta, C and García-Esteban, MT and Murciano-Cespedosa, A and Muñoz-Rodríguez, D and Quarta, E and Mateos González, Á and Juan-Llamas, C and Rantsiou, K and Geuna, S and Cocolin, L and Herrera-Rincon, C},
title = {An in vitro neurobacterial interface reveals direct modulation of neuronal function by gut bacteria.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25535},
pmid = {40664808},
issn = {2045-2322},
support = {FPU23/02273//Spanish Ministry of Universities FPU Predoctoral Fellowship/ ; PID2023-147361NA-I00//Ministerio de Ciencia e Innovación/ ; PR3/23-30827//Universidad Complutense de Madrid/ ; },
mesh = {Animals ; *Neurons/microbiology/metabolism/physiology/cytology ; Rats ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; *Lactobacillus plantarum/physiology ; Transcriptome ; Cells, Cultured ; Calcium Signaling ; Neuronal Plasticity ; },
abstract = {Interactions between bacteria and somatic cells are increasingly important for understanding cellular communication mechanisms. While the gut microbiome's influence on the gut-brain axis is established, direct interactions between bacteria and neurons are poorly explored, especially regarding bidirectional information exchange. We developed an in vitro model using the foodborne bacterium Lactiplantibacillus plantarum and rat cortical neural cultures to study neuronal responses to bacterial presence through morphological, functional, and transcriptomic analyses. We found that L. plantarum adheres to neuronal surfaces without penetrating the soma. Real-time calcium imaging showed enhanced Ca[2][+] signaling dependent on bacterial concentration and active metabolism. Neurons exhibited changes in neuroplasticity-related proteins such as Synapsin I and pCREB, indicating functional modulation. Transcriptomic profiling revealed significant gene expression changes affecting networks linked to neurological conditions and bioelectrical signaling. Together, our results provide proof-of-concept for targeted neuronal responses induced by bacterial contact, offering key resources and transcriptomic data to advance the study of bacteria-driven neural modulation within the gut-brain axis.},
}

Animals
*Neurons/microbiology/metabolism/physiology/cytology
Rats
*Gastrointestinal Microbiome
Gene Expression Profiling
*Lactobacillus plantarum/physiology
Transcriptome
Cells, Cultured
Calcium Signaling
Neuronal Plasticity

@article {pmid40664314,
year = {2025},
author = {Li, Y and Zhang, S and Li, C and Shen, J and Cao, P and Sun, Y and Ma, X and An, B},
title = {Prebiotics chronotherapy alleviates depression-like behaviors in FMT mice through enhancing short-chain fatty acids receptors and intestinal barrier.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {119885},
doi = {10.1016/j.jad.2025.119885},
pmid = {40664314},
issn = {1573-2517},
abstract = {BACKGROUND: Prebiotics interventions to restore microbiome homeostasis may have long-lasting benefits for mental health especially in adolescence. However, the anti-depressants of prebiotics, particularly in prebiotics chronotherapy, orchestrated remain unknown. We aimed to elucidate the underlying mechanisms of prebiotics in light of maximum antidepressant effects by appropriate dosing timing.

METHODS: Adolescent depression mouse model was made by fecal microbiota transplantation (FMT) from major depressive disorder (MDD) adolescent patients. Sodium Butyrate (SB), one of SCFAs, was intragastrically administrated to mice at Zeitgeber time 4 (ZT4: the highest short-chain fatty acids (SCFAs) receptor-activated timing) or ZT16 (the lowest SCFA receptor-activated timing) for the last 2 weeks within 4-week-FMT exposure. The success of modeling and antidepressant effects of SB chronotherapy were determined by changes in depression-like behaviors, inflammation, neurotrophy, neuron functions, circadian rhythm, and barrier systems.

RESULTS: SB alleviated depressive symptoms at ZT4 with better efficacy over ZT16. SB decreased inflammation, upregulated neurotrophy, restored functions, and re-established circadian rhythm. Notably, SB increased the expressions of SCFAs receptors to repair the intestinal barrier and blood-brain barrier, thereby alleviating depressive symptoms.

LIMITATION: Only one prebiotic with one disease was involved.

CONCLUSION: SB supplementation could be a promising therapeutic tactic for restoring the integrity of barrier systems by enhancing the intestinal SCFAs receptors. Alignment SB supplementation with circadian clocks might help to obtain better antidepressant efficacy, which may generate novel insights into diseases related to diseases with barrier system impairment and optimize interventions to improve health and human well-being.},
}

@article {pmid40664260,
year = {2025},
author = {Mac Aogáin, M},
title = {Beyond ORBIT: Mapping the Constellation of Pseudomonas Endotypes in Bronchiectasis Clinical Trials.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.202506-1388ED},
pmid = {40664260},
issn = {1535-4970},
}

@article {pmid40664089,
year = {2025},
author = {Zhu, Y and Xi, Q and Liu, Y and Zhou, Y and Liao, J and Wu, Q},
title = {Recent advances in exosome-based nanodelivery systems for Parkinson's disease.},
journal = {Biomaterials},
volume = {325},
number = {},
pages = {123548},
doi = {10.1016/j.biomaterials.2025.123548},
pmid = {40664089},
issn = {1878-5905},
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder that primarily affects dopaminergic neurons in the substantia nigra. Its multifactorial pathogenic mechanisms include oxidative stress, mitochondrial dysfunction, α-synuclein aggregation, neuroinflammation, and alterations in the gut microbiome, ultimately leading to neuronal deficits and debilitating motor and nonmotor symptoms. Although conventional therapies provide temporary relief, their efficacy tends to wane over time or produce adverse effects. Exosome-based therapeutic strategies are a promising alternative, and we highlight the unique advantages of exosomes, including their biocompatibility, low immunogenicity, and ability to cross the blood-brain barrier, thereby facilitating the targeted delivery of neuroprotective and anti-inflammatory medications to affected regions. We also discuss recent advances in exosome engineering to improve cargo loading, enhance cell specificity and improve efficacy. However, large-scale exosome production, targeted delivery and long-term safety remain major challenges. Early-phase clinical trials of exosome-based therapies in other neurodegenerative conditions have demonstrated acceptable tolerability, and ongoing preclinical studies in PD models suggest potential efficacy, laying the groundwork for future clinical translation.},
}

@article {pmid40663917,
year = {2025},
author = {El-Keblawy, A and Jarrar, H and Manikandan, SK and Abideen, Z and Sheteiwy, MS},
title = {Rhizosheaths in desert plants: Natural mechanisms and bioinspired technologies for water harvesting and dryland restoration.},
journal = {The Science of the total environment},
volume = {994},
number = {},
pages = {180064},
doi = {10.1016/j.scitotenv.2025.180064},
pmid = {40663917},
issn = {1879-1026},
abstract = {Rhizosheaths, which are sand sheaths formed around plant roots, represent a critical adaptation in many desert species, enabling survival under arid conditions through enhanced water and nutrient retention. Although rhizosheaths also occur in crops such as wheat and maize, this review emphasizes desert-adapted grasses and sedges that exhibit highly specialized rhizosheath structures and functions. We synthesize current knowledge on rhizosheath formation, microbial and biochemical interactions, and mechanisms of soil and atmospheric water harvesting. Our analysis shows that rhizosheaths significantly enhance local moisture availability, support beneficial microbial communities, and contribute to nutrient cycling in sandy soils. We also highlight the key role of mucilage chemistry and root-microbe interactions in stabilizing rhizosheaths under drought. The review highlights their ecological functions as nutrient-rich microhabitats and their role in supporting drought-adapted microbial consortia. We further explore how rhizosheath biology inspires bioinspired technologies such as hydrogels, root-zone irrigation systems, and exopolysaccharide-based seed coatings. In conclusion, we identify key knowledge gaps-particularly in mucilage composition, microbiome specificity, and the scalability of synthetic rhizosheaths-and propose future directions for climate-resilient agriculture and dryland restoration.},
}

@article {pmid40663882,
year = {2025},
author = {Khattak, F and Galgano, S and Pearson, R and Houdijk, JGM and Short, F and Leigh, A},
title = {Enhancing key broiler welfare indicators, meat quality, and gut microbiome composition using oxygen-enriched drinking water under commercially relevant housing conditions.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105550},
doi = {10.1016/j.psj.2025.105550},
pmid = {40663882},
issn = {1525-3171},
abstract = {Water is a critical nutrient in poultry production, yet its quality, particularly dissolved oxygen (DO) content, is often overlooked. This study is the first to comprehensively evaluate the impact of oxygen-enriched drinking water on broiler welfare, breast muscle myopathies, and gut microbiome composition under commercially relevant housing conditions. A total of 840 male Ross 308 broiler chicks were randomly assigned to two treatment groups (oxygenated water vs. tap water), with 12 replicate pens per treatment. Oxygenated water was enriched to a DO level of approximately 32 mg/L, compared to around 9.5 mg/L in tap water. Birds were reared to 36 days of age. The consistently high performance of both treatment groups under controlled experimental conditions is demonstrated by final body weights and feed conversion ratios surpassing Ross 308 breed standards by approximately 19-22 % from day 24 onward. Although growth performance remained unaffected under these optimal conditions, oxygenated water significantly improved welfare indicators, including feather condition, hock burn scores, and breast cleanliness (P< 0.05). Birds on oxygenated water also showed lower abdominal fat (-12 %) and higher thigh yield (+2.6 %) without compromising breast yield. Carcass fat deposition was significantly lower (abdominal fat pad reduced by ∼12 %), and thigh yield was higher in the oxygenated water treatment (P < 0.05), although overall carcass weight and breast yield were unchanged. No major differences were detected in breast meat nutrient composition (P > 0.05). The prevalence of white striping in breast fillets was markedly reduced in birds receiving oxygenated water, 32 mg/L indicating enhanced muscle integrity (P < 0.05). Metagenomic analysis revealed that some bacterial lipid metabolism pathways where differentially abundant in oxygenated-water birds. Following up on previous knowledge suggesting the interplay between lipid metabolism and broiler welfare, these findings suggest that supplementing broiler drinking water with 32 mg/L DO levels may offer a practical, non-pharmaceutical strategy to mitigate breast muscle myopathies and improve overall animal welfare and meat quality.},
}

@article {pmid40663629,
year = {2025},
author = {Kriete, AL and Scott, MJ},
title = {Direct and trans-generational effects of tetracyclines on the microbiome, transcriptome, and male mating behavior of the sheep blowfly Lucilia cuprina.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf160},
pmid = {40663629},
issn = {2160-1836},
abstract = {Tetracyclines are broad-spectrum antibiotics widely used in agriculture, medicine, and research. However, they are associated with harmful side effects. In arthropods, parental exposure to tetracyclines has been linked to reduced health and fitness in untreated offspring. These trans-generational effects of tetracyclines could jeopardize the success of pest control programs that use tetracyclines to control gene expression. In this study, we investigated the transgenerational effects of two tetracyclines, doxycycline (DOX) and anhydrotetracycline (ATC), in the blowfly Lucilia cuprina, a significant pest of sheep. To simulate the rearing conditions of a transgenic male-only release program, blowflies were reared on standard diet alone, or on standard diet plus DOX or ATC, for three generations, then reared for an additional fourth generation on standard diet alone. We used behavioral assays, 16S amplicon sequencing, and mRNA sequencing to determine how DOX and ATC influenced male sexual competitiveness, microbiome composition and gene expression in the third and fourth generations. We found that three generations of DOX treatment led to lower sexual competitiveness in both third- and fourth-generation males. In addition, DOX and ATC shifted the composition of the blowfly microbiome and altered the expression of numerous mitochondria- and immunity-related genes in both generations. Our study supports an emerging body of evidence that tetracyclines exert not only direct but also trans-generational effects, and sheds light on the transcriptional and microbial responses to antibiotic exposure and removal. Our findings emphasize the need for pest control programs that use tetracyclines to evaluate the long-term effects of these antibiotics.},
}

@article {pmid40663456,
year = {2025},
author = {Novák, Á and Zajta, E and Csikós, M and Halmos, E and Horváth, M and Tildy, O and Szekeres, A and Svorenj, G and Gémes, N and Szebeni, GJ and Tóth, R and Gacser, A},
title = {Comprehensive analysis of human keratinocyte interactions with Candida albicans and Candida parapsilosis.},
journal = {Virulence},
volume = {},
number = {},
pages = {2532815},
doi = {10.1080/21505594.2025.2532815},
pmid = {40663456},
issn = {2150-5608},
abstract = {In recent years, microbiome studies revealed that Candida species are common colonisers of the human skin. The distribution of species however varies greatly. Although C. parapsilosis is more likely to resemble skin commensals, opinions are divided, and discrepancies are present regarding C. albicans, that is also often associated with cutaneous candidiasis. Therefore, we aimed to thoroughly assess the nature of skin epithelial cell - Candida interactions. To study species-specific host responses, we examined internalization, cytokine and metabolic responses in different keratinocytes (HaCaT, HPV-KER) along with host cell damage following fungal stimuli. To rigorously examine yeast-keratinocyte interactions, we applied two distinct isolates of both C. albicans (SC5314, WO-1) and C. parapsilosis (GA1, CLIB214). Comparison of the two fungi's virulence revealed that while C. albicans effectively adheres to human keratinocytes and causes subsequent damage, C. parapsilosis is unable to establish lasting physical contact and causes less harm. In terms of keratinocyte response, both cell lines showed significantly enhanced cellular (internalization), humoral (IL-6, IL-8) and metabolic responses (2-ketoglutaric acid, citric acid, threorine, hypotaurine) to C. albicans strains, while those towards C. parapsilosis remained relatively low or similar to the control condition. Under certain conditions strain preference was also detected. Of the two cell lines, HPV-KER was more sensitive, as besides interspecies differences, intraspecies differences were also measurable. These results suggest that C. albicans triggers an enhanced antifungal response, thus does not closely resemble skin commensals, like C. parapsilosis. Furthermore, HPV-KER might serve as a more applicable tool for studying keratinocyte antifungal responses.},
}

@article {pmid40663222,
year = {2025},
author = {Chen, Q and Wang, G and Shu, J and Zou, X and Miao, W and Nong, W and Li, M and Lan, G and Huang, W and Huang, X and Luo, H and Qu, S},
title = {Mendelian randomization analysis of gut microbiota-immune cell interactions in malignant neoplasm of nasopharynx.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {106},
pmid = {40663222},
issn = {2191-0855},
support = {2024GXNSFBA010070//Guangxi Natural Science Foundation/ ; },
abstract = {Observational studies have suggested associations among the gut microbiome, immune cells, and the risk of malignant neoplasms of nasopharynx. However, the causality of these relationships remains unclear. Thus, we conducted multiple Mendelian Randomization analyses to estimate the causal association of gut microbiota with the risk of malignant neoplasms of nasopharynx and to evaluate the mediating effect of immune cells on this causal pathway. Genetic variants extracted from genome-wide association studies of human gut microbiota compositions (n = 211), immune cell traits (n = 731) and malignant neoplasms of nasopharynx served as instrumental variables for calculating causal associations and mediating effects. Four gut microbiota compositions and eight immune cell traits exhibited detrimental causal effects, while three gut microbiota compositions and fifteen immune cell traits demonstrated protective effects. Interestingly, the causal association of genus Candidatus Soleaferrea id.11350 was no longer significant after adjusting for two established immune cell traits (HLA DR + + monocyte %leukocyte and HLA DR + + monocyte % monocyte). Moreover, HLA DR + + monocyte %leukocyte exhibited a mediating effect (OR 0.75, 95% CI 0.59-0.96) on the causal pathway of genus Candidatus Soleaferrea id.11350-malignant neoplasms of nasopharynx, with a mediating proportion of 21.59%. To our knowledge, this study is the first to identify potential therapeutic targets and elucidate mechanistic insights for malignant neoplasms of nasopharynx interventions involving gut microbiota and immune cell traits; however, these findings warrant further validation through adequately powered randomized clinical trials (RCTs).},
}

@article {pmid40662747,
year = {2025},
author = {Touceda-Suárez, M and Ponsero, AJ and Barberán, A},
title = {Differences in the genomic potential of soil bacterial and viral communities between urban greenspaces and natural arid soils.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0212424},
doi = {10.1128/aem.02124-24},
pmid = {40662747},
issn = {1098-5336},
abstract = {Urban green spaces provide essential ecosystem services that are ever more important in arid cities. However, the design and management of these greenspaces often require physicochemical transformations, whose effect in the balance of the arid urban ecosystems is normally not accounted for. In this project, we leverage metagenomic data from soil microbial communities of urban greenspaces and neighboring natural areas in a city from the arid Southwestern USA (Tucson, Arizona) to understand the differences in microbial (bacterial and viral) community structure, taxonomy, and function in urban greenspaces compared to natural arid soils. We found bacterial and viral communities to be distinct between urban greenspace and natural arid soils, with urban greenspace bacteria displaying reduced metabolic versatility and higher genetic potential for simple carbohydrate consumption and nitrogen reduction. Moreover, bacteria in urban greenspaces exhibit higher genetic potential for resistance to heavy metals and certain clinical antibiotics. Our results suggest that the conversion of arid natural land to urban greenspaces determines the soil microbiome structure and functioning, and potentially its ability to adapt to the changing environment.IMPORTANCEUrban green spaces are critical for the sustainability of arid cities. Nevertheless, they require deep soil physicochemical transformations. Soil bacterial and viral communities are responsible for soil functioning and provision of some ecosystem services, but they are also highly influenced by changes in the soil environment. The significance of our research is in illustrating the structural and functional changes that microbial and viral communities undergo in urban soils of arid cities and their potential impacts on urban greenspace soil processes.},
}

@article {pmid40662685,
year = {2025},
author = {Verstraete, W and Strubbe, L and Pikaar, I and Vinestock, TW and Lee, PH and Matassa, S and Chong, J and Zhou, J and Daigger, GT and Guo, M},
title = {Escaping Historical Lock-in─Redesigning Wastewater Treatment Plants and Their Microbiomes for the 21st Century.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06208},
pmid = {40662685},
issn = {1520-5851},
abstract = {Wastewater treatment plants (WWTPs) have gradually, over the last hundred years, been designed and extended to deal with a sequence of problems, including a) odor, b) suspended solids, c) organics, d) ammonia, e) nitrate and phosphate, and f) recalcitrant pollutants. The line of historical developments was piecemeal rather than holistic and did not focus on sustainability, resource recovery, and water reuse. On the contrary, microbial processes that accelerated the removal of nitrogen were incorporated and heralded as a positive part of the "cleanup" agenda, despite their relatively large energy consumption and substantial production of nitrous oxide, a potent greenhouse gas. The time has come to examine the historical, technological, and microbiological lock-in present in today's WWTPs, so that a more coherent integrated system can be developed for future generations. Some disruptive strategies are outlined, and a categorization of processes in terms of their potential for the future is formulated.},
}

@article {pmid40662582,
year = {2025},
author = {Li, B and Fu, M and Jin, G and Liu, Z},
title = {Rare bacterial subcommunity drives nutrient cycling in phyllosphere habitat of evergreen conifers.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0051825},
doi = {10.1128/spectrum.00518-25},
pmid = {40662582},
issn = {2165-0497},
abstract = {UNLABELLED: Phyllosphere bacteria are crucial for pathogen resistance, stress tolerance, and productivity maintenance of host plants and further have potential effects on ecosystem functions. However, whether and how assembly patterns of both abundant and rare subcommunities changed across needle age cohorts, and their relative contributions to nutrient cycling in phyllosphere habitat of evergreen conifers are still unclear. Here, we examined both phyllosphere abundant and rare bacterial subcommunities in three needle age cohorts of the representative evergreen conifers in mixed broadleaved-Korean pine forests throughout Northeast China. We found that dispersal limitation and ecological drift dominated abundant and rare subcommunities, respectively. Deterministic assembly gradually increased with needle aging, which was mainly attributed to the increased needle chemical defense traits such as flavonoids. We further showed that multiple nutrient cycling in phyllosphere habitat was regulated by the rare subcommunity, closely related to the variations in diversity and composition. Collectively, our findings facilitate us in clarifying the mechanisms underlying the formation and succession of phyllosphere bacterial subcommunities across needle age cohorts and emphasize the vital role of rare subcommunities in promoting ecosystem functions.

IMPORTANCE: Host-associated microbial communities are critical for host health. However, the relative importance of abundant and rare subcommunities in driving nutrient cycling in phyllosphere habitat across needle age cohorts of evergreen conifers remains unknown. Here, we showed the different assembly mechanisms of abundant and rare subcommunities and emphasized the ecological role of rare subcommunities in promoting ecosystem functions. This is useful for understanding the formation and succession dynamics of plant microbiome to advance future applications with microbial agents to sustainable productivity and reduce diseases.},
}

@article {pmid40662533,
year = {2025},
author = {Jiang, J and Hu, D and Hu, S and Huang, K and Zheng, J and Pei, E},
title = {Age-Related Differences in Gut Microbiome and Fecal Metabolome of Captive African Penguins (Spheniscus demersus).},
journal = {Zoo biology},
volume = {},
number = {},
pages = {},
doi = {10.1002/zoo.70014},
pmid = {40662533},
issn = {1098-2361},
support = {//This study was supported by a Project of Shanghai Zoo (SZ220302) and Special Fund for Scientific Research of Shanghai Landscaping & City Appearance Administrative Bureau (G250407)./ ; },
abstract = {The purpose of the present study was to characterize the profiles of gut microbiota and fecal metabolites in African penguins (Spheniscus demersus) of different ages. The combination of metagenome and metabolome was performed on the feces of captive African penguins of varying age groups, including juvenile (1-3 years old), adult (4-15 years old) and senior (16-20 years old) individuals. The results of the metagenome showed that microbial abundance was significantly different between groups. Adult penguins had higher abundances of Gallilactobacillus and Ligilactobacillus compared to juvenile penguins. Senior penguins exhibited higher abundances of Gammaproteobacteria and Escherichia coli than adult penguins. We further identified differentially expressed metabolites across the groups using liquid chromatography-mass spectrometry analysis. Correlation analysis showed that age was correlated significantly with certain differential microbial species and fecal metabolites. The results revealed that age is a key factor influencing gut microbiota and metabolism in African penguins. Our results provide baseline information on gut microbial structure and fecal metabolite characteristics in African penguins of different ages, which is vital for the management and ex situ conservation of this endangered species.},
}

@article {pmid40662501,
year = {2025},
author = {Bai, L and Wen, Y and Han, G and Tang, J and Xu, Z and Wang, Z and Jiang, L and Ren, H},
title = {Long-term climate warming and nitrogen deposition increase leaf epiphytic and endophytic bacterial diversity.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.13965},
pmid = {40662501},
issn = {1744-7909},
support = {2022YFF1302300//National Key Research and Development Program of China/ ; YLXKZX-NND-002//First-Class Discipline Research Program/ ; 2023JQ09//Distinguished Young Scholars Program of Inner Mongolia/ ; BR230301//Distinguished Young Scholars Program of Inner Mongolia/ ; 32260301//National Natural Science Foundation of China/ ; NMGIRT2403//Program for Innovative Research Team in Universities of Inner Mongolia Autonomous Region/ ; },
abstract = {Plant microbiome plays a vital role in plant fitness and ecosystem functioning, yet its response to global environmental change remains poorly understood. Using an 18-year field experiment, we investigated the effects of climate warming and nitrogen deposition on the diversity of leaf epiphytic and endophytic bacterial communities in two dominant plant species (Stipa breviflora and Cleistogenes songorica) of a temperate desert steppe. We found that warming and nitrogen addition increased both epiphytic and endophytic bacterial diversity, but via different mechanisms. Specifically, epiphytic diversity increased with leaf temperature and transpiration rate, whereas greater endophyte diversity was linked to higher leaf carbon and nitrogen concentrations. Structural equation modeling revealed that both epiphytic and endophytic diversity were negatively associated with plant diversity. Our results demonstrate different mechanisms driving similar responses of leaf epiphytic and endophytic bacterial diversity to global change, and point to a negative feedback loop between phyllosphere bacterial and plant diversity.},
}

@article {pmid40662393,
year = {2025},
author = {Wilson, EJ and Lee, STM and Zeglin, LH and Arias Rodriguez, L and Tobler, M},
title = {Host-Microbiome Associations in Livebearing Fishes Adapted to Toxic Environments Rich in Hydrogen Sulfide.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70034},
doi = {10.1111/mec.70034},
pmid = {40662393},
issn = {1365-294X},
support = {//Friends of the Sunset Zoo Conservation Scholar Program/ ; IOS-1931657//National Science Foundation/ ; IOS-2423844//National Science Foundation/ ; //Des Lee Collaborative Vision in Zoological Studies/ ; W911NF-15-1-0175//Army Research Office/ ; W911NF-16-1-0225//Army Research Office/ ; },
abstract = {Organisms inhabiting extreme environments must tolerate a variety of physiochemical stressors. In some cases, host-associated microbial communities facilitate the survival of their hosts in extreme environments, but extremophile symbioses have not been identified in vertebrates. We used 16S rRNA amplicon sequencing to investigate commonalities and differences in the gut bacterial communities of livebearing fishes (Poecilia mexicana species complex, Poeciliidae) that have repeatedly colonised toxic sulfide streams in southern Mexico. We found shared gut microbial taxa across habitat types and drainages but also differences in the microbiomes between sulfidic and nonsulfidic populations, both in terms of patterns of diversity and community composition. Most importantly, we documented convergent changes in microbiome composition across evolutionarily independent sulfide spring lineages. These patterns were consistent when we analysed the gut microbiomes as well as primarily host-associated microbiomes that excluded taxa that are commonly found in the environment. Our analyses also revealed several microbial taxa associated with sulfide spring coloniation that have previously been implicated in symbioses and may influence the host's tolerance to the extreme environmental conditions. Our study sheds light on how shared environmental pressures can give rise to convergent host-microbiome associations in fishes, and it provides a foundation for investigating the role of host-microbiome interactions in vertebrate adaptation to extreme environments.},
}

@article {pmid40662304,
year = {2025},
author = {Byrne, K and Lisiecka, D and Moran, G and Daly, B and Fleischmann, I and McCallion, P and McCarron, M and Phadraig, CMG},
title = {Oral Health and Pneumonia in Adults With Intellectual and Developmental Disabilities: A Scoping Review.},
journal = {Journal of intellectual disability research : JIDR},
volume = {},
number = {},
pages = {},
doi = {10.1111/jir.70013},
pmid = {40662304},
issn = {1365-2788},
support = {//School of Dental Science PhD scholarship fund/ ; //Trinity College Dublin/ ; },
abstract = {INTRODUCTION: Pneumonia is a leading cause of death for people with intellectual and developmental disabilities (IDD), who also have increased risk of oral disease. Given the known relationship between oral disease and pneumonia in similar populations, this review aims to explore what is known about the association between oral health and pneumonia among people with IDD.

METHODS: This systematic scoping review was carried out in accordance with the Joanna Briggs Institute methods and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews checklist (PRISMA-ScR). A systematic search of Medline (Ovid), Embase, Cochrane Trials, Cochrane Review, CINAHL and PubMed was conducted, guided by a registered protocol. The PCC framework informed the search and inclusion criteria. Titles and abstracts were independently screened by two reviewers, with full texts assessed for relevance to oral health and pneumonia in adults with IDD.

RESULTS: Following a protocol and defined criteria, (2544) articles were abstract screened; a further (31) reached full-text review, with (7) included in this review. Study designs included cross-sectional studies (2), retrospective cohorts (2), prospective cohorts (2) and one RCT pilot (1). Six studies reported oral carriage of respiratory pathogens such as Streptococcus pneumoniae, Pseudomonas aeruginosa and Klebsiella pneumoniae. Two studies reported predictive relationships between oral pathogens and pneumonia, with increased odds of respiratory illness associated with positive PCR results for specific pathogens (OR 9.0, 95% confidence interval [CI] 2.3-38.8). Two studies identified poor oral health as a predictor of pneumonia, using validated tools such as the ROAG (OR 1.6, 95% CI 1.1-2.5). Mediating factors included enteral feeding, level of IDD, and history of oral disease.

CONCLUSIONS: Research consistently finds carriage of potential respiratory pathogens in the oral microbiome of people with IDD. Despite this, there is a significant lack of research into the relationship between the oral microbiome, poor oral health, and pneumonia in this population, though the latter two are both prevalent and consequential. There is an urgent need for further research exploring the role that oral health and the oral microbiome play in pneumonia among people with IDD.},
}

@article {pmid40662048,
year = {2025},
author = {Pai, HD and Baid, R and Palshetkar, NP and Pai, R and Pai, A and Palshetkar, R},
title = {Role of Vaginal and Gut Microbiota in Human Papillomavirus (HPV) Progression and Cervical Cancer: A Systematic Review of Microbial Diversity and Probiotic Interventions.},
journal = {Cureus},
volume = {17},
number = {6},
pages = {e85880},
pmid = {40662048},
issn = {2168-8184},
abstract = {Cervical cancer remains a major global health concern, primarily associated with persistent infection by high-risk human papillomavirus (HrHPV) types. Both gut and vaginal microbiome may influence the progression from HPV infection to cervical intraepithelial neoplasia (CIN) and cervical cancer. We performed a systematic review to study the relevant literature on gut and cervical microbiota in patients with HPV infection, CIN, and cervical cancer, as well as the role of probiotics in managing these conditions. The protocol was registered in the PROSPERO database (#CRD42024584685). We searched PubMed, the Cochrane Library, Web of Science, and Google Scholar from their inception to September 2024. Two reviewers independently checked study eligibility. Both reviewers were responsible for data extraction. Disagreements were resolved by a third senior reviewer. The review was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for reporting systematic reviews. The Joanna Briggs Institute (JBI) checklist was used to assess the risk of bias of the included studies. In total, 82 papers were included in this review. Microbial dysbiosis plays a significant role in HPV infection, its progression, and clearance. The analysis of the microbiome reveals that the transition from HPV infection to CIN to cervical cancer involves a shift from a Lactobacillus-dominated, healthy microbiome to one dominated by pathogenic genera. Women with CIN and cervical cancer demonstrated increased microbial diversity compared to HPV-positive individuals. Pathogenic organisms such as Gardnerella, Prevotella, Sneathia, Streptococcus, and Porphyromonas were more prevalent in the patient population compared to controls. Probiotics were effective in restoring vaginal microbiota and managing HPV clearance, and were also associated with cytological and inflammatory improvement rates. Patients with HPV, CIN, and cervical cancer exhibited a microbial community characterised by an increased abundance of pathogenic genera and reduced levels of beneficial Lactobacillus species. Probiotics could be used as a prophylactic or an adjuvant therapy while treating HPV infection, CIN, and cervical cancer.},
}

@article {pmid40661986,
year = {2025},
author = {Wu, Z and Li, X and Wang, Y and Zhang, J and Ji, L and Gan, L},
title = {Microbiome analysis reveals gut bacterial alterations in adult Tibetan pigs with diarrhea.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1524727},
pmid = {40661986},
issn = {1664-302X},
abstract = {Diarrhea is a significant ailment that causes heavy economic losses in the pig industry. The Tibetan pig is a native Chinese breed that is unique to high-altitude regions and displays strong disease resistance. However, scientific research on the structural characteristics of the gut microbiota and key genera associated with diarrhea in Tibetan pigs is still scarce, especially those involving adult Tibetan pigs. In this study, fresh fecal samples from diarrheic (case, N = 9) and healthy adult Tibetan pigs (control, N = 10) were collected and sequenced using 16S rRNA gene sequencing. Our results revealed that the gut microbial community of the case pigs exhibited lower alpha diversities but higher intragroup variability in microbiota composition. The genera Treponema and Prevotellaceae_UCG-001 were underrepresented in the pigs, serving as hallmarks of diarrhea, while Lactobacillus, Escherichia-Shigella, and Muribaculaceae showed increased abundance. Moreover, the genera Lactobacillus and Ignatzschineria were significantly enriched biomarkers in the case pigs. Notably, these changes were not consistent with those observed in Tibetan piglets and other commercial pigs. Furthermore, the decreased abundance of Treponema in the diarrheic pigs indicated that this disease was associated with a high-fiber diet and environmental adaptability. The differentially enriched pathways in the case and control pigs further revealed that gut dysbiosis exacerbated immune and inflammatory responses to promote the development of diarrhea. In conclusion, this study characterized the distribution of gut microbiota composition in adult Tibetan pigs with different health status, which may enhance our understanding of the role of the gut microbiota in intestinal issues.},
}

@article {pmid40661978,
year = {2025},
author = {Rutkowska, N and Daroch, M and Marchut-Mikołajczyk, O},
title = {Exploring the diversity and genomics of cultivable Bacillus-related endophytic bacteria from the medicinal plant Galium aparine L.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1612860},
pmid = {40661978},
issn = {1664-302X},
abstract = {INTRODUCTION: Endophytes are crucial partners that contribute to the plants' health and overall wellbeing. Apart from the elucidation of the relationship between plants and their microbiota, the metabolic potential of endophytes is also of a special interest. Therefore, it is crucial to isolate and taxonomically identify endophytes, as well as to investigate their genomic potential to determine their significance in plant health and potential as bioactive metabolite producers for industrial application.

METHODS: In this study, we isolated ten endophytic bacterial strains from different tissues of medicinal plant Galium aparine L. and performed de novo assembly of their genomes using short and long reads. Comparative genomic analysis was conducted to assess the accurate taxonomic identification of the strains. The investigation also focused on the presence of mobile genetic elements and their significance concerning endophytic lifestyles. We performed functional annotation of coding sequences, particularly targeted genes that encode carbohydrate enzymes and secondary metabolites within gene clusters.

RESULTS: Through sequencing using two complementary methods, we obtained 10 bacterial genomes, ranging in size, coding density and number of mobile genetic elements. Our findings provide a first insight into the cultivable bacterial community of the medicinal plant Galium aparine L., their genome biology, and potential for producing valuable bioactive metabolites. Obtained whole genome sequences allowed for complete phylogenetic analysis, which revealed crucial insights into the taxonomic status of bacteria and resulted in the discovery of two putatively novel bacterial species from the Bacillus and Priestia genera, suggesting that plants are hiding a reservoir of novel species with potentially useful properties and unknown mechanisms related to their relationship with plant host.},
}

@article {pmid40661950,
year = {2025},
author = {Ma, Y and Suo, J and Sheng, S and Chen, L},
title = {PD-L1 deficiency exacerbates colitis severity by remodeling gut microbiota in inflammatory bowel disease.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1622744},
pmid = {40661950},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *B7-H1 Antigen/genetics/deficiency ; Mice ; Mice, Knockout ; *Colitis/pathology/microbiology/chemically induced/genetics/immunology/metabolism ; *Inflammatory Bowel Diseases/microbiology/immunology/pathology/genetics/metabolism ; Dysbiosis ; Disease Models, Animal ; Severity of Illness Index ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic autoimmune disorder driven by gut microbiota dysbiosis. As an essential immune checkpoint, Programmed death-ligand 1 (PD-L1) has been implicated in modulating gut microbiota composition. However, the precise role of PD-L1 in shaping metagenomic profiles during IBD-associated colitis remains unexplored.

METHODS: DSS-induced colitis was established in both PD-L1 knockout (Pdcd1lg1-/-) mice and wild-type (wt) control mice. Clinical parameters, including disease activity index (DAI), body weight changes, colon length, and histopathological alterations, were systematically evaluated using non-parametric Kruskal-Wallis tests and ANOVA to compare colitis severity between genotypes.

RESULTS: PD-L1 knockout mice exhibited exacerbated colitis, manifesting significantly greater weight loss (p<0.05 vs. wt_DSS), colonic shortening (p<0.05), and DAI scores (p<0.05) and inflammatory changes. PD-L1 knockout mice showed distinct dysbiosis, with enriched pathobionts (Escherichia coli, p=0.006; Bacteroides thetaiotaomicron, p=0.015) and depletion of commensals (Tritrichomonas foetus, p<0.001; Ligilactobacillus murinus). Alpha diversity analysis using Chao1 index revealed statistically significant differences between experimental groups (p=0.05). The transporters downregulate anti-inflammatory SCFA metabolism. KEGG enrichment analysis of differentially expressed genes (DEGs) revealed significant associations with immune and inflammatory pathways in PD-L1 knockout mice.

CONCLUSION: PD-L1 deficiency aggravates colitis by driving pathogenic microbiota alterations and impairing microbial metabolic homeostasis, highlighting its dual regulatory roles in immune homeostasis and microbiome dynamics.},
}

Animals
*Gastrointestinal Microbiome/immunology
*B7-H1 Antigen/genetics/deficiency
Mice
Mice, Knockout
*Colitis/pathology/microbiology/chemically induced/genetics/immunology/metabolism
*Inflammatory Bowel Diseases/microbiology/immunology/pathology/genetics/metabolism
Dysbiosis
Disease Models, Animal
Severity of Illness Index
Mice, Inbred C57BL
Dextran Sulfate
Male

@article {pmid40661942,
year = {2025},
author = {Yin, J and Kaakoush, NO and Massey, J and Danta, M},
title = {Understanding the microbiome in autologous haemopoietic stem cell transplant for multiple sclerosis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1590601},
pmid = {40661942},
issn = {1664-3224},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/methods ; Adult ; Female ; *Gastrointestinal Microbiome ; Male ; *Multiple Sclerosis/therapy/microbiology ; Middle Aged ; Transplantation, Autologous ; Natalizumab/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; },
abstract = {BACKGROUND: MS is a chronic inflammatory and degenerative disease of the central nervous system (CNS) resulting in neurological deficits associated with physical and/or cognitive disability. The gut microbiome can interact with the CNS and immune system through various molecular pathways and has been previously implicated in MS. Autologous Haematopoietic Stem Cell Transplant (AHSCT) in MS arrests inflammatory disease and has evidence of long-term therapeutic benefit. To date, no study has explored the effect of AHSCT on the gut microbiome in people with MS.

METHOD: The microbiome of people with MS (pwMS) undergoing AHSCT was compared with pwMS on Natalizumab (NTZ). Longitudinal microbiome analysis was also conducted within the AHSCT cohort at two timepoints. Amplicon sequencing of the 16S ribosomal RNA V3-4 region (Illumina MiSeq) was used to evaluate alpha and beta diversity, oral-stool microbiota distances, and relative taxa abundances on both oral and stool microbiota.

RESULTS: The pre-transplant, baseline samples from the AHSCT cohort (n=8) was compared to the Natalizumab group (n=22). The AHSCT cohort had lower oral species richness compared to the NTZ cohort (p=0.026). There was a significant difference in oral beta diversity between the two cohorts (p=0.043). The oral taxa analysis of AHSCT subjects showed increased relative abundances of Porphyromonas and decreased Veillonella.

CONCLUSION: This pilot study identified specific microbiome changes, particularly in the oral alpha diversity and abundance of specific bacteria which may reflect treatment status or disease activity in MS.},
}

Humans
*Hematopoietic Stem Cell Transplantation/methods
Adult
Female
*Gastrointestinal Microbiome
Male
*Multiple Sclerosis/therapy/microbiology
Middle Aged
Transplantation, Autologous
Natalizumab/therapeutic use
RNA, Ribosomal, 16S/genetics
Feces/microbiology

@article {pmid40661744,
year = {2025},
author = {Wang, X and Liu, X and Gong, F and Jiang, Y and Zhang, C and Zhou, W and Zhang, W},
title = {Targeting gut microbiota for diabetic nephropathy treatment: probiotics, dietary interventions, and fecal microbiota transplantation.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1621968},
pmid = {40661744},
issn = {1664-2392},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Probiotics/therapeutic use ; *Gastrointestinal Microbiome/physiology ; *Diabetic Nephropathies/therapy/microbiology ; Animals ; Dysbiosis/therapy ; },
abstract = {Diabetic nephropathy (DN) stands as a prominent microvascular complication of diabetes mellitus and presents a significant global health challenge. Despite advancements in glycemic control and renin-angiotensin system inhibition, current treatments merely delay disease progression without targeting fundamental pathological processes. This review explores gut microbiota modulation as a promising treatment strategy for DN through probiotic supplementation, dietary interventions, and fecal microbiota transplantation(FMT) protocols. The gut microbiota, integral to the "gut-kidney axis," is critically implicated in DN pathogenesis. DN is associated with gut dysbiosis-characterized by reduced microbial diversity, depletion of beneficial short-chain fatty acid (SCFA)-producing bacteria, and proliferation of opportunistic pathogens. This dysbiosis impairs gut barrier integrity, fostering systemic inflammation and the accumulation of uremic toxins like indoxyl sulfate. Furthermore, translocated bacterial lipopolysaccharides activate Toll-like receptors and the NLRP3 inflammasome, exacerbating kidney damage and fibrosis. Interventions targeting the microbiota, including dietary strategies (e.g., enhancing fermentable fibers, low-protein diets) and FMT, show promise in preclinical and early clinical studies, though FMT requires stringent safety and donor screening protocols. Significant challenges persist, such as managing inter-individual microbiota variability for personalized therapies, fully elucidating molecular mechanisms like SCFA-GPR43 signaling, and leveraging multiomics for biomarker discovery. Advancing microbiota-focused interventions for DN towards microbiome-centered precision medicine necessitates addressing standardization, deepening mechanistic understanding, and validating combination therapies, heralding a potential shift from traditional nephroprotective approaches.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Probiotics/therapeutic use
*Gastrointestinal Microbiome/physiology
*Diabetic Nephropathies/therapy/microbiology
Animals
Dysbiosis/therapy

@article {pmid40661523,
year = {2025},
author = {Siegel, SJ and Pomerantz, D and Heimburg-Molinaro, J and Mahmood, SD and Korzenik, JR and Cummings, RD and Rakoff-Nahoum, S},
title = {A glycan atlas of the mammalian intestine through ontogeny and inflammation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.06.641959},
pmid = {40661523},
issn = {2692-8205},
abstract = {UNLABELLED: The muco-epithelial interface in the mammalian gut is composed of a mucus and epithelial lining fundamental to barrier function, microbe-host interactions, and intestinal homeostasis. This barrier is heavily glycosylated by O-linked sugars covalently linked to mucin glycoproteins, and N-linked sugars that coat epithelial surface proteins. Gut O- and N-glycans are thought to play central roles in barrier function, host defense, nutrition and attachment for commensals and pathogens, immunoregulation and cell-cell interactions. However, the precise nature of the glycans and how glycan composition changes through development, as a function of diet, and during inflammation, remains incompletely understood. Here, we apply O- and N-glycomic platforms to profile glycans on mucus and intestinal epithelium. By mapping individual glycan species spatially and temporally we identify 57 O- and 18 N-glycans in the mouse intestine, and observe that fucosylation and sialylation varies according to intestinal region and developmental stage. We identify a subset of glycans regulated by the gut microbiome, and observe a constriction of the glycan repertoire during inflammation in both mice and humans. Together, these results provide an atlas of individual intestinal glycans and their dynamic range through ontogeny and inflammation, and represent a significant resource for our understanding of the role of intestinal glycans in health and disease and glycan-focused therapies for intestinal inflammation and shaping the gut microbiome.

HIGHLIGHTS: - Individual glycans vary across gut region and developmental stage- Terminal fucose and sialic acid residues vary across space and time- The microbiome influences gut glycan composition early in life- Gut inflammation in mice and humans converge on a restricted glycan repertoire.

ETOC BLURB: Microbes colonizing the mammalian intestines encounter mucus and an epithelial layer highly decorated by glycans. Siegel et al. use glycomics to map these sugars in high resolution across gut region, microbial colonization, development and inflammation in both humans and mice.},
}

@article {pmid40661479,
year = {2025},
author = {Parajuli, B and Midya, V and Kiddle, R and De Jager, N and Eggers, S and Spakowicz, D and Hoyd, R and Salhia, B and Chan, CHF and Churchman, ML and Rounbehler, RJ and Yao, S and Rutkowski, MR and Tarhini, AA and Mudaranthakam, DP and Masood, A and Bocklage, TJ and Lentz, RW and Hatoum, H and Ilozumba, MN and Hardikar, S and Ulrich, CM and Round, JL and Riedlinger, G and Shriver, CD and Bosch, DE},
title = {Primary tumor microbiomes predict distant metastasis of colorectal cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.02.654060},
pmid = {40661479},
issn = {2692-8205},
abstract = {Metastasis causes most cancer-related deaths in colorectal carcinoma (CRC), and microbiome markers may have prognostic value. We hypothesized that primary tumor microbiomes predict distant metastases. We analyzed 5-year metastasis-free survival (MFS) in a retrospective cohort of 900 ORIEN CRC tumor microbiomes (RNAseq). ORIEN findings were validated on an independent cohort using 16S rDNA sequencing and pathobiont-specific qPCR. Microbiome alpha diversity was higher in primary tumors than metastases and positively correlated with metastasis risk. Microbiome beta diversity distinguished primary vs. metastasis and predicted 5-year MFS. High primary tumor abundance of B. fragilis and low F. nucleatum were associated with short MFS. Enterobacteriaceae, including E. coli, were enriched in metastases. qPCR identified increased enterotoxigenic B. fragilis and pks+ E. coli detection in CRC metastasizers. Microbial co-occurrence analysis identified a 3-species clique that predicts metastasis (OR 1.9 [1.4-2.6]). Results suggest that primary tumor microbiomes and specific pathobionts are precision markers for metastasis risk.},
}

@article {pmid40661243,
year = {2025},
author = {Xing, H and Lin, WJ and Hu, WL and Cao, JS and Cui, LY and Lyu, W and Zhu, HK and Wu, AJ and Xu, QX and Zhao, Y and Bao, SY},
title = {Insights of acupuncture in modulating gut microbiota in stroke treatment.},
journal = {Frontiers in neurology},
volume = {16},
number = {},
pages = {1579585},
pmid = {40661243},
issn = {1664-2295},
abstract = {Stroke, an acute neurological disorder caused by the interruption of cerebral blood flow, is the second leading cause of death and a major contributor to long-term disability worldwide. Recent research has increasingly highlighted the role of gut microbiota in stroke recovery. Post-stroke gut microbiota dysbiosis, characterized by an imbalance in microbial composition, exacerbates neuroinflammation and neuronal injury. Restoring the balance of the gut microbiome may facilitate neurological recovery. Acupuncture, a traditional therapeutic modality, has shown potential in stroke rehabilitation. Evidence suggests that acupuncture modulates gut microbiota composition, restores gut barrier integrity, and reduces endotoxin translocation into the bloodstream, which collectively reduces systemic inflammation and alleviates neurological damage. Additionally, acupuncture may influence immune responses through the gut-brain axis, a bidirectional communication system between the gut and brain, thereby suppressing neuroinflammation and promoting neuronal repair. Despite these promising findings, current evidence is limited by methodological inconsistencies, including variability in acupuncture protocols and heterogeneous patient populations, which may confound result interpretation. The precise mechanisms underlying acupuncture's modulation of gut microbiota and its role in stroke recovery remain unclear. Future studies should adopt standardized protocols and larger sample sizes to improve reproducibility, validate these findings, explore the molecular pathways involved, and determine the clinical efficacy of acupuncture in stroke rehabilitation.},
}

@article {pmid40661167,
year = {2025},
author = {Oba, PM and Roberts, LJ and Geary, EL and Suchodolski, JS and Swanson, KS},
title = {Effects of diet type on the core fecal bacterial taxa and the dysbiosis index of healthy adult dogs.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1572875},
pmid = {40661167},
issn = {2297-1769},
abstract = {There is great interest in studying the canine gastrointestinal microbiome. In healthy dogs versus those with acute and chronic enteropathies, specific bacterial taxa have been identified that are consistently associated with shifts in the microbiome. A qPCR-based dysbiosis index (DI) that assesses microbiome shifts was developed based on a subset of these taxa. Because most dogs consume kibble diets, published data on core bacteria and the DI were largely derived from dogs consuming that diet form. Because dietary composition impacts the microbiome, it was unknown whether data from dogs consuming other diet types would adhere to reported core taxa abundance and DI guidelines. The study's aim was to determine the fecal abundance of core bacteria and DI of dogs fed commercially available kibble vs. mildly-cooked human-grade (fresh) diets. Fecal samples collected from adult dogs across four experiments were used (4 kibble diets, n = 10-12/treatment; 4 fresh diets, n = 10-24/treatment). Moderate correlations were observed between total dietary fiber (TDF) and Fusobacterium (positive correlation), Lactobacillus (negative), and DI (negative). Dietary protein was correlated with fecal Ruminococcus gnavus (negative), while dietary fat was correlated with fecal Bacteroides and C. perfringens abundance (both positive). Dogs fed fresh diets exhibited higher (p < 0.01) abundances of Streptococcus, Escherichia coli, and Clostridium perfringens, while those fed kibble diets had higher (p < 0.05) abundances of Fusobacterium, Clostridium hiranonis, and Bacteroides. Dogs fed fresh diets had a greater (p < 0.0001) DI, but the majority of scores remained within the normal range. Dogs fed animal protein-based kibble diets had higher (p < 0.05) fecal Faecalibacterium and Fusobacterium, while dogs fed animal protein-based fresh diets had higher (p < 0.05) Streptococcus, E. coli, and C. perfringens. Bifidobacterium and Bacteroides were more abundant (p < 0.01) in dogs fed animal protein-based kibble and plant protein-based fresh diets. Dogs fed animal protein-based fresh diets had a greater (p < 0.0001) DI. Even though microbiota populations were statistically different among diets, all mean DI were <0, with only a few individual dogs consuming fresh diets having DI >0 (5 dogs >0; 1 dog >2). Overall, these data demonstrate the utility of the DI across different diet types in healthy dogs.},
}

@article {pmid40660964,
year = {2025},
author = {Ng, HM and Wall, CL and Bayer, SB and Gearry, RB and Roy, NC},
title = {The interconnection between dietary fibre, gut microbiome and psychological well-being.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-10},
doi = {10.1017/S002966512510061X},
pmid = {40660964},
issn = {1475-2719},
abstract = {This review highlights the importance of dietary fibres (DF) intake and its interconnection with the gut microbiome and psychological well-being, while also exploring the effects of existing DF interventions on these aspects in adults. The gut microbiota is a complex and diverse ecosystem in which microbial species interact, influencing the human host. DF are heterogeneous, requiring different microbial species to degrade the complex DF structures. Emerging evidence suggests that microbial fermentation of DF produces short-chain fatty acids (SCFA), which may play a role in regulating psychological well-being by affecting neurotransmitter levels, including serotonin. The effectiveness of DF interventions depends on factors such as baseline gut microbiota composition, the dosage and the source of DF consumed. Although the gut microbiota of adults is relatively stable, studies have shown that the abundance of the species in the gut microbiota can change within 24 h of an intervention and may return to baseline following the termination of DF intervention. This review underscores the need for larger and well-powered dietary clinical trials incorporating longitudinal biological sample collections, advanced sequencing and omic techniques (including novel dietary biomarkers and microbial metabolites), validated subjective questionnaires and dietary records. Furthermore, mechanistic studies driven by clinical observations are crucial to understanding gut microbiota function and its underlying biological pathways, informing targeted dietary interventions.},
}

@article {pmid40660619,
year = {2025},
author = {Armstrong, R},
title = {Microbes as Teachers: Rethinking Knowledge in the Anthropocene.},
journal = {Microbial biotechnology},
volume = {18},
number = {7},
pages = {e70195},
doi = {10.1111/1751-7915.70195},
pmid = {40660619},
issn = {1751-7915},
support = {101114746//European Innovation Council (EIC), Pathfinder Challenges/ ; },
mesh = {Humans ; Ecosystem ; *Microbiology/education ; },
abstract = {This opinion piece proposes that the environmental crises of our time arise from a failure to recognise the vital role of microbes in sustaining life on Earth, where ecosystems have been shaped for billions of years by microbial processes, including oxygen production, nutrient cycling and climate regulation. Yet the idea that microbes can 'teach' us how to navigate complexity, adapt across scales, and sustain planetary systems is still marginalised in science, policy, and education. A paradigm shift is proposed: microbes must be reframed as active collaborators in solving global challenges. This perspective is grounded in microbial ecology, Indigenous knowledge, and ethical philosophy, advocating for 'learning' through and with microbial life. To institutionalise this transition, policy and educational reforms are urged, centring microbial literacy as a foundation for ecological understanding. By integrating microbial agency into human knowledge systems, societal actions could be realigned with the biochemical and evolutionary logics that have sustained life for millennia. Ultimately, a deeper engagement with microbial knowledge is called for-one that informs a more sustainable future.},
}

Humans
Ecosystem
*Microbiology/education

@article {pmid40660416,
year = {2025},
author = {Grosche, A and Selci, M and Smedile, F and Giovannelli, D and Borin, S and Le Bris, N and Vetriani, C},
title = {The chemosynthetic biofilm microbiome of deep-sea hydrothermal vents across space and time.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {88},
pmid = {40660416},
issn = {2524-6372},
support = {OCE 1948623//National Science Foundation/ ; },
abstract = {Microbial biofilms colonize mineral and biological substrates exposed to fluid circulation at deep-sea hydrothermal vents, providing a biologically active interface along redox boundaries. Since many biofilms at deep-sea vents are associated with invertebrates, microbial distribution and abundance are not only constrained by local fluid geochemistry, but also through host-microbe interactions. This study examined the spatial distribution and diversity of established microbial biofilm communities collected from three distinct biological regimes characteristic of the East Pacific Rise (9°50 N, 104°17 W) vent system, as well as newly established biofilms on experimental microbial colonization devices. Transcripts from 16S rRNA-based amplicon sequencing revealed that Campylobacterota of the Sulfurimonas and Sulfurovum genera dominated newly-formed biofilms across all biological regimes. Statistical analyses using environmental chemistry data from each sampling site suggest that community composition is significantly impacted by biofilm age, temperature and sulfide concentration ranges, and to a lesser extent, locality. Further, metatranscriptomic analyses were used to investigate changes in community gene expression between seafloor and subseafloor biofilms. Our findings revealed differences in the type and abundance of transcripts related to respiratory pathways, carbon fixation and reactive oxygen species (ROS) detoxification. Overall, this study provides a novel conceptual framework for evaluating biofilm structure and function at deep-sea vents by showing a transition from a niche-specific pioneer microbial community in newly-formed biofilms, to a complex population of increased diversity in established biofilms and by identifying key changes in gene expression in taxonomically similar biofilms during the transition from the shallow subseafloor to the seafloor.},
}

@article {pmid40660385,
year = {2025},
author = {Ji, X and Zhi, M and Gu, X and Han, Y and Lan, X and Song, L and Sun, P and Li, J and Qi, X and Feng, Q},
title = {DnaK of Parvimonas micra extracellular vesicles interacts with the host fibroblasts BAG3-IKK-γ axis to accelerate TNF-α secretion in oral lichen planus.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {164},
pmid = {40660385},
issn = {2049-2618},
support = {ZR2023MH045//Shandong Natural Science Foundation/ ; YJRC2021002//the start-up fund for introduction of talents to Jinan Central Hospital/ ; 2022-2-7//Science and Technology Development Program of Jinan Municipal Health Commission/ ; 82270980//National Natural Science Foundation of China/ ; 2019//he National Young Scientist Support Foundation/ ; ZR2021JQ29//Excellent Young Scientist Foundation of Shandong Province/ ; 2021SFGC0502//Major Innovation Projects in Shandong Province/ ; 2021GXRC021//the Periodontitis innovation team of Jinan City/ ; 2019//Taishan Young Scientist Project of Shandong Province/ ; 2020KJK001//Oral Microbiome Innovation Team of Shandong Province/ ; 2021ZDSYS18//Shandong Province Key Research and Development Program/ ; },
mesh = {Humans ; *Fibroblasts/metabolism/microbiology ; *Extracellular Vesicles/metabolism ; *Tumor Necrosis Factor-alpha/metabolism ; *Lichen Planus, Oral/microbiology/metabolism/pathology ; *Adaptor Proteins, Signal Transducing/metabolism/genetics ; Mouth Mucosa/microbiology ; *I-kappa B Kinase/metabolism/genetics ; Male ; Signal Transduction ; Female ; NF-kappa B/metabolism ; Middle Aged ; *Bacterial Proteins/metabolism/genetics ; *HSP70 Heat-Shock Proteins/metabolism/genetics ; Apoptosis Regulatory Proteins ; },
abstract = {BACKGROUND: Oral lichen planus (OLP) is one of the most frequent oral mucosal diseases associated with chronic inflammation, despite a profoundly limited understanding of its underlying pathogenic mechanisms.

RESULTS: The microbiome analysis was conducted on buccal and lip mucosae, tongue dorsum, and saliva in nonerosive/erosive OLP patients and healthy individuals. Significant variations were observed in the oral microbiome of OLP patients, particularly in the buccal mucosa. Network, random forest, and NetShift analysis collectively indicated that Parvimonas micra (P. micra) emerged as a crucial bacterium in OLP. In vivo analysis further demonstrated that P. micra was abundant at the junction of epithelial and connective tissue layers in OLP lesions. Single-cell RNA sequencing data implicated fibroblasts as potential targets, characterized by upregulation of the NF-κB pathway linked to TNF-α. Co-culturing of P. micra or its extracellular vesicles (EVs) with fibroblasts showed that P. micra and EVs could activate the NF-κB signaling pathway and suppress autophagy in buccal mucosal fibroblasts. Among the pathogenic effectors, DnaK from P. micra EVs was identified to interact with BAG3 in fibroblasts. The interaction of DnaK with BAG3 subsequently activated the NF-κB pathway and decreased autophagy flux. Additionally, we identified that IKK-γ was the key downstream protein that could bind with DnaK-BAG3, thereby inhibiting autophagy and promoting TNF-α secretion.

CONCLUSIONS: We initially revealed that P. micra was a crucial pathogen in the development of OLP and demonstrated that P. micra's EVs induce the inhibition of autophagy and enhanced TNF-α secretion in OLP fibroblasts via the DnaK-BAG3-IKK-γ axis. This study offers novel insights into the pathogenic mechanisms underlying OLP. Video Abstract.},
}

Humans
*Fibroblasts/metabolism/microbiology
*Extracellular Vesicles/metabolism
*Tumor Necrosis Factor-alpha/metabolism
*Lichen Planus, Oral/microbiology/metabolism/pathology
*Adaptor Proteins, Signal Transducing/metabolism/genetics
Mouth Mucosa/microbiology
*I-kappa B Kinase/metabolism/genetics
Male
Signal Transduction
Female
NF-kappa B/metabolism
Middle Aged
*Bacterial Proteins/metabolism/genetics
*HSP70 Heat-Shock Proteins/metabolism/genetics
Apoptosis Regulatory Proteins

@article {pmid40660333,
year = {2025},
author = {Yang, Z and Zhang, Y and Ran, S and Zhang, J and Gao, Y and Zhang, Y and Li, X and Ai, B and Wei, S and Tian, F and Jia, G and Lin, H and Chen, Z and Zhang, Z},
title = {Exposure to ambient air pollution over developmental stages induced neurodevelopmental impairment in mice offspring via microbiome-gut-brain axis.},
journal = {Particle and fibre toxicology},
volume = {22},
number = {1},
pages = {20},
pmid = {40660333},
issn = {1743-8977},
support = {2024A1515010465//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2022A1515010695//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 82203988//National Natural Science Foundation of China/ ; 2023A04J2071//Guangzhou Municipal Science and Technology Project/ ; 23qnpy107//Fundamental Research Funds for the Central Universities of Sun Yat-sen University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Female ; *Air Pollution/adverse effects ; Mice ; Male ; *Neurodevelopmental Disorders/chemically induced/microbiology ; Pregnancy ; *Prenatal Exposure Delayed Effects/chemically induced ; *Brain/drug effects/growth & development ; *Air Pollutants/toxicity ; Mice, Inbred C57BL ; Behavior, Animal/drug effects ; *Brain-Gut Axis/drug effects ; },
abstract = {Exposure to air pollution has been increasingly recognized as a risk factor for neurodevelopmental disorders, and gut microbiome may play a critical role. However, current evidence still remains scarce. In the present study, mice were exposed to real-time ambient air pollution from conception through young adulthood, with neurobehavioral performance and gut microbiome being assessed across different developmental stages. Neurodevelopmental changes including emotional and cognitive impairments were observed in behavioral tests, accompanied by pathological and inflammation changes in brain, which were more pronounced in adolescence than in young adulthood. Alterations in the compositions and functions of gut microbiome were also revealed by fecal metagenomic sequencing. Mediation analysis showed that gut microbiome alterations significantly contributed to the observed neurodevelopmental changes induced by air pollution. Furthermore, after antibiotic (ABX) intervention, the observed neurobehavioral, pathological and inflammatory differences between the exposed and control groups diminished. These findings indicate that the gut microbiome mediates the neurodevelopmental damage caused by exposure to air pollution during developmental stages, adding novel insights on the underlying mechanisms linking air pollution and neurodevelopmental disorders.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Female
*Air Pollution/adverse effects
Mice
Male
*Neurodevelopmental Disorders/chemically induced/microbiology
Pregnancy
*Prenatal Exposure Delayed Effects/chemically induced
*Brain/drug effects/growth & development
*Air Pollutants/toxicity
Mice, Inbred C57BL
Behavior, Animal/drug effects
*Brain-Gut Axis/drug effects

@article {pmid40660288,
year = {2025},
author = {Qin, W and Yin, N and Xu, B and Mei, Q and Fu, Y and Fan, J and Lu, Y and Wang, G and Ai, L and Lu, Z and Zeng, Y and Huang, C},
title = {Faecalibacterium prausnitzii enhances intestinal IgA response by host-microbe derived inecalcitol in colitis.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {425},
pmid = {40660288},
issn = {1741-7015},
support = {No. 81970555//National Natural Science Foundation of China/ ; No.CCTR-2022B02//Shanghai General Hospital/ ; 202440170//Shanghai Municipal Health Commission/ ; No.22SJKGGG28//Science and Technology Commission of Songjiang District/ ; No.KY-2023-03-02//Shanghai Jiao Tong University School of Medicine, Digestive Institute/ ; },
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/immunology ; Humans ; *Faecalibacterium prausnitzii/immunology ; Mice, Knockout ; Mice, Inbred C57BL ; *Colitis, Ulcerative/microbiology/immunology ; Male ; *Immunoglobulin A/metabolism/immunology ; Dextran Sulfate ; Disease Models, Animal ; *Colitis/microbiology/immunology ; *Immunoglobulin A, Secretory ; Female ; Feces/microbiology ; },
abstract = {BACKGROUND: Faecalibacterium prausnitzii plays a crucial role in ulcerative colitis (UC) remission, but its action mechanism is unknown. Here, we aimed to explore the potential mechanisms focusing on the interaction of F. prausnitzii with host immune response and its potential modulation on gut microbiome.

METHODS: RNA-seq analysis together with 16S rRNA sequencing and metabolomics were performed in a dextran sodium sulfate (DSS)-induced colitis mouse model followed by F. prausnitzii gavage. To present evidence of sIgA involved in the anti-inflammatory effects of F. prausnitzii, we further applied immunoglobulin A (IgA) knockout mice and secretory IgA (sIgA) depletion mouse models using polymeric immunoglobulin receptor (pIgR) neutralizing antibody. Colonic immune cells were characterized by flow cytometry. The fecal relative abundance of F. prausnitzii, inecalcitol, and colonic IgA expression were assessed in UC patients.

RESULTS: F. prausnitzii markedly ameliorated colitis by alleviating intestinal inflammation and barrier dysfunction, with significantly decreased abundance of pro-inflammatory taxa (Enterococcus, Desulfovibrio, Escherichia-Shigella, and Enterorhabdus) and increased abundance of Lachnospiraceae NK4A136_group. Functions related to intestinal immune network for IgA production pathway were up-regulated shown by transcriptomics and KEGG pathway analysis. Increased expression of IgA production associated genes including MHCII-related genes, Aicda, and Tnfrsfl3c were verified, accompanied by up-regulated colonic IgA and pIgR. The IgA knockout mice and sIgA depletion model weakened the anti-inflammation and microbiota-modulation effects of F. prausnitzii, which was further proved by fecal microbiota transplantation (FMT). The shift profile of fecal metabolites after F. prausnitzii supplement was characterized by increased production of inecalcitol, which may account for the enhanced IgA response. In a cohort of UC patients, the relative abundance of F. prausnitzii was decreased and positively correlated with colonic IgA expression and negatively correlated with disease severity.

CONCLUSIONS: F. prausnitzii effectively alleviated colonic inflammation and modulated dysbiosis via enhancing colonic IgA response, thus showing promise as a UC treatment.},
}

Animals
Mice
*Gastrointestinal Microbiome/immunology
Humans
*Faecalibacterium prausnitzii/immunology
Mice, Knockout
Mice, Inbred C57BL
*Colitis, Ulcerative/microbiology/immunology
Male
*Immunoglobulin A/metabolism/immunology
Dextran Sulfate
Disease Models, Animal
*Colitis/microbiology/immunology
*Immunoglobulin A, Secretory
Female
Feces/microbiology

@article {pmid40660153,
year = {2025},
author = {Cui, X and Wang, Y and Yu, G and He, B and Huang, L and Liu, Y and Zhan, Z},
title = {Integrated morphological observation, metabolomics, and transcriptomics to investigate the effect of growth years on the quality of Atractylodes macrocephala Koidz.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {912},
pmid = {40660153},
issn = {1471-2229},
support = {CI2023E002//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; CI2023E002//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; CI2023E002//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; CI2023E002//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; CI2023E002//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; 2060302//Ministry of Finance Central Level of the Special/ ; 2060302//Ministry of Finance Central Level of the Special/ ; 2060302//Ministry of Finance Central Level of the Special/ ; 2060302//Ministry of Finance Central Level of the Special/ ; 2060302//Ministry of Finance Central Level of the Special/ ; },
abstract = {BACKGROUND: Atractylodes macrocephala Koidz. is a medicinal plant in high clinical demand due to its pharmacological efficacy. However, research on its quality dynamics across different growth years remains limited, primarily focusing on transcriptomics, microbiome analysis, and photosynthetic capacity, with studies only extending to three-year-old plants.

RESULTS: This study examines A. macrocephala over a broader growth span (1, 2, 3, 5, and 10 years), integrating morphological, microstructural, metabolomic, spatial metabolite distribution, and transcriptomic analyses. Morphologically, rhizome weight and length increased with age, and the characteristic "Hejing" structure became more pronounced. Microstructural analysis revealed progressively developed xylem. Metabolomic profiling indicated a decline in sucrose content, alongside increased accumulation of bioactive sesquiterpenoids and phenolic acids over time. Transcriptomic analysis showed that genes involved in the biosynthesis of these active compounds-terpenoid backbone (HMGR, DXS, idi, GPS, and GGPS), phenylpropanoid (PAL, 4CL, and HCT), and sucrose metabolism (SPS and SPP)-were upregulated in older plants. Desorption electrospray ionisation mass spectrometry imaging (DESI-MSI) revealed an expanded distribution of key metabolites with increasing growth years.

CONCLUSION: The findings suggest that A. macrocephala aged 5 and 10 years exhibit superior quality, with a more distinct "Hejing" morphology and higher levels of bioactive compounds. The quality stabilises after five years, indicating that older plants may possess enhanced medicinal value.},
}

@article {pmid40659807,
year = {2025},
author = {Ledford, H},
title = {Found: a human gut microbe that makes cancer therapy more effective in mice.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40659807},
issn = {1476-4687},
}

@article {pmid40659728,
year = {2025},
author = {Rehner, J and Molano, LG and Christodoulou, C and Holländer, S and Förster, MO and Keller, V and Jäger, J and Volz-Willems, S and Becker, SL and Glanemann, M and Jelden, M},
title = {Examining spatial microbiome variations across gastrointestinal tract regions in obesity.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25423},
pmid = {40659728},
issn = {2045-2322},
mesh = {Humans ; *Obesity/microbiology/surgery ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; *Gastrointestinal Tract/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Bariatric Surgery ; Feces/microbiology ; Bacteria/genetics/classification ; },
abstract = {Obesity, a global health concern, is associated with alterations in the gut microbiome, yet its spatial dynamics across the gastrointestinal (GI) tract remain poorly understood. This study provides the first comprehensive analysis of the spatial microbiome in individuals with obesity, encompassing samples from the stomach, peritoneum, jejunum (50 cm and 150 cm post-Treitz), and feces before and after bariatric surgery. Using 16 S rRNA sequencing, we analyzed microbial composition and diversity after computational decontamination in 172 high-quality samples from 51 participants. Our results reveal significant differences in alpha diversity across GI sites, with stool samples exhibiting the highest diversity, which decreased post-surgery. The presence of microbial DNA in traditionally sterile compartments, such as the peritoneum and stomach, suggests potential microbial-host interactions warranting further exploration. Contaminants, including Nitrotoga sp., were identified in low-biomass samples and excluded using computational decontamination, emphasizing the need for rigorous controls. This study establishes a foundation for spatial microbiome analysis in obesity, highlighting the impact of bariatric surgery and the importance of advanced multi-omics approaches to unravel host-microbiome dynamics.},
}

Humans
*Obesity/microbiology/surgery
*Gastrointestinal Microbiome/genetics
Male
Female
*Gastrointestinal Tract/microbiology
Adult
RNA, Ribosomal, 16S/genetics
Middle Aged
Bariatric Surgery
Feces/microbiology
Bacteria/genetics/classification

@article {pmid40659339,
year = {2025},
author = {Singh, A and Juyal, G and Gacesa, R and Joshi, MC and Midha, V and Thelma, BK and Weersma, RK and Sood, A},
title = {Cross-ethnic evaluation of gut microbial signatures reveal increased colonization with oral pathobionts in the north Indian inflammatory bowel disease cohort.},
journal = {Intestinal research},
volume = {},
number = {},
pages = {},
doi = {10.5217/ir.2024.00216},
pmid = {40659339},
issn = {1598-9100},
abstract = {BACKGROUND/AIMS: Inflammatory bowel disease (IBD) has become a global health concern. With the growing evidence of the gut microbiota's role in IBD, studying microbial compositions across ethnic cohorts is essential to identify unique, populationspecific microbial signatures.

METHODS: We analyzed stool samples and clinical data from 254 IBD patients (226 ulcerative colitis, 28 Crohn's disease) and 66 controls in northern India using metagenomic shotgun sequencing to assess microbiota diversity, composition, and function. Results were replicated in 436 IBD patients and 903 controls from the Netherlands using identical workflows. Using machine learning, we evaluated the generalizability of Indian IBD signals to the Dutch cohort, and vice versa.

RESULTS: Indian IBD patients exhibited reduced bacterial diversity and an abundance of opportunistic pathogens, including Clostridium, Streptococcus, and oral bacteria like Streptococcus oralis and Bifidobacterium dentium. There was a significant loss of energy metabolic pathways and distinct co-occurrence patterns among microbial species. Notably, 39% of these signals replicated in the Dutch cohort. Unique to the Indian cohort were oral pathobionts such as Scardovia, Oribacterium, Actinomyces dentalis, and Klebsiella pneumoniae. Both Indian and Dutch IBD patients shared reduced butyrate producers. Machine-learning diagnostic models trained on the Indian cohort achieved high predictive accuracy (sensitivity 0.84, specificity 0.95) and moderately generalized to the Dutch cohort (sensitivity 0.77, specificity 0.69).

CONCLUSIONS: IBD patients across populations exhibit shared and unique microbial signatures, suggesting a role for the oral-gut microbiome axis in IBD. Crossethnic diagnostic models show promise for broader applications in identifying IBD.},
}

@article {pmid40659293,
year = {2025},
author = {Laguna-Marín, C and Escolà-Casas, M and Subirats, J and Matamoros, V},
title = {Biochar enhanced floating root mats to reduce recalcitrant contaminants of emerging concern from wastewater effluents.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132960},
doi = {10.1016/j.biortech.2025.132960},
pmid = {40659293},
issn = {1873-2976},
abstract = {This bench-scale study assessed a novel biochar-intensified floating root mat (FRM) system to reduce contaminants of emerging concern (CEC) from secondary-treated wastewater. Three configurations were evaluated: (1) FRM with plants (Cyperus alternifolius) and biochar, (2) FRM with plants only, and (3) unplanted control reactors, under two hydraulic loading rates (12 and 24 mm/day) over six months. The planted FRM enhanced CEC removal by 15 and 28 %, while the addition of biochar further increased removal by 35 % and 41 %, achieving CEC attenuation ranging from 41-99 %. Untargeted analysis corroborated this performance, and microbiological analysis linked CEC reduction to increased abundance of genera such as Exiguobacterium, Nocardia, Rodobacter and Amaricoccus, associated with biodegradation processes. This work therefore demonstrates that integrating biochar into FRMs enhances the attenuation of CEC and, for the first time, links biochar addition to microbial community shifts, offering a new strategy to tackle CEC pollution in wastewater treatment plants.},
}

@article {pmid40659121,
year = {2025},
author = {Eapen, AA and Shankhwar, S and von Mutius, E and Johnson, CC},
title = {Environmental Risk Factors and Asthma Primary Prevention: from Birth Cohort Studies to Clinical Trials.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2025.07.002},
pmid = {40659121},
issn = {1097-6825},
abstract = {With the prevalence of pediatric asthma and allergy rising substantially since last mid-century, birth cohort studies starting in pregnancy have been pivotal in identifying prenatal and early life environmental factors that influence risk of these diseases. With these findings, researchers have been able to identify biological mechanisms at play with the eventual goal of engineering tailored interventions to optimize immune system development and decrease the risk of allergic disorders. In this review, we describe the critical role birth cohort studies have played in starting to disentangle the environmental epidemiology and etiology of childhood-onset asthma and other allergic diseases, and how these studies have guided ongoing clinical trials for asthma and allergy prevention. Lastly, we highlight important questions that remain unanswered and potential approaches to help fill these gaps in knowledge.},
}

@article {pmid40659087,
year = {2025},
author = {Wang, Y and Zhao, D and Li, Z and Yang, Y and Peng, Z and Meng, C and Ma, S and Xu, K and Li, Y and Ding, G and Zheng, Y and Zhang, CS},
title = {Kaempferol drives genotype-specific microbiota Bacillaceae to enhance nitrogen acquisition in rapeseed.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.07.018},
pmid = {40659087},
issn = {2090-1224},
abstract = {INTRODUCTION: Host genotype is a key driver in shaping plant microbiome in response to dynamic changes in soil nitrogen (N) availability. However, the effects of rapeseed (Brassica napus) genotypes with different N use efficiency characteristics on microbiome assembly, as well as the underlying plant-microbe interaction mechanisms, remain poorly understood.

OBJECTIVES: This study aims to: (1) assess microbial assembly differences between N-use efficient and inefficient genotypes; (2) identify specific microbiota associated with plant N acquisition; and (3) reveal the molecular mechanisms driving plant-microbe interactions.

METHODS: We conducted comparative microbiome profiling of N-use efficient and inefficient genotypes, followed by functional validation of microbial roles in plant N uptake. Multi-omics approaches, including RNA-seq and metabolomics, were used to uncover the regulatory interactions between the host and rhizosphere microbiota.

RESULTS: The N-use efficient genotype constructed more diverse root-associated microbes than the inefficient genotype, with Bacillaceae emerging as the most enriched taxon. A representative isolate, Bacillus sp. 41S2 from the N-use efficient genotype, markedly enhanced root biomass and N uptake in the N-use inefficient genotype, as confirmed by [15]N tracer assays. RNA-Seq analysis further demonstrated that genes involved in jasmonic acid and ethylene signaling pathways were upregulated in strain 41S2-inoculated plants, likely contributing to enhanced root development. Metabolomic profiling identified kaempferol, a flavonol with the highest fold-change between genotypes, as a key root exudate promoting the growth and biofilm formation of strain 41S2. Furthermore, the fls1 mutant (deficient in kaempferol biosynthesis) failed to recruit Bacillaceae, confirming the role of kaempferol in mediating genotype-specific microbial enrichment.

CONCLUSIONS: Our findings reveal a novel, microbe-dependent N acquisition pathway in N-use efficient rapeseed genotypes, driven by kaempferol-mediated recruitment of Bacillaceae. This work highlights the potential of host genotype and metabolite signaling to shape beneficial microbiota for improved nutrient efficiency and sustainable crop production.},
}

@article {pmid40659044,
year = {2025},
author = {Nolan, M and Chan, B and Loc-Carrillo, C and Parker, A and France, D and Grubb, PH and Drews, F},
title = {Increased Caregiver Interaction with the NICU Environment during Medication Administration May Contribute to Higher Infection Rates: A Pilot Observational Study.},
journal = {American journal of perinatology},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2641-9863},
pmid = {40659044},
issn = {1098-8785},
abstract = {After nearly 3 years without a single central line-associated bloodstream infection (CLABSI), our neonatal intensive care unit (NICU) experienced a significant rise in CLABSI rates beginning in 2019. The increase coincided with changes made to the intravenous (IV) medication pump integration process, which added more safety checks and procedural steps. This study aimed to investigate the potential association between these process changes and increased CLABSI and non-CLABSI (bloodstream infection, BSI) rates prior to inclusion in a future QI project Key Driver Diagram.This observational pilot study used a mixed-methods approach, including statistical process control analysis to confirm a special-cause increase in CLABSI rate, human factors observations, and environmental microbiome sampling focusing on the equipment involved in the IV pump integration. We compared these findings to the CLABSI and BSI rates to identify temporal and geographic associations.Following the 2019 implementation of IV pump integration, statistically significant increases in CLABSI and BSI rates were observed. The enhanced safety checks added steps to IV medication administrations, with timestamp observation indicating up to 14 location changes around the bed spaces and a mean of 5.5 minutes for any IV medication administration. Environmental microbial sampling showed a 27% positivity rate. The highest microbial burden was found on patient-specific mobile equipment (30%) used during IV medication administration, including isolettes, IV hubs, and glove boxes, compared with other equipment (26%) like nursing computers or ventilators (p = 0.093). A strong overlap was observed between the microorganisms found in the NICU environment and those responsible for positive patient blood cultures, particularly coagulase-negative Staphylococcus (CONS).Though not statistically significant, the findings suggest that the added complexity and extended duration of the modified IV pump integration process may have increased the frequency of caregiver interactions with the NICU environment, exposing immune-vulnerable NICU patients to a higher risk of infection. Further human factors analysis and quality improvement efforts are necessary to simplify the IV medication administration process, reduce environmental microbial loads, and decrease infection rates. · Increased CLABSI/BSI rates post-IV pump integration.. · High microbial load on equipment related to the IV medication administration process.. · Process changes with IV pump integration to enhance patient safety may have unintended consequences, like increasing caregiver-environment interaction and patient infection rates..},
}

@article {pmid40658810,
year = {2025},
author = {Allegretti, AS and Levitsky, J and Sharma, P and Ouyang, T and Jamil, K and Silvey, S and Bajaj, JS},
title = {Predictors of response to terlipressin therapy in hepatorenal syndrome: Metabolomic and proteomic analysis from the CONFIRM trial.},
journal = {Hepatology communications},
volume = {9},
number = {8},
pages = {},
pmid = {40658810},
issn = {2471-254X},
mesh = {Humans ; *Hepatorenal Syndrome/drug therapy/blood/urine/metabolism ; *Terlipressin/therapeutic use ; Male ; Female ; Middle Aged ; *Vasoconstrictor Agents/therapeutic use ; Proteomics ; Metabolomics ; Treatment Outcome ; Biomarkers/blood/urine ; Aged ; Creatinine/blood ; Adult ; },
abstract = {BACKGROUND: Terlipressin is the only FDA-approved vasoconstrictor for hepatorenal syndrome (HRS). The CONFIRM study is the largest trial of terlipressin versus placebo. Novel predictors of HRS response are required to enrich patient selection and optimize outcomes.

METHODS: Samples at treatment initiation were tested using (a) liquid chromatography-mass spectrometry of 1594 plasma/1420 urine metabolites (Metabolon Inc.), (b) aptamer-based array of 7289 plasma proteins (SomaScan), and (c) 14 plasma/urine pre-specified assays. The CONFIRM trial's original definition of HRS response [2 serum creatinine (SCr) <1.5 mg/dL separated by >2 h] was used as the primary outcome.

RESULTS: In all, 115 patients [79 terlipressin-treated (TT) and 36 placebo-treated (PT)] provided samples. Baseline characteristics, outcomes, and 2:1 TT:PT allocation were preserved from the original 300-patient trial. A total of 36 out of 116 (31.0%) patients achieved HRS reversal. HRS reversal was associated with lower SCr (p=0.001), cystatin C (p=0.005), angiopoietin-2 (p=0.04), and beta-2 microglobulin (p=0.006). In metabolite analysis, PT had the most significant differences in HRS reversal [n=26 plasma, n=50 urine, including lower urine levels of those centered on sulfated secondary bile acids (microbiome-derived), N-acetylated amino acids, catechols (both uremic toxins), and phosphocholines (cell membrane integrity)], with fewer in TT (n=1 plasma, n=2 urine), and in all patients (n=3 plasma, n=7 urine). There were no significant aptamers associated with HRS reversal after false-discovery correction.

CONCLUSIONS: SCr, cystatin C, angiopoietin-2, and beta-2 microglobulin were associated with HRS reversal. Protein and metabolite signals centered on microbiome function and uremic toxins appeared more robust in PT patients, likely selecting a subgroup that may recover without terlipressin. Use of novel biomarkers may enrich for terlipressin response.},
}

Humans
*Hepatorenal Syndrome/drug therapy/blood/urine/metabolism
*Terlipressin/therapeutic use
Male
Female
Middle Aged
*Vasoconstrictor Agents/therapeutic use
Proteomics
Metabolomics
Treatment Outcome
Biomarkers/blood/urine
Aged
Creatinine/blood
Adult

@article {pmid40658737,
year = {2025},
author = {Lundberg, DS and Kersten, S and Mehmetoğlu Boz, E and Pramoj Na Ayutthaya, P and Zhu, W and Poersch, K and Yuan, W and Swartz, S and Müller, D and Bezrukov, I and , and Weigel, D},
title = {A major trade-off between growth and defense in Arabidopsis thaliana can vanish in field conditions.},
journal = {PLoS biology},
volume = {23},
number = {7},
pages = {e3003237},
doi = {10.1371/journal.pbio.3003237},
pmid = {40658737},
issn = {1545-7885},
abstract = {When wild plants defend themselves from pathogens, this often comes with a trade-off: the same genes that protect a plant from disease can also reduce its growth and fecundity in the absence of pathogens. One protein implicated in a major growth-defense trade-off is ACCELERATED CELL DEATH 6 (ACD6), an ion channel that modulates salicylic acid (SA) synthesis to potentiate a wide range of defenses. Wild Arabidopsis thaliana populations maintain significant functional variation at the ACD6 locus, with some alleles making the protein hyperactive. In the greenhouse, plants with hyperactive ACD6 alleles are resistant to diverse pathogens, yet they are of smaller stature, their leaves senesce earlier, and they set fewer seeds compared to plants with the standard allele. We hypothesized that ACD6 hyperactivity would not only affect the growth of microbial pathogens but also more generally change leaf microbiome assembly. To test this in an ecologically meaningful context, we compared plants with hyperactive, standard, and defective ACD6 alleles in the same field-collected soil, both outdoors and in naturally lit and climate-controlled indoor conditions, taking advantage of near-isogenic lines as well as a natural accession and a CRISPR-edited derivative. We surveyed visual phenotypes, gene expression, hormone levels, seed production, and the microbiome in each environment. The genetic precision of CRISPR-edited plants allowed us to conclude that ACD6 genotype had no effect on mature field plants in our setting, despite reproducibly dramatic effects on greenhouse plants. We conclude that additional abiotic and/or microbial signals present outdoors-but not in the greenhouse-greatly modulate ACD6 activity. This raises the possibility that the fitness costs of other commonly studied immune system genes may be grossly misjudged without field studies.},
}

@article {pmid40658721,
year = {2025},
author = {Mahajan, T and Maslov, S},
title = {Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013222},
doi = {10.1371/journal.pcbi.1013222},
pmid = {40658721},
issn = {1553-7358},
abstract = {Many microbial communities in nature are complex, with hundreds of coexisting strains and the resources they consume. We currently lack the ability to assemble and manipulate such communities in a predictable manner in the lab. Here, we take a first step in this direction by introducing and studying a simplified consumer resource model of such complex communities in serial dilution experiments. The main assumption of our model is that during the growth phase of the cycle, strains share resources and produce metabolic byproducts in proportion to their average abundances and strain-specific consumption/production fluxes. We fit the model to describe serial dilution experiments in hCom2, a defined synthetic human gut microbiome with a steady-state diversity of 63 species growing on a rich media, using consumption and production fluxes inferred from metabolomics experiments. The model predicts serial dilution dynamics reasonably well, with a correlation coefficient between predicted and observed strain abundances as high as 0.8. We applied our model to: (i) calculate steady-state abundances of leave-one-out communities and use these results to infer the interaction network between strains; (ii) explore direct and indirect interactions between strains and resources by increasing concentrations of individual resources and monitoring changes in strain abundances; (iii) construct a resource supplementation protocol to maximally equalize steady-state strain abundances.},
}

@article {pmid40658705,
year = {2025},
author = {Cui, X and Martinez Luna, AA and Gillone, A and Wu, Q and Serag, M and Murata, RM},
title = {Correlation between pre-extraction periodontal diagnosis and peri-implant microbiome for patients treated with implant-retained overdenture - A retrospective cohort pilot study.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0325711},
doi = {10.1371/journal.pone.0325711},
pmid = {40658705},
issn = {1932-6203},
mesh = {Humans ; Female ; Male ; Aged ; Pilot Projects ; *Microbiota ; Middle Aged ; *Denture, Overlay/microbiology ; Retrospective Studies ; *Dental Implants/microbiology ; RNA, Ribosomal, 16S/genetics ; *Periodontitis/diagnosis/microbiology ; Aged, 80 and over ; Peri-Implantitis/diagnosis/microbiology ; },
abstract = {Limited clinical data exists on the peri-implant microbiome in edentulous patients with implant-retained overdentures (IRO). This study aimed to examine the peri-implant microbiome and its correlation with pre-treatment periodontal diagnosis. A total of twenty-five patients with 50 implants were included, with demographic information and pre-treatment periodontal diagnosis collected. Clinical measurements and subgingival plaque samples were obtained from each implant, followed by 16S rRNA gene-targeted sequencing. Peri-implant parameters and microbiome were analyzed in relation to gender, remaining teeth prior to treatment, IRO function time, implant system, bone graft at implant placement, and peri-implant diagnosis. The mean age of patients was 71 years, with pre-extraction diagnoses including clinical healthy gingiva on a reduced periodontium (4 patients), localized periodontitis (4 patients), generalized periodontitis (7 patients), and generalized Stage IV Grade C periodontitis (10 patients). Nineteen implants were diagnosed with peri-implant mucositis, while 31 were healthy. The predominant genera detected were Streptococcus, Rothia, Veillonella, Actinomyces, and Schaalia. No significant correlation was found between pre-treatment periodontal diagnosis and peri-implant diagnosis. The findings suggest that while pre-extraction periodontal diagnosis might influence the peri-implant subgingival microbiome in IRO patients, it may not correlate with the clinical peri-implant diagnosis.},
}

Humans
Female
Male
Aged
Pilot Projects
*Microbiota
Middle Aged
*Denture, Overlay/microbiology
Retrospective Studies
*Dental Implants/microbiology
RNA, Ribosomal, 16S/genetics
*Periodontitis/diagnosis/microbiology
Aged, 80 and over
Peri-Implantitis/diagnosis/microbiology

@article {pmid40658627,
year = {2025},
author = {Ma, T and Wang, W and Li, S and Li, D and Shen, L and Qu, G and Chiang, VL and Zhang, Q and Wu, D and Niu, B},
title = {A Workflow for the Quantitative Assessment of the Endophytic and Epiphytic Bacterial Microbiomes of the Bark of Populus trichocarpa.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {220},
pages = {},
doi = {10.3791/66318},
pmid = {40658627},
issn = {1940-087X},
mesh = {*Populus/microbiology ; *Plant Bark/microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Workflow ; DNA, Bacterial/genetics ; Polymerase Chain Reaction/methods ; Endophytes/genetics/isolation & purification ; },
abstract = {Microorganisms colonizing plant surfaces and internal tissues may possess beneficial functions in promoting plant growth and health. However, information on the microbiome of bark tissues of woody plants remains limited, especially regarding the endophytic and epiphytic bacterial microbiota of the bark of Populus. To overcome this limitation, we established a workflow to quantify the composition and diversity of the endophytic and epiphytic bacterial microbiota colonizing the bark of Populus trichocarpa. Briefly, the epidermis of the stem of P. trichocarpa was repeatedly wiped with a cotton ball dipped in 0.1% Tween 20 to acquire epiphytic bacterial samples. The stripped epidermis was sterilized and then repeatedly frozen and crushed using liquid nitrogen and a bead beater, respectively, to collect endophytic bacterial samples. Genomic DNA was extracted from the cotton-adhered epiphytic bacterial communities and the crushed bark of P. trichocarpa, and underwent ploymerase chain reaction (PCR) amplification with primers targeting the hypervariable V5-V7 and V4 regions of the bacterial 16S rRNA gene. Three replicates of the obtained PCR products of each endophytic or epiphytic sample were mixed in equal concentrations to build the amplicon library, which was then sequenced. The obtained sequences were analyzed by sequence splicing, quality filtering, chimera removal, and taxonomic annotations. In summary, we established a reliable and efficient workflow from sample collection to data analysis for determining the endophytic and epiphytic bacterial microbiomes of the bark of P. trichocarpa through 16S rRNA gene profiling. Together with the methods for exploring microbiota colonizing barks established in the previous study, our methodology may serve as a blueprint for designing protocols for investigating the bark microbiome of other woody plant species, particularly economically important trees of forests.},
}

*Populus/microbiology
*Plant Bark/microbiology
*Microbiota
*Bacteria/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
Workflow
DNA, Bacterial/genetics
Polymerase Chain Reaction/methods
Endophytes/genetics/isolation & purification

@article {pmid40658318,
year = {2025},
author = {Yu, S and Li, J and Ye, Z and Zhang, M and Guo, X and Wang, X and Liu, L and Wang, Y and Zhou, X and Fu, W and Zhang, MQ and Chen, YG},
title = {Identification of a 10-species microbial signature of inflammatory bowel disease by machine learning and external validation.},
journal = {Cell regeneration (London, England)},
volume = {14},
number = {1},
pages = {32},
pmid = {40658318},
issn = {2045-9769},
support = {2023YFA1800603//National Key Research and Development Program of China/ ; 31988101//Natural Science Foundation of China/ ; 92354306//Natural Science Foundation of China/ ; Z231100007223006//Beijing Science and Technology Plan/ ; B2302022//Shenzhen Medical Research Fund/ ; 20224ACB209001//Natural Science Foundation of Jiangxi Province/ ; O0390302//Guangdong Provincial Postdoctoral Science Foundation/ ; },
abstract = {Genetic and microbial factors influence inflammatory bowel disease (IBD), prompting our study on non-invasive biomarkers for enhanced diagnostic precision. Using the XGBoost algorithm and variable analysis and the published metadata, we developed the 10-species signature XGBoost classification model (XGB-IBD10). By using distinct species signatures and prior machine and deep learning models and employing standardization methods to ensure comparability between metagenomic and 16S sequencing data, we constructed classification models to assess the XGB-IBD10 precision and effectiveness. XGB-IBD10 achieved a notable accuracy of 0.8722 in testing samples. In addition, we generated metagenomic sequencing data from collected 181 stool samples to validate our findings, and the model reached an accuracy of 0.8066. The model's performance significantly improved when trained on high-quality data from the Chinese population. Furthermore, the microbiome-based model showed promise in predicting active IBD. Overall, this study identifies promising non-invasive biomarkers associated with IBD, which could greatly enhance diagnostic accuracy.},
}

@article {pmid40658295,
year = {2025},
author = {Li, B and Lin, W and Hu, R and Bai, S and Ruan, Y and Fan, Y and Qiao, S and Wen, X and Liu, R and Chen, H and Cui, W and Cai, Z and Zhang, G},
title = {Crosstalk between lung and extrapulmonary organs in sepsis-related acute lung injury/acute respiratory distress syndrome.},
journal = {Annals of intensive care},
volume = {15},
number = {1},
pages = {97},
pmid = {40658295},
issn = {2110-5820},
support = {No. 82470068, No. 82270086//National Natural Science Foundation of China/ ; LZ25H150001//Natural Science Foundation of Zhejiang Province/ ; WKJ-ZJ-2526//National Health Commission Scientific Research Fund/ ; },
abstract = {Sepsis-related acute lung injury/acute respiratory distress syndrome (ALI/ARDS) is associated with considerable morbidity and mortality, yet the efficacy of current treatments is limited. Previous studies have predominantly focused on the lung itself as an isolated organ, whereas the role of organ crosstalk in the pathogenesis of sepsis-related ALI/ARDS cannot be overlooked. Meanwhile, neglecting the discussion of heterogeneity in sepsis caused by different sources of infection may be another important obstacle to translating previous studies into clinical efficacy. In this review, we initially delineated the distinctions in pathogenesis between pulmonary and extrapulmonary sepsis-related ALI/ARDS in microbial species, pathogenesis, host response, and clinical manifestations. Additionally, systemic organ crosstalk mechanisms are summarized, including the commonality and specificity of systemic inflammation, lung and gut microbiome, as well as cascade cell injury and death in distant organs. Subsequently, organ crosstalk between lung and extrapulmonary in pulmonary sepsis and extrapulmonary sepsis-related ALI/ARDS are discussed by organs, including immunity, neuroendocrine, metabolism, and so forth. Furthermore, extracellular vesicles represent a promising avenue of research as potential players and targets in organ-lung crosstalk in sepsis. While the complexity of multi-organ interactions and the heterogeneity of septic patients present significant challenges, these issues are expected to be addressed by the emergence of organ-on-a-chip platforms, 3D organoid cultures, and multi-omics techniques.},
}

@article {pmid40658186,
year = {2025},
author = {You, L and Huang, W and Chen, S},
title = {Unveiling the anticancer potential of flavonoids in hepatocellular carcinoma through microbiome and spatially resolved metabolomics analysis.},
journal = {Discover oncology},
volume = {16},
number = {1},
pages = {1327},
pmid = {40658186},
issn = {2730-6011},
abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) causes a large worldwide health burden, needing novel ways to prevention and treatment. Traditional Chinese medicine, which is rich in bioactive substances, has emerged as a viable approach to tackling HCC difficulties. Artemisia rupestris L. (AR), a perennial plant, has received interest for its immunoregulatory qualities and potential protection against viral influenza and hepatocellular cancer.

METHODS: In this work, we looked at the pharmacological effects of Artemisia rupestris L. extract (ARE) on HCC mice. We used 16 S rRNA sequencing and computational biology approaches to investigate ARE-induced changes in bacterial composition inside HCC mouse tissues. Furthermore, we used liquid chromatography tandem mass spectrometry (UPLC-MS/MS) to identify metabolic changes caused by ARE.

RESULTS: Our data indicate that ARE affects hepatocellular cancer via several pathways. AR offers a multi-faceted strategy to combating HCC by influencing critical metabolic pathways such α-linolenic acid and glycerophospholipid metabolism.

CONCLUSIONS: This research sheds new light on Artemisia rupestris L.'s anticancer potential, setting the platform for a more in-depth knowledge of its influence on hepatocellular carcinoma using a multi-omics approach.},
}

@article {pmid40658106,
year = {2025},
author = {Chen, G and Wang, Y and Zhang, X and Jiang, K and Yu, M and Fang, L and Li, F},
title = {Periphyton-Driven Arsenic Methylation in Paddy Soils: The Crucial Role of Trophic Interactions.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06047},
pmid = {40658106},
issn = {1520-5851},
abstract = {Arsenic (As) methylation facilitated by periphyton in paddy soils is crucial for its biogeochemical cycling and thus its bioavailability. However, the key functional taxa and underlying interactive metabolisms remain unclear due to the high complexity of the periphytic microbiome. Here, we employ DNA-stable isotope probing with metagenomic binning analysis to uncover the critical role of intrinsic trophic interactions in stimulating As methylation within the periphyton in association with soil inorganic carbon. Abundance of As-methylating microorganisms in the periphyton increases by 2.1-fold after bicarbonate addition. Members of phototrophs are predominantly responsible for regulating the stability of the periphytic microbiome, of which photoautotrophs (e.g., Oscillatoriales) initiate carbon fixation and constitute a major portion of As-methylating populations. These phototrophs further offer requisite organic substrates such as polysaccharides for heterotrophic bacteria (e.g., Chitinophagales) that in return foster the growth of the periphytic community, while these taxa simultaneously detoxify As through biomethylation to secure their ecological niches in periphyton. Such a symbiotic metabolism between phototrophs and heterotrophs facilitates carbon sequestration and shapes the functional community, collaboratively determining methylated As production in paddy soils. These findings offer new insights into the influence of trophic interactions within the periphyton on As speciation with potential implications for element cycling and soil remediation in paddy soils.},
}

@article {pmid40657987,
year = {2025},
author = {Van Dyke, TE and Baima, G and Romandini, M},
title = {Periodontitis: Microbial Dysbiosis, Non-Resolving Inflammation, or Both?.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.13424},
pmid = {40657987},
issn = {1600-0765},
support = {DE025020/DE/NIDCR NIH HHS/United States ; DE032406/DE/NIDCR NIH HHS/United States ; },
abstract = {The central question addressed in this review revisits the historical chicken-and-egg debate: "In periodontitis, does microbial dysbiosis drive inflammation, or does inflammation shape the subgingival microbiome?" This question is reframed through the lens of inflammation resolution. Specialized pro-resolving mediators (SPMs) provide a mechanistic framework for understanding how inflammation intersects with microbial dysbiosis. Derived from omega-3 and omega-6 fatty acids, SPMs actively promote the resolution of inflammation through binding of specific cell surface receptors rather than nonspecifically suppressing it, highlighting their therapeutic potential as side-effect-free host modulators, with implications beyond periodontitis to other chronic inflammatory diseases. The evidence reviewed shows how SPMs can: (1) control inflammation by resolution rather than inhibition, (2) reverse microbial dysbiosis as a consequence of inflammation control, and (3) promote tissue regeneration through diverse biological pathways. Whether the primary dysregulation in periodontitis lies solely in resolution failure or involves additional-possibly still unidentified-mechanisms, remains unclear. All individuals harbor periodontal pathobionts, yet only a subset develop severe disease. Why do some individuals with significant biofilm accumulation maintain attachment levels, while others with reasonable plaque control become edentulous? This remains one of the most significant unanswered questions in periodontology. What is evident, however, is the need for a paradigm shift. While bacteria initiate the inflammatory process in all individuals, it is the host response that ultimately determines the progression to periodontitis.},
}

@article {pmid40657968,
year = {2025},
author = {Morandi, SC and Uldry, AC and Eldridge, N and Kreuzer, M and Herzog, EL and Zinkernagel, M and Zysset-Burri, DC},
title = {Toward the Characterization of the Human Core Ocular Surface Microbiome.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {9},
pages = {40},
doi = {10.1167/iovs.66.9.40},
pmid = {40657968},
issn = {1552-5783},
mesh = {Humans ; *Microbiota/genetics ; Middle Aged ; Adult ; *Tears/microbiology/metabolism ; *Conjunctiva/microbiology ; Female ; Male ; Tandem Mass Spectrometry ; *Eyelids/microbiology ; *Bacteria/genetics/isolation & purification ; Chromatography, Liquid ; Eye Proteins/metabolism ; },
abstract = {PURPOSE: The field of ocular surface microbiome (OSM) research suggests its involvement in ocular surface (OS) health and disease. However, existing OSM data are heterogeneous. This study aims to provide a whole-metagenome shotgun sequencing-based description of the healthy core ocular surface microbiome (COSM), encompassing all taxonomic kingdoms at species-level resolution.

METHODS: Swabs from the conjunctiva and lower lid margin, and tear fluid of 27 individuals without OS disease aged 40 to 60 years were collected at 3 time points. The OSM was sequenced and taxonomically and functionally profiled using Kraken2 and HUMAnN3, respectively. To validate sequencing results, human and microbial proteins of the tear fluid, termed the tear proteome (TP), were characterized by nano liquid chromatography-tandem mass spectrometry (nLC-MS/MS) and profiled by gene ontology. The COSM was defined as the microbiome present in most of the study population over time. Therefore, species present in > 50% of all samples across the three time points were considered to form the COSM.

RESULTS: At species level, Cutibacterium acnes, Malassezia restricta, and Staphylococcus epidermidis formed the COSM, with Corynebacterium segmentosum additionally being part of the core lid microbiome (LM). No significant differences in the OSM and human TP were observed between the left and right eyes on individual levels. However, the variance between subjects mostly exceeded that between eyes within subjects, suggesting an individual-specific COSM and TP.

CONCLUSIONS: The description of the COSM provides the basis for future OSM research and potential targets for preventive and therapeutic interventions of the OS and associated diseases.},
}

Humans
*Microbiota/genetics
Middle Aged
Adult
*Tears/microbiology/metabolism
*Conjunctiva/microbiology
Female
Male
Tandem Mass Spectrometry
*Eyelids/microbiology
*Bacteria/genetics/isolation & purification
Chromatography, Liquid
Eye Proteins/metabolism

@article {pmid40657928,
year = {2025},
author = {Knotek, AAU and Kristich, CJ},
title = {Phosphorylation of the cell wall hydrolase MltG in response to cell wall stress modulates resistance toward cephalosporins in Enterococcus faecalis.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0009925},
doi = {10.1128/jb.00099-25},
pmid = {40657928},
issn = {1098-5530},
abstract = {Enterococcus faecalis is an opportunistic pathogen that colonizes the human gut microbiome. E. faecalis commonly establishes infection subsequent to antibiotic therapy in patients due to intrinsic resistance exhibited by E. faecalis toward cephalosporins and acquired resistance to many clinically used antibiotics. Intrinsic resistance toward cephalosporins in E. faecalis depends on the kinase activity of IreK, a transmembrane serine/threonine PASTA kinase that mediates responses to cell wall stress, including stress caused by cephalosporins, by phosphorylating downstream effector proteins. Our previous phosphoproteomics analysis identified MltG, a transmembrane protein with an extracellular catalytic domain that cleaves nascent peptidoglycan strands, as a putative substrate for phosphorylation by IreK in E. faecalis, suggesting the hypothesis that IreK-mediated phosphorylation of MltG might regulate cell wall homeostasis and possibly intrinsic cephalosporin resistance. Here we report that MltG is a bona fide direct substrate of IreK in E. faecalis. We found that MltG phosphorylation in vivo is enhanced in response to cell wall stress in an IreK-dependent manner, requiring a specific residue in the MltG cytoplasmic domain for phosphorylation by IreK both in vivo and in vitro. Finally, phosphoablative and phosphomimetic substitutions of MltG reciprocally influence resistance of E. faecalis to ceftriaxone, pointing to functional consequences of MltG phosphorylation. Collectively, our results reveal a novel pathway by which IreK senses antibiotic-mediated cell wall stress and responds by phosphorylating the cytoplasmic segment of MltG to enhance antibiotic resistance.IMPORTANCEInfections caused by Enterococcus faecalis are increasingly prevalent and difficult to treat due to the multi-drug resistance exhibited toward common antibiotics. A greater understanding of the mechanisms underlying antibiotic resistance can enable the development of new drugs or strategies to overcome antibiotic-resistant infections. E. faecalis exhibits intrinsic resistance toward cephalosporins. This intrinsic resistance requires activity of the PASTA kinase IreK; however, few substrates for phosphorylation by IreK have been rigorously identified. Here, we report that MltG is directly phosphorylated by IreK in response to cell wall stress. This phosphorylation event acts to promote cephalosporin resistance as part of the IreK signaling network. Our results thereby validate a new substrate and expand knowledge of the IreK signaling pathway contributing to cephalosporin resistance.},
}

@article {pmid40657927,
year = {2025},
author = {Robinson, JM and Crino, OL and Camargo, A and Breed, MF},
title = {Does a microbial-endocrine interplay shape love-associated emotions in humans? A hypothesis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0041525},
doi = {10.1128/msystems.00415-25},
pmid = {40657927},
issn = {2379-5077},
abstract = {Emerging evidence suggests that the human gut microbiome plays a regulatory role in the endocrine system, influencing hormone activity and potentially shaping the emotional and physiological dimensions of behaviors such as aggression and emotional states, including love. Here, we review the hypothesis that microbial-endocrine interactions shape love-associated emotions by modulating hormone levels and activity. While the division of love into discrete components such as lust, attraction, and attachment is somewhat artificial and may not fully capture the complexity of human experience, the associated emotions nevertheless correspond to well-characterized neuroendocrine processes. Psycho-endocrinological theory proposes that the complex and nonlinear interplay between testosterone, estradiol, and other hormones drives emotions associated with lust; serotonin and dopamine play a role in emotions linked to attraction; and oxytocin and vasopressin influence the modulation of attachment and social bonds. Microbial communities may influence emotions and relationship dynamics through effects on the hormonal pathways linked to love-associated emotions. While non-human animal studies suggest microbiota can impact social bonding, sexual preferences, and stress-related behaviors, direct evidence in humans remains limited. Investigating the evolutionary underpinnings of microbial-endocrine interactions could provide insights into how microbes influence emotions beyond love, including hate and aggression-with important societal implications. Indeed, understanding these mechanisms could have profound implications for human relationships, mental health, and even therapeutic interventions targeting the microbiota-gut-brain axis. Future research is needed to unravel the extent to which microbiomes contribute to the neurobiology of love (and other emotions) and whether manipulating microbial communities could modulate emotional and social behaviors.IMPORTANCELove is often considered an abstract emotion, but emerging science suggests that it may be shaped by the microscopic inhabitants of our bodies: microbes. This paper explores the intriguing hypothesis that microbes can influence the hormonal and neural systems linked to love-associated emotions-via the microbiota-gut-brain axis. Drawing on animal studies and early human microbiome and endocrine research, we highlight how microbes modulate neurohormones like oxytocin, dopamine, and testosterone, which play key roles in social bonding. By regulating these systems, microbes may also shape emotional and behavioral responses. This research opens new avenues for understanding not just the (micro)biology of love but also the potential for microbiome-targeted therapies to support relational well-being. By linking microbiome and emotion science, the article raises the important question of whether love is a phenomenon influenced by our resident symbionts, adding an intriguing and potentially impactful dimension to our understanding of human connection and behavior.},
}

@article {pmid40657876,
year = {2025},
author = {Strachan, CR and Bowers, CM and Kim, BC and Movsesijan, T and Neubauer, V and Mueller, AJ and Yu, XA and Pereira, FC and Nagl, V and Faas, J and Wagner, M and Zebeli, Q and Weimer, PJ and Candry, P and Polz, MF and Lawson, CE and Selberherr, E},
title = {Distinct lactate utilization strategies drive niche differentiation between two co-existing Megasphaera species in the rumen microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf147},
pmid = {40657876},
issn = {1751-7370},
abstract = {Lactate utilization mitigates rumen acidosis and is associated with decreased methane production in the rumen. While several lactate utilization pathways exist across different microbial species in the rumen, how they are metabolically differentiated remains unclear. Here, we show that the key lactate-utilizing species Megasphaera hexanoica and Megasphaera elsdenii display distinct growth strategies based on their fermentative end products. This allows them to co-exist and play distinct metabolic roles, which appear particularly relevant in the early stages of rumen development, as both species are highly enriched in the calf. Specifically, M. hexanoica is more strongly associated with rumen microbiome states that involve increased lactate utilization and preferentially runs reverse beta-oxidation (termed chain elongation) to produce butyrate and medium-chain fatty acids from lactate. As M. elsdenii instead utilizes lactate via the acrylate pathway to produce propionate, we leverage Enzyme Cost Minimization to predict how this pathway relates to a distinct growth strategy. We find that M. elsdenii maximizes growth rate when lactate transiently accumulates, which contrasts M. hexanoica's invariably high-yield strategy. This trade-off, which is supported by the analysis of growth kinetics, metabolic flux, and bioreactors simulating the rumen microbiome, ultimately contributes to co-existence on lactate and may have driven niche differentiation. Lastly, we demonstrate how lactate utilization in the Megasphaera is threatened by toxins widespread in feed, which points to dietary interventions to support calf health.},
}

@article {pmid40657740,
year = {2025},
author = {Miyako, E},
title = {Reply to "Exploring Bacteria-Based Cancer Immunotherapy"-Comment on "Discovery of Intratumoral Oncolytic Bacteria Toward Targeted Anticancer Theranostics".},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e11325},
doi = {10.1002/advs.202511325},
pmid = {40657740},
issn = {2198-3844},
support = {23H00551//Japan Society for the Promotion of Science/ ; 25K21827//Japan Society for the Promotion of Science/ ; JPMJSF2318//Japan Science and Technology Agency/ ; },
abstract = {This manuscript is a formal response to the commentary by A/Prof. Dr. Chen-xi Li and colleagues regarding our previous publication in Advanced Science. We clarify the rationale, methods, and outcomes of our original study and highlight ongoing work in the field of bacterial cancer immunotherapy.},
}

@article {pmid40657642,
year = {2025},
author = {Wu, W and Meng, T and Han, L and Jin, F and Han, P and Zhou, Y},
title = {Bridging traditional Chinese medicine and Alzheimer's disease: the pivotal role of gut microbiota in multitarget therapeutic mechanisms.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1630205},
pmid = {40657642},
issn = {1663-9812},
abstract = {Microbiota-gut-brain axis communication represents another crucial pathway in the pathogenesis of Alzheimer's disease (AD), whereby gut microbiota significantly impacts AD pathology by modulating immune, metabolic, digestive, and neurological functions. Although research on treating AD through gut microbiota interventions is advancing, substantial breakthroughs remain limited. Given AD's complex pathological mechanisms, Traditional Chinese Medicine (TCM) presents a clear advantage with its multi-target effects. During the processes of TCM intake, absorption, and therapeutic action, the gut microbiota serves both as a mediator and as a therapeutic target. However, the mechanisms by which TCM interacts with gut microbiota to exert beneficial effects on AD remain largely unclarified. Here, we review the mechanisms through which TCM may intervene in AD from the perspective of gut microbiota, examining the potential mechanisms and clinical application prospects of Chinese herbal medicine in regulating the gut microbiome. This provides a novel theoretical foundation and methodological support for further research into herbal therapies for AD.},
}

@article {pmid40657495,
year = {2025},
author = {Bruins-van Sonsbeek, LGR and Verschuren, MCM and Kaal, S and Lindenburg, PW and Rodenburg, KCW and Clauss, M and Speksnijder, AGCL and Rutten, VPMG and Bonnet, BFJ and Wittink, F},
title = {Correction: Rhinoceromics: a multi-amplicon study with clinical markers to transferrin saturation levels in ex-situ black rhinoceros (Diceros bicornis michaeli).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1644681},
doi = {10.3389/fmicb.2025.1644681},
pmid = {40657495},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1515939.].},
}

@article {pmid40656962,
year = {2025},
author = {Gunawan, SP and Huang, SY and Hsu, JW and Lin, CY and Nguyen, NN and Tung, TH and Liang, SL and Lee, GA and Su, CT and Chen, YC},
title = {Chronic sleep deprivation is associated with delayed puberty onset in rats, activation of proinflammatory cytokines and gut dysbiosis.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19668},
pmid = {40656962},
issn = {2167-8359},
mesh = {Animals ; *Sleep Deprivation/complications/physiopathology ; *Gastrointestinal Microbiome ; Male ; Rats ; *Cytokines/metabolism/blood ; *Dysbiosis ; Female ; Rats, Sprague-Dawley ; *Sexual Maturation ; *Puberty, Delayed/etiology ; Inflammation ; },
abstract = {Chronic sleep deprivation (CSD) in adolescents has become a trend with adverse health outcomes. Previous studies have demonstrated that sleep deprivation causes inflammation, alters puberty onset, and changes the gut microbiome composition; however, the relationship between these is still unknown. Therefore, we hypothesized that CSD delays the onset of puberty via elevating proinflammatory cytokines and alter ation of gut microbiome composition. Using the modified multiple platform method, we conducted a 4-week CSD experiment in juvenile rats and assessed pubertal markers, antioxidant activity, cytokine levels, and gut microbiome profiles. CSD significantly reduces body weight, delays onset of puberty, and elevated antioxidant enzyme activities in both sexes. In the sleep-deprivation female (SDF) rats, plasma levels of lipopolysaccharide-binding protein (LBP), interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) were significantly elevated; mRNA levels of TNF-α and IL-1β were also significantly elevated in the colon and reproductive organs, respectively. In the sleep-deprivation male (SDM) rats, only plasma levels of IL-6 were elevated considerably; in addition, mRNA levels of IL-1β and TNF-α were also significantly elevated in the colon and reproductive organs, respectively. Gut microbiome analysis revealed that the predominant bacteria at the genus level were Muribaculaceae, Prevotellaceae UCG-001, and Ruminococcaceae UCG-005 in the SDF rats; Prevotellaceae NK3B31, Ruminococcaceae UCG-010, Eubacterium coprostanoligenes, and Shuttleworthia in the SDM rats. CSD rats with abundant genera were positively correlated with antioxidant enzyme activities and mRNA levels of proinflammatory cytokines. Overall, CSD is associated with delayed puberty onset, possibly via an increase in the expression levels of proinflammatory cytokines and altering the gut microbiome composition, indicating proinflammatory cytokines and gut microbiome play an important role in pubertal timing change. These findings may guide the future studies to intervene sleep deprivation-related delays in the onset of puberty.},
}

Animals
*Sleep Deprivation/complications/physiopathology
*Gastrointestinal Microbiome
Male
Rats
*Cytokines/metabolism/blood
*Dysbiosis
Female
Rats, Sprague-Dawley
*Sexual Maturation
*Puberty, Delayed/etiology
Inflammation

@article {pmid40656088,
year = {2024},
author = {Schneider, E and Leigh, SJ and Lynch, CMK and Hilbert, A and Clarke, G and Higgs, S and Cryan, JF},
title = {Microbiota-gut-brain axis in binge-eating disorder: Towards microbiome-based therapies.},
journal = {Neuroscience applied..},
volume = {3},
number = {},
pages = {104088},
pmid = {40656088},
issn = {2772-4085},
abstract = {Binge-eating disorder (BED) is the most common eating disorder, but the mechanisms that underlie this disorder are still largely unknown. There is tentative evidence to suggest that the gut microbiota, which communicates to the brain via the gut-brain axis, plays a role in the pathogenesis of BED. However, more mechanistic research is urgently required to gain greater clarity and inform the development of superior management strategies. In this review, we sought to develop a new conceptual model that incorporates the gut microbiota to provide valuable guidance for future research in this area. In BED, the large quantities of hyper-palatable, energy-dense foods rapidly consumed reduces microbial diversity and their associated metabolites alongside promotions in microbial volatility and inflammation. These dietary-induced effects on the microbiota alter pathways implicated in BED including satiety, reward, impulsivity, and mood. The biological mechanisms underpinning the psychological effects include actions of microbial components and metabolites, alongside effects on the hypothalamic-pituitary-adrenal axis and the dopaminergic and serotonergic systems. Importantly, individual baseline characteristics such as genetics and environmental stressors can moderate the relationship between one's diet, the gut microbiota, and BED. A growing body of evidence suggests that microbiota-targeted interventions, so called psychobiotics, may affect these pathways to modulate brain and behaviour. While further research is necessary to test this hypothesis, the gut microbiota represents a novel avenue for future BED therapeutics.},
}

@article {pmid40655582,
year = {2025},
author = {Patel, SP and Bhoraniya, SJ and Kalola, SD and Rukadikar, A and Ravi, R and Farooqui, S and Rukadikar, C},
title = {Gut Microbiota and its Impact on Chronic Diseases: A Comprehensive Review.},
journal = {Journal of pharmacy & bioallied sciences},
volume = {17},
number = {Suppl 2},
pages = {S1080-S1082},
pmid = {40655582},
issn = {0976-4879},
abstract = {The intricate community of bacteria that live in the gastrointestinal system, known as the gut microbiota, is essential to preserving human health and equilibrium. The pathophysiology of several chronic illnesses, including as neurological, cardiovascular, immunological, and metabolic disorders, has been progressively associated with its dysbiosis. This thorough analysis looks at the complex relationships that exist between gut microbiota and host physiology, examining processes including metabolic signaling, immunological regulation, and gut-brain axis communication. We discuss current developments in the study of the microbiome, with an emphasis on the role that the variety and makeup of gut microbes play in the development of chronic diseases. In order to restore microbial balance and lessen the severity of the condition, the study also covers new treatment approaches such as dietary changes, probiotics, prebiotics, and fecal microbiota transplantation. The development of novel, microbiome-based diagnostic and therapeutic strategies is made possible by an understanding of the complex link between the gut microbiota and chronic illnesses, highlighting the vital role that personalized medicine plays in enhancing health outcomes.},
}

@article {pmid40655378,
year = {2025},
author = {Sreehari, OK and Jose, RM and Menon, DB and Saranya, MK and Anilkumar, TR},
title = {Comparative Analysis of Faecal Bacteria in Captive Asian Elephants of Various Age Groups and Musth.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {1225-1233},
pmid = {40655378},
issn = {0046-8991},
abstract = {UNLABELLED: Study of gut microbiome is an emerging area in modern research with over one trillion population is known to inhabit the gut of organisms. The gut microbiome constitutes bacteria, viruses, protozoa and fungi and their collective genetic material present in the gastrointestinal tract. It is an essential part of a species' ecology and influenced by the diet and phylogeny of the host. Most studies on the significance of gut microbiota and its association with physiology were done in humans than animals, and even fewer in elephants. Here in this study, we ventured to study the diversity of faecal bacteria of elephants of various age groups and musth. Bacteriological analysis of faecal samples from elephants of various age groups and musth were done and a total viable count was determined. Bacterial colonies obtained from elephant faecal samples of various age groups and musth were identified employing 16S rDNA sequencing. Here we evolved a PCR based strategy to amplify partial gene which encodes 16S rRNA was sequenced and the sequence obtained was analyzed by NCBI BLAST to identify these bacterial strains. Stenotrophomonas maltophilia, Lactococcus lactis and Staphylococcus arlettae were the major species of bacteria identified from the samples of captive elephants, of which, Stenotrophomonas maltophilia is an opportunistic pathogen that dominates in all the age groups. Lactococcus lactis is the major bacteria in the fecal samples of four years old elephant (Juvenile) and found to constitute nearly 68%. Fecal samples collected from 25 years old constitute Stenotrophomonas maltophilia as the major bacteria (73%) followed by Lactococcus lactis while 45 years old showed the higher occurrence of Staphylococcus arlettae followed by Lactococcus lactis. Elephant of the very old age group (84 years) showed high diversity in the fecal bacteria with Stenotrophomonas maltophilia dominating in this group (72%). Elephant in musth, a condition characterized by the high level of testosterone, temporal secretion and high gastric acidity was shown the dominance of acidophilic Stenotrophomonas maltophilia in the gut while alkalophilic Lactococcus lactis which was prevalent in other groups was not detected in musth condition.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01391-7.},
}

@article {pmid40655373,
year = {2025},
author = {Sabarish, S and Dhanasekaran, D},
title = {Bacterial Community Profile of Bovine Mastitis Infected Dairy Cow Milk by 16S rRNA Amplicon Sequencing.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {1142-1151},
pmid = {40655373},
issn = {0046-8991},
abstract = {UNLABELLED: The prevalence of Bovine mastitis, an important disease of cow, causing huge economic loss in dairy industries, was tested in cows and other types of breeds reared at Salem and Trichirappalli district. It was interesting to note that the country breed cow was free from disease. The presence of mastitis microbes was identified by culture dependent method. Staphylococcus aureus, Staphylococcus agalactiae, Klebsiella sp. and Pseudomonas sp. were the most common bacteria found in mastitis-infected milk. Opportunistic anaerobic bacteria such as Fusobacterium necrophorum and Porphyromonas levii were found in abundance in mastitis milk samples, but not in non-mastitis milk samples. Milk samples from a mastitis-infected Jersey cow and healthy cow as a control cow were utilized to construct V3-V4 sections of 16S rRNA gene profiles, which were compared to bacterial diversity and abundance. A total of 16,000 sequence numbers were acquired from the 16S rRNA dataset, with a cumulative length of base pairs (bp) of 250. About 321 OTUs were created from these readings. Among these, 190 OTUs are similar in milk from both uninfected healthy and infected Jersey cow. A total of 70 OTUs and 61 OTUs were unique to milk obtained from healthy milk and mastitis infected milk respectively. The hierarchically clustered heat map depicted the overall perspective of the found relationships of bacterial populations among milk samples. The relative abundance of the Ochrobactrum, Pseudomonas and Stenotrophomonas (Kamilari) were associated in the milk. The Shannon index of a healthy cow milk sample was greater (4.136), suggesting the quantity and evenness of the microbial species present. The Simpson index also revealed that during a cow infection, the species richness and evenness declined. Metagenomic analysis can help us better understanding the pathophysiology of bovine mastitis, and it has the potential to be employed as a diagnostic tool as well.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01310-w.},
}

@article {pmid40655369,
year = {2025},
author = {Hoda, S and Aggarwal, KK},
title = {Impact of Organophosphates on Diversity and Functional Characteristics of Phyllosphere Bacterial Communities of Solanum melongena.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {1161-1172},
pmid = {40655369},
issn = {0046-8991},
abstract = {UNLABELLED: The phyllosphere harbours a distinctive microbial community that is influenced by plant species, geological locations, and biotic and abiotic environmental factors. Organophosphates represent a significant category of pesticides that are applied to plant surfaces for pest management. Despite substantial research into phyllosphere microorganisms, little is known about the influence of pesticides on the phyllosphere bacterial ecosystem. In the present study, the effect of chlorpyrifos, monocrotophos, and malathion was studied on the phyllosphere bacterial community of Solanum melongena. The plant-inhabitant bacterial population was explored using culturable and high-throughput 16S rRNA gene amplicon sequencing, with and without pesticide application. A total of 165 genera belonging to 14 phyla were observed in the control and 108 genera belonging to 11 phyla in the treated sample. In total, 28 morphologically distinct bacteria were isolated from the abaxial and adaxial surfaces of leaf, and 4 bacteria were found tolerant to pesticides. An increased abundance of Psychrobacter, Janthinobacterium, Sphingomonas, Flavobacterium, and Pedobacter were observed from the pesticide-treated phyllosphere. Overall pesticide impacted the evenness and diversity of the bacterial communities colonizing the S. melongena phyllosphere.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01322-6.},
}

@article {pmid40655366,
year = {2025},
author = {Yadav, S and Kapley, A},
title = {Profiling of Pharmaceutical Sludge Microbiome, Resistome and Secondary Metabolites Using Metagenomics.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {1181-1200},
pmid = {40655366},
issn = {0046-8991},
abstract = {UNLABELLED: Antibiotic manufacturing sites act as the hotspot for the dissemination of antibiotic resistance. The present study explores the resistome and secondary metabolites profile associated with the sludge of two pharmaceutical industries located in Delhi and Mysore, India. It confirmed that the pharma sludge contains complex microbiome and resistome. The presence of antibiotic-resistant genes (ARGs), class I integrons, and secondary metabolite genes (NRPs and PKs) was confirmed using PCR. Metagenomic tools like ResFinder 3.2, DeepARG, BusyBee, MG-RAST, and CoMET universe were used to analyze pharmaceutical sludge metagenome. Proteobacteria was found abundant in both metagenomes, followed by firmicutes & bacteriodetes. KEGG analysis predicted the expression of vancomycin, Pandrug, antifolate resistance pathway in both metagenomes. Resfinder predicted the presence of aminoglycoside, macrolide, and sulphonamide resistance genes in both metagenomes. DeepARG analysis classified ARGs in 28 (Arbro) & 27 (Mysore) ARG category and 431 & 368 ARG class. Further, CoMET universe indicated the presence of biosynthetic gene clusters like type II polyketide biosynthesis, Nonribosomal polypeptide biosynthesis, vancomycin & tetracycline, and macrolide biosynthesis. The present study provides primary insight about the diversity of secondary metabolites clusters present in pharmaceutical sludge. Microbes residing in such environment grows under higher selection pressure and produce various secondary metabolites. These metabolites could be exploited for the discovery of novel metabolites with antimicrobial potential and combating AMR. In future, the author aims to clone metagenome in expression vector (BAC/YAC vectors) for the discovery of novel secondary metabolites.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01349-9.},
}

@article {pmid40655336,
year = {2025},
author = {Yata, VK},
title = {From Bioreactors to Organoids: Tools for Culturing and Understanding Microbiota.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {623-644},
pmid = {40655336},
issn = {0046-8991},
abstract = {Emerging evidence on the role of gut microbiota on human health necessitated the investigations on gut microbial composition and functions. The diet, drug and disease are the major factors that influence the gut microbial composition and subsequent changes in gut physiology. The consequences of external factors on gut microbiota leads to immunological and neurological disorders. The in vivo studies and animal models are associated with difficulties such as surgical procedures, differences in animal and human tissue responses and ethical issues. Microbiota culture outside the in vivo systems provides mechanistic insights on the effect of external factors on gut microbiota function. In order to provide more information on gut microbiota, researchers have developed intestinal gut models that allow the culture of microbiota under controlled conditions. The multistage, dynamic in vitro fermenters have been developed to simulate the stomach, intestine and colon conditions to culture microbiota. The co-culture of host and microbiome is difficult in in vitro models due to differences in the culture media and oxygen requirements for both the cultures. Microfluidics based gut on chip models demonstrated co-culture of host and microbiota in separate channels connected by semipermeable membranes. Host-microbiota interactions play an important role in deciphering the mechanisms of microbiota related human diseases. The ex-vivo systems show more resemblance to the host signaling as these systems use the individual's explants or host tissues. This review discusses the design considerations, pros and cons of the existing in vitro, microfluidic and ex-vivo intestinal microbiota culture models. The collective information provided in this review would be helpful to design novel in vitro microbiota culture models or methods.},
}

@article {pmid40654961,
year = {2025},
author = {Medeiros, MJ and Schoville, S and Price, D and Yew, JY},
title = {Abiotic factors are the primary determinants of endemic Hawaiian Drosophila microbiome assembly.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.06.652154},
pmid = {40654961},
issn = {2692-8205},
abstract = {The Hawaiian Drosophila radiation exemplifies rapid adaptation and species diversification. Many factors have been attributed to these phenomena, including allopatry, sexual selection, and ecological specialization. In recent years, the microbiome has come to the forefront as an important driver of adaptation that is capable of facilitating host survivorship, enhancing resilience to local environmental challenges, and enabling the use of different dietary resources. To determine how microbial communities assemble in natural populations and potentially contribute to the rapid adaptation of Hawaiian drosophilids, we conducted a survey of bacterial and fungal communities from over 500 wild flies collected from across six islands of the Hawaiian archipelago. These samples represent a breadth of host plant specializations, habitats, lifestyles, and endemicity. Our findings reveal that microbiome assembly is largely driven by abiotic factors including elevation, temperature, rainfall, and evapotranspiration, but is not strongly constrained by phylogenetic relatedness. Identical species inhabiting two separate locations exhibited different microbiomes. By contrast, distantly related species inhabiting the same site had more similar microbiomes. The microbiomes of native species also differ from recently introduced, non-native Drosophila in terms of diversity, composition, and function. Given the myriad roles of the microbiome in nutrition, reproduction, and mate choice, these results support a role for the microbiome in the remarkable ecological divergence of Hawaiian Drosophila .},
}

@article {pmid40654884,
year = {2025},
author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS},
title = {Discovering Broader Host Ranges and an IS-bound Prophage Class Through Long-Read Metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.09.652943},
pmid = {40654884},
issn = {2692-8205},
abstract = {Gut bacteriophages profoundly impact microbial ecology and human health, yet they are greatly understudied. Using deep, long-read bulk metagenomic sequencing, a technique that overcomes fundamental limitations of short-read approaches, we tracked prophage integration dynamics in 12 longitudinal stool samples from six healthy individuals, spanning a two-year timescale. While most prophages remain stably integrated into their host over two years, we discover that ∼5% of phages are dynamically gained or lost from persistent bacterial hosts. Within the same sample, we find evidence of population heterogeneity in which identical bacterial hosts with and without a given integrated prophage coexist simultaneously. Furthermore, we demonstrate that phage induction, when detected, occurs predominantly at low levels (1-3x coverage compared to the host region). Interestingly, we identify multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phage are specific to a host of a given species or strain. Lastly, we describe a new class of phages, which we name "IScream phages". These phages co-opt bacterial IS30 transposases to mediate their integration, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity in this ecosystem.},
}