@article {pmid40476565,
year = {2025},
author = {Fu, J and Chen, J and Ni, J and Liu, X and Yao, Q and Shou, Q and Fu, H},
title = {Dietary supplementation with beetroot modulates gut microbiota-derived diacylglycerol biosynthesis to enhance anti-tumor immunity in MMTV-PyMT (FVB) mice.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo01116g},
pmid = {40476565},
issn = {2042-650X},
abstract = {Recent studies have established a strong connection between gut microbiota and the tumor immune microenvironment. Beetroot (BRT) has emerged as a promising functional food for cancer prevention and treatment, although its specific effects on breast cancer remain unclear. This study investigates the impact of BRT on polyomavirus middle T antigen (PyMT)-induced breast cancer by examining the gut microbiome, metabolites, and immune responses. Dietary supplementation of 80 g BRT powder per 1000 g of standard diet (8% w/w, 80 g per kg) significantly inhibited tumor growth and metastasis in mouse mammary tumor virus (MMTV)-PyMT (FVB) mice, while simultaneously enhancing anti-tumor immunity. 16S rRNA sequencing revealed that BRT supplementation altered the gut microbiota, notably increasing the abundance of Lachnospiraceae and Ruminococcaceae. An antibiotic (ABX) experiment confirmed that BRT restores gut microbiota balance, thereby enhancing anti-tumor immunity. Metabolomics and ELISA assays demonstrated that BRT regulates diacylglycerol (DAG) biosynthesis through microbiota modulation. Notably, diacylglycerol kinase ζ (DGKζ) inhibitors enhance CD8+ T cell responses by increasing DAG levels, thereby activating Mitogen-Activated Protein Kinase (MAPK) and Protein Kinase C (PKC) signaling pathways. Collectively, our findings suggest that microbiota-derived DAG plays a key role in BRT-mediated enhancement of anti-tumor immunity.},
}

@article {pmid40476383,
year = {2025},
author = {Kim, N and Kim, J and Choi, J and Kim, R},
title = {A collagen hydrogel-based intestinal model enabling physiological epithelial-immune cell interactions in host-microbe studies.},
journal = {Biomaterials science},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5bm00612k},
pmid = {40476383},
issn = {2047-4849},
abstract = {The human intestine orchestrates complex immune responses to external stimuli, including trillions of gut microbes. Understanding host-microbiota interactions remains challenging due to the complex cellular composition of intestinal tissues. In this study, we present InTRIC (Intestinal model with Tissue-Resident Immune Components), a three-dimensional intestinal model incorporating tissue-resident immune cells within a biomimetic extracellular matrix. We developed a hydrogel system by combining UV-crosslinked methacrylated collagen with a native collagen blend that prevents matrix shrinkage while maintaining physiologically relevant mechanical properties, a fibrillar microstructure and minimal toxicity for cell embedding. Prior to establishing InTRIC, we validated THP-1 viability in the collagen hydrogel (>14 days), verified their differentiation into distinct macrophage phenotypes, and confirmed appropriate gene expression in Caco-2 cells on the collagen substrates. The integrated model comprises THP-1 macrophages embedded within the collagen matrix and Caco-2 cells forming a functional epithelium with intact junctions and physiologically relevant TEER values. The InTRIC platform enables both the assessment of cytokine profiles and the visualization of transepithelial macrophage infiltration in response to commensal (Lacticaseibacillus rhamnosus) and pathogenic (Pseudomonas aeruginosa) bacteria. Notably, P. aeruginosa exposure induced a four-fold increase in macrophage infiltration and elevated IL-8 secretion. Compared to conventional cocultures without collagen, InTRIC exhibited attenuated inflammatory cytokine secretion, suggesting microenvironmental modulation of epithelial-immune communication. Additionally, M2-polarized macrophages showed reduced basal IL-8 secretion but increased responsiveness to bacterial stimulation. This proof-of-concept model demonstrates the importance of incorporating both immune cells and appropriate extracellular matrices in recapitulating intestinal conditions and offers a physiologically relevant test platform for applications in drug discovery, toxicology, and microbiome research.},
}

@article {pmid40476348,
year = {2025},
author = {Ducatelle, R and Goossens, E and Eeckhaut, V and Van Immerseel, F},
title = {The Gordon Memorial Lecture: Steering the gut microbiome for improved health and welfare in broilers.},
journal = {British poultry science},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/00071668.2025.2488014},
pmid = {40476348},
issn = {1466-1799},
abstract = {1. In fast growing broilers, intestinal health is continuously under pressure due to extremely high feed intake and environmental/management conditions that cause (oxidative) stress to the intestinal epithelium.2. The following review focuses on the contributions of the Livestock Gut Health Team at Ghent University into understanding the mechanisms governing the interactions between the intestinal microbiota and the host intestinal mucosa. It covers the development of tools to support intestinal health of broilers through nutritional manipulation of the microbiota.3. In the duodenum and jejunum, microbiota are suppressed by the secretion of enzymes and antibacterial peptides in order to avoid competition for the nutrients. These defence mechanisms can be re-enforced and/or the epithelial cells can be protected from damage by different feed additives.4. Metabolism in the caecal microbial network is fuelled by the fibre fraction in feed. Whenever this network is incomplete or the feed is lacking fibre, this may lead to a distortion of the microbiota, followed by insufficient production of beneficial microbial metabolites, such as butyrate. This can contribute to inflammation and leakage of the gut barrier, with, in severe cases, wet litter, foot pad lesions and poor performance as common consequences. Reenforcing the caecal microbial network can be achieved using prebiotics, probiotics and postbiotics, which will improve the health and well-being of the birds.5. Steering towards optimal microbial fermentation will help to protect the birds from Clostridium perfringens-associated necrotic enteritis and Salmonella spp. colonisation since both interact with the intestinal microbiota.},
}

@article {pmid40476157,
year = {2025},
author = {Rashid, M and Pereira, HS and Alissa, A and Keraidi, S and Wipf, N and Sowa, AM and McDonnell, JM and Darwish, S and Butler, JS},
title = {Microbiome dysbiosis in spinal pathology: Mechanisms, evidence, and research limitations.},
journal = {Brain & spine},
volume = {5},
number = {},
pages = {104272},
pmid = {40476157},
issn = {2772-5294},
abstract = {INTRODUCTION: The microbiome's relevance has become increasingly discussed amid the rising prevalence of chronic illnesses. Microbiome research to date focuses predominantly on its relationship with the GI tract while largely ignoring any impact on the rest of the body. This narrative review aims to lay a foundation of knowledge to fill this gap in the literature and discuss other microbiomes within the human body and their relation to spinal health.

RESEARCH QUESTION: What is the relationship between the human microbiome and spinal pathologies?

MATERIALS AND METHODS: A narrative review of all available literature (written or translated to English) was performed using PubMed, MEDLINE, and Google Scholar using relevant search terms including: "microbiome", "spine", "spinal pathology", "ankylosing spondylitis", and "seronegative arthropathies".

RESULTS: This review found that with dysbiosis, specific bacterial such as Bacteroidaceae and Rikenellaceae proliferate, altering the cytokine microenvironment and subsequently increasing gut wall permeability. This immune overactivation and improper cell function results in an increased susceptibility to autoimmunity; specifically ankylosing spondylitis and seronegative arthropathies. This review also highlights the significant gaps in the available literature.

DISCUSSION AND CONCLUSION: This review aims to equip clinicians with an understanding of how the collection of microbiomes in the human body have specific implications for spinal health. By building on the current literature and integrating this knowledge into practice, more patient-specific practices in the treatment of spinal pathologies can be implemented, ultimately improving and optimizing patient care in a field in which the microbiome is not currently at the forefront of pathology.},
}

@article {pmid40475999,
year = {2025},
author = {Hwang, D and Chong, E and Li, Y and Li, Y and Roh, K},
title = {Deciphering the gut microbiome's metabolic code: pathways to bone health and novel therapeutic avenues.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1553655},
pmid = {40475999},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bone and Bones/metabolism ; Animals ; Probiotics/therapeutic use ; *Bone Remodeling/physiology ; *Osteoporosis/metabolism/microbiology/therapy ; Prebiotics ; Fecal Microbiota Transplantation ; Bone Diseases/metabolism/microbiology/therapy ; },
abstract = {The gut microbiome plays an important role in the protection against various systemic diseases. Its metabolic products profoundly influence a wide range of pathophysiological events, including the regulation of bone health. This review discusses the recently established connections between the gut microbiome and bone metabolism, focusing on the impact of microbiome-derived metabolites such as SCFAs, Bile Acids, and tryptophan to the control of bone remodeling and immunoreactions. Recent advances in metagenomics and microbiome profiling have unveiled new exciting therapeutic opportunities, ranging from the use of probiotics, prebiotics, engineered microbes, and to fecal microbiota transplantation. Understanding of the interplay among diet, microbiota, and bone health provides new avenues for tailored interventions aimed at reducing disease risk in osteoporosis and other related disorders. By drawing knowledge from microbiology, metabolism, and bone biology, this review highlights the potential of microbiome-targeted therapies to transform skeletal health and the management of bone diseases.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bone and Bones/metabolism
Animals
Probiotics/therapeutic use
*Bone Remodeling/physiology
*Osteoporosis/metabolism/microbiology/therapy
Prebiotics
Fecal Microbiota Transplantation
Bone Diseases/metabolism/microbiology/therapy

@article {pmid40475850,
year = {2025},
author = {Liu, Y and Li, R and Liu, J and Liang, X and Su, M and Wang, S and Mu, B},
title = {Exploring the role of the vaginal microbiome in HPV infection dynamics: A prospective cohort study.},
journal = {iScience},
volume = {28},
number = {5},
pages = {112476},
pmid = {40475850},
issn = {2589-0042},
abstract = {Persistent human papillomavirus (HPV) infection is a key risk factor for cervical cancer, often associated with changes in the vaginal microbiome (VMB). High-throughput 16S rRNA sequencing was used to study the VMB in a prospective cohort of 731 individuals. Participants were monitored through two follow-up screenings and then categorized into two groups: 22 female patients with persistent HPV infection (PHI), 31 female patients who cleared the infection (HC). After excluding those with HPV and other urogenital infections, 43 female patients were selected as controls, and their samples were analyzed using the same high-throughput sequencing method. Results indicate that high-risk HPV infections correlate with increased microbial diversity and reduced Lactobacillus levels. Even after HPV clearance, distinct microbial differences persist, suggesting that VMB could serve as a biomarker for monitoring infection and cervical health management, especially in populations at higher risk.},
}

@article {pmid40475770,
year = {2025},
author = {Varghese, A and Hess, SM and Chilakapati, S and Conejo-Garcia, JR and McGray, AJR and Zsiros, E},
title = {Tertiary lymphoid structures: exploring opportunities to improve immunotherapy in ovarian cancer.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1473969},
pmid = {40475770},
issn = {1664-3224},
mesh = {Humans ; *Tertiary Lymphoid Structures/immunology/pathology ; Female ; *Ovarian Neoplasms/immunology/therapy/pathology ; Tumor Microenvironment/immunology ; *Immunotherapy/methods ; Animals ; Immune Checkpoint Inhibitors/therapeutic use ; Lymphocytes, Tumor-Infiltrating/immunology ; },
abstract = {Tertiary lymphoid structures (TLS) are organized ectopic lymphoid clusters of immune cells that develop in non-lymphoid tissue to promote antigen presentation, drive cytotoxic immune responses, and enhance humoral immunity via B cell clonal expansion. Their presence within the tumor microenvironment (TME) correlates with increased patient survival and an improved response to immune checkpoint inhibitors (ICIs), positioning TLS as potential predictive and prognostic biomarkers. Despite the widespread use of ICIs across various cancers, their effectiveness remains limited in gynecological malignancies, including ovarian cancer (OC), a notably challenging disease characterized by poor responses to both single and combination ICI therapies. Interestingly, the infiltration of T cells into the OC TME is linked to enhanced progression-free survival (PFS) and overall survival (OS), yet an immunosuppressive TME frequently impedes therapeutic efficacy, suggesting cell activity within localized immune niches can impact antitumor immunity. This review explores the roles of TLS, their maturity, functionality, identification, and related gene signatures; specific immune cells and cytokines that play a role in TLS formation and antitumor response; and other modifiable elements, including gut microbiota, that may drive improving OC survival by leveraging a TLS-driven antitumor response to bolster immunotherapy outcomes.},
}

Humans
*Tertiary Lymphoid Structures/immunology/pathology
Female
*Ovarian Neoplasms/immunology/therapy/pathology
Tumor Microenvironment/immunology
*Immunotherapy/methods
Animals
Immune Checkpoint Inhibitors/therapeutic use
Lymphocytes, Tumor-Infiltrating/immunology

@article {pmid40475712,
year = {2025},
author = {Zhou, R and Wu, Q and Qian, H and Wang, L and Liu, G and Zhang, B and Wu, W and Zhang, S},
title = {Long-term Metformin Alters Gut Microbiota and Serum Metabolome in Coronary Artery Disease Patients After Percutaneous Coronary Intervention to Improve 5-year Prognoses: A Multi-omics Analysis.},
journal = {Reviews in cardiovascular medicine},
volume = {26},
number = {5},
pages = {26835},
pmid = {40475712},
issn = {2153-8174},
abstract = {BACKGROUND: About 20% of patients with coronary artery disease (CAD) experience adverse events within five years of undergoing percutaneous coronary intervention (PCI) for acute myocardial infarction. In these patients, the impact of metformin on long-term prognosis remains uncertain.

METHODS: This study enrolled 22 metformin (Met)-CAD patients with diabetes mellitus (DM) who had been administered metformin for at least six months before PCI, 14 non-Met CAD-DM patients with DM who had never taken metformin or had stopped taking metformin for a year before PCI, and 22 matched healthy controls. A 5-year follow-up was conducted to collect clinical prognosis data. Fecal 16S rRNA sequencing and serum untargeted metabolomics analyses were performed. BugBase was utilized to analyze the possible functional changes in the gut microbiome. Multi-omics analysis was conducted using Spearman's correlation to explore the interactions between metformin, gut microbiome, serum metabolites, and clinical prognosis.

RESULTS: Metformin significantly lowered the 5-year major adverse cardiac events (MACEs) in Met CAD-DM patients. We found a higher abundance of Bacteroides coprocola, Bacteroides massiliensis, Phascolarctobacterium succinatutens, and Eubacterium coprostanoligenes in the Met CAD-DM patients, as well as an increase in hydroxy-alpha-sanshool (HAS) and decenoylcarnitine and a decrease in tridec-10-enoic acid, Z-vad-fmk (benzyloxycarbonyl-Val-Ala-Asp (OMe)-fluoromethylketone), 3,9-dimethyluric acid in blood serum. Multi-omics analysis revealed that alterations in the gut microbiome and serum metabolites are significantly associated with the 5-year prognosis of CAD-DM.

CONCLUSIONS: Metformin significantly improved the 5-year prognosis of CAD patients following PCI. Metformin tended to have more positive effects on the commensal flora and metabolic profiles, which may explain its beneficial effects on cardiovascular health. This study revealed the potential associations between metformin and the gut microbiome, an associated alteration in serum metabolome, and the impact on the host immune system and metabolic pathways.},
}

@article {pmid40475637,
year = {2025},
author = {Nia, LH and Alqudah, S and Markley, RL and DeLucia, B and Bobba, V and Elmallah, J and Nemet, I and Sangwan, N and Claesen, J},
title = {The antimicrobial metabolite nisin Z reduces intestinal tumorigenesis and modulates the cecal microbiome in Apc [Min/+] mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.18.654755},
pmid = {40475637},
issn = {2692-8205},
abstract = {UNLABELLED: Nisin Z, an antimicrobial metabolite produced by Lactococcus lactis spp., has been safely used as a food preservative for many years. Nisin Z also showed promising activity against various cancer types in vitro , and significantly reduced tumor size in an ectopic head and neck cancer model. Here, we investigate the activity of nisin Z for colorectal cancer treatment and observed an in vitro reduction in cellular proliferation, and a moderate enhancement in cell death. We next analyzed the effect of oral nisin Z administration in the Apc [min/+] intestinal adenoma mouse model. We measured tumor burden along the gastrointestinal tract and observed a decrease in tumor burden in the middle region of the small intestine, but not in the lower region or colon. Since tumor progression in the Apc [min/+] model is exacerbated by an inflammatory environment, we next determined whether nisin Z impacts this in a direct or indirect manner. We show that nisin Z can directly reduce NF-κB activation in a dose-dependent manner. In addition, nisin Z impacted the cecal microbiome composition as well as microbiota-associated plasma metabolites, causing an overall shift towards a more health-associated profile. Interestingly, the Apc [min/+] genotype differentially impacted the nisin Z-mediated differences in cecal microbiome composition and plasma metabolites compared to wildtype animals. In summary, our data suggest that the reduction in small intestinal tumor burden could be due to nisin Z's contribution to a reduced pro-inflammatory environment. Future studies will reveal whether nisin's localized effect is due to degradation of the peptidic compound in more distal regions of the gastrointestinal tract and focus on development of delivery systems to increase efficacy.

IMPORTANCE: With the increased incidence of colorectal cancer, especially among younger individuals, it is critical to study approaches that help with the prevention and treatment of this debilitating disease. Our study indicates that nisin Z, a bacterially produced peptide antibiotic, decreases the growth of colorectal cancer cells and moderately increases cell death in vitro . Oral administration of nisin Z in an intestinal adenoma mouse model revealed a reduction of tumor burden in the middle region of the small intestine. This decreased tumor burden might in part be attributed to a direct anti-inflammatory effect, as well as an indirect effect on the gut microbiota and their metabolites due to nisin Z's antibacterial activity. Overall, we demonstrate a potential activity for nisin Z in the prevention or amelioration of inflammation-associated colorectal cancer, underscoring the significance of investigating the properties of bacterial natural products in human health.},
}

@article {pmid40475569,
year = {2025},
author = {Rajczewski, AT and Mehta, S and Wagner, R and Gabriel, W and Johnson, J and Do, K and Vintila, S and Wilhelm, M and Kleiner, M and Searle, BC and Griffin, TJ and Jagtap, PD},
title = {Benchmarking Spectral Library and Database Search Approaches for Metaproteomics Using a Ground-Truth Microbiome Dataset.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.15.654320},
pmid = {40475569},
issn = {2692-8205},
abstract = {Mass spectrometry-based metaproteomics, the identification and quantification of thousands of proteins expressed by complex microbial communities, has become pivotal for unraveling functional interactions within microbiomes. However, metaproteomics data analysis encounters many challenges, including the search of tandem mass spectra against a protein sequence database using proteomics database search algorithms. We used a ground-truth dataset to assess a spectral library searching method against established database searching approaches. Mass spectrometry data collected by data-dependent acquisition (DDA-MS) was analyzed using database searching approaches (MaxQuant and FragPipe), as well as using Scribe with Prosit predicted spectral libraries. We used FASTA databases that included protein sequences from microbial species present in the ground-truth dataset along with background protein sequences, to estimate error rates and assess the effects on detection, peptide-spectral match quality, and quantification. Using the Scribe search engine resulted in more proteins detected at a 1% false discovery rate (FDR) compared to MaxQuant or FragPipe, while FragPipe detected more peptides verified by PepQuery. Scribe was able to detect more low-abundance proteins in the microbiome dataset and was more accurate in quantifying the microbial community composition. This research provides insights and guidance for metaproteomics researchers aiming to optimize results in their analysis of DDA-MS data.},
}

@article {pmid40475515,
year = {2025},
author = {De Allende, CC and Salter, SJ and Brigg, SE and Claassen-Weitz, S and Mwaikono, KS and Workman, L and Zar, HJ and Nicol, MP and Parkhill, J and Dube, FS},
title = {Characterisation of Ornithobacterium hominis colonisation dynamics and interaction with the nasopharyngeal microbiome in a South African birth cohort.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.24.655922},
pmid = {40475515},
issn = {2692-8205},
abstract = {UNLABELLED: Ornithobacterium hominis is a recently described Gram-negative bacterium that colonises the human nasopharynx and may be associated with poor upper respiratory tract health. Here, we describe the isolation of O. hominis from samples collected from a South African birth cohort, creating the first archive of cultured strains of the species from Africa. Sequenced genomes from this archive reveal that South African O. hominis is more similar to Australian strains than those from Southeast Asia, and that it may share genes with other members of the microbiome that are relevant for virulence, colonisation, and antibiotic resistance. Leveraging existing microbiome data from the cohort, O. hominis was found to be closely associated with bacterial co-colonisers that are rare in non-carrier individuals, including Suttonella , Helcococcus , Moraxella spp., and Gracilibacteria. Their collective acquisition has a significant impact on the diversity of nasopharyngeal communities that contain O. hominis . Individuals who have not yet acquired O. hominis have a higher abundance of Moraxella (particularly M. lincolnii) than individuals who never acquire O. hominis , suggesting that this could be a precursor state for successful colonisation. Finally, a novel co-coloniser species, Helcococcus ekapensis , was successfully isolated and sequenced.

DATA SUMMARY: Ornithobacterium hominis data have been deposited under project accession ERP149886. This comprises genome sequences for isolates SA-OH-C1 (ERR13967269), SA-OH-C2 (ERR13967270), SA-OH-C3 (ERR13967271), SA-OH-C4 (ERR13967272, ERR13967275), SA-OH-C5 (ERR13967273), SA-OH-C6 (ERR13967274, ERR13967276). Previously published 16S rRNA gene data are deposited under project accessions PRJNA790843 and PRJNA548658. Helcococcus ekapensis genome data are deposited under project accession PRJEB85661.

SOFTWARE USED: AMRFinderPlus v3.12.8: https://github.com/ncbi/amr AssembleBAC-ONT v1.1.1: https://github.com/avantonder/assembleBAC-ONT BAKTA v1.8.1: https://bakta.computational.bio/ BLAST v2.16.0: https://blast.ncbi.nlm.nih.gov/Blast.cgi Comprehensive Antibiotic Resistance Database (CARD) Resistance Gene Identifier (RGI) tool v1.2.1: https://card.mcmaster.ca/analyze/rgi Decontam v1.12 (R package): https://github.com/benjjneb/decontam Eggnog-mapper v2.0.1: http://eggnog-mapper.embl.de/ FastANI v1.1.0: https://github.com/ParBLiSS/FastANI Flye v2.9.2: https://github.com/fenderglass/Flye Guppy v6.5.7: https://community.nanoporetech.com/downloads/guppy/release_notes ISEScan v1.7.2.3: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1 Medaka v1.9.1: https://github.com/nanoporetech/medaka MEGA11: https://www.megasoftware.net/ MMseqs2 v17: https://github.com/soedinglab/MMseqs2 Mothur v1.44.3: https://github.com/mothur/mothur NetCoMi v1.2.0 (R package): https://github.com/stefpeschel/NetCoMi Panaroo v1.4.3: https://github.com/gtonkinhill/panaroo PHASTEST: https://phastest.ca/submissions/new Prowler (commit ID c3041ba): https://github.com/ProwlerForNanopore/ProwlerTrimmer R v4.4.3: https://www.r-project.org/.

DATABASES USED: Comprehensive Antibiotic Resistance Database (CARD): https://card.mcmaster.ca/ European Nucleotide Archive: https://www.ebi.ac.uk/ena/ Genome Taxonomy Database (GTDB) release 09-RS220: https://gtdb.ecogenomic.org/ RefSeq release 228: https://www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/ SILVA v132: https://www.arb-silva.de/.

IMPACT STATEMENT: First described in 2019, Ornithobacterium hominis is an understudied bacterium that may be associated with poor respiratory health in children. The study builds upon existing knowledge of O. hominis by describing the first African isolates of the species, its potential as a reservoir of virulence and antibiotic resistance genes in the upper respiratory tract, and the unique microbiome profile of O. hominis carriers.},
}

@article {pmid40475494,
year = {2025},
author = {Mirji, G and Bhat, SA and El Sayed, M and Reiser, SK and Gavara, SP and Ye, Y and Miyamoto, T and Liu, Q and Goldman, AR and Kossenkov, A and Zhang, N and Shinde, RS},
title = {Aromatic Microbial Metabolite Hippuric Acid Potentiates Pro-Inflammatory Responses in Macrophages through TLR-MyD88 Signaling and Lipid Remodeling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.19.654724},
pmid = {40475494},
issn = {2692-8205},
abstract = {The gut microbiome generates a diverse array of metabolites that actively shape host immunity, yet the pro-inflammatory potential of microbial metabolites remains poorly understood. In this study, we identified hippuric acid, an aromatic gut microbe-derived metabolite, as a potent enhancer of pro-inflammatory responses using a murine bacterial infection model and a non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomics. Administering hippuric acid intraperitoneally in murine models of Escherichia coli infection or LPS-induced inflammation significantly heightened pro-inflammatory responses and innate immune cell activation. In vitro , hippuric acid selectively potentiated M1-like macrophage polarization (LPS + IFNγ) but had no effect on M2-like polarization (IL-4). Hippuric acid further enhanced responses to diverse MyD88-dependent TLR ligands, but not TRIF-dependent TLR3, implicating a possible mechanism of action via activation of TLR-MyD88 signaling. Genetic deletion of MyD88 abrogated the pro-inflammatory effects of hippuric acid both in vitro and in vivo , confirming its dependence on the MyD88 pathway. Transcriptomic and lipidomic analyses revealed that hippuric acid promoted cholesterol biosynthesis and lipid accumulation, linking microbial metabolism to lipid-driven immune activation. Notably, hippuric acid similarly enhanced pro-inflammatory responses in human macrophages, and its elevated levels correlated with increased sepsis mortality, highlighting its potential clinical relevance. These findings establish hippuric acid as a previously unrecognized microbial-derived inflammatory modulator, bridging gut microbial metabolism, lipid remodeling, and innate immune signaling, and offer new insights into its role in infection and inflammation.},
}

@article {pmid40475488,
year = {2025},
author = {Price, A and Rasolofomanana-Rajery, S and Manpearl, K and Robertson, CE and Krebs, NF and Frank, DN and Krishnan, A and Hendricks, AE and Tang, M},
title = {Network-based representation learning reveals the impact of age and diet on the gut microbial and metabolomic environment of U.S. infants in a randomized controlled feeding trial.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.01.621627},
pmid = {40475488},
issn = {2692-8205},
abstract = {While studies have explored differences in gut microbiome development for infant liquid diets (breastmilk, formula), little is known about the impact of complementary foods on infant gut microbiome development. Here, we investigated how different protein-rich foods (i.e., meat vs. dairy) affect fecal metagenomics and metabolomics during early complementary feeding from 5-12 months in U.S. formula-fed infants from a randomized controlled feeding trial. We used a network representation learning approach to model the time-dependent, complex interactions between microbiome features, metabolite compounds, and diet. We then used the embedded space to detect features associated with age and diet type and found the meat diet group was enriched with microbial genes encoding amino acid, nucleic acid, and carbohydrate metabolism. Compared to a more traditional differential abundance analysis, which analyzes features independently and found no significant diet associations, network node embedding represents the infant samples, microbiome features, and metabolites in a single transformed space revealing otherwise undetected associations between infant diet and the gut microbiome.},
}

@article {pmid40475274,
year = {2025},
author = {Lv, Y and Peng, S and Liu, Y and Yang, H and Li, G and Peng, Y},
title = {Cross-omics analysis reveals microbe-metabolism interactions characteristic of gingival enlargement associated with fixed orthodontic in adolescents.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2513739},
pmid = {40475274},
issn = {2000-2297},
abstract = {OBJECTIVES: To investigate the oral microbiome and metabolome longitudinal changes associated with orthodontic treatment-induced gingival enlargement (OT-GE).

METHODS: Twenty-six subjects were divided into case and control groups based on the gingival overgrowth index (GOi). The OT-GE group was divided into the no gingival enlargement (OT-GE0, n = 5) and persistent gingival enlargement (OT-GE1, n = 11). The control group included orthodontic treatment periodontal health (OT-GH, n = 5), and no orthodontic treatment periodontal health (NOT-GH, n = 5). Microbial composition and metabolites in saliva were investigated using cross-omics.

RESULTS: Longitudinal analysis linked orthodontic treatment-induced gingival enlargement to distinct oral microbiome and metabolome shifts. The OT-GE group showed significantly higher bleeding on probing (BOP), plaque scores (p < 0.001), probing depth, GOi, and ligature wire differences (p < 0.05) versus controls. Microbial diversity and species richness were elevated in OT-GE (p < 0.05), though no differences emerged between OT-GE0 and OT-GE1) subgroup (p > 0.05). Cross-omics identified specific periodontal pathogens and metabolites linked to gingival enlargement. Disrupted amino acid biosynthesis pathways, particularly citrulline metabolism, correlated with functional gene dysregulation and microbial imbalance. Aberrant citrulline intake appeared to drive dysbiosis, potentially contributing to gingival overgrowth.

CONCLUSIONS: OT-GE pathogenesis involves functional gene-regulated metabolite metabolism influencing periodontal pathogens.},
}

@article {pmid40475154,
year = {2025},
author = {Cotto, I and Durán-Viseras, A and Jesser, KJ and Zhou, NA and Hemlock, C and Albán, V and Ballard, AM and Fagnant-Sperati, CS and Lee, GO and Hatt, JK and Royer, C and Eisenberg, JNS and Trueba, G and Konstantinidis, KT and Levy, K and Fuhrmeister, ER},
title = {Environmental Exposures and the Human Gut Resistome in Northwest Ecuador.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.23.25327954},
pmid = {40475154},
abstract = {Inadequate water, sanitation, and hygiene (WASH) infrastructure may increase exposure to antimicrobial resistance (AMR). In addition, close human-animal interactions and unregulated antibiotic use in livestock facilitate the spread of resistant bacteria. We used metagenomic sequence data and multivariate models to assess how animal exposure and WASH conditions affect the gut resistome and microbiome in 53 pregnant women and 84 children in Ecuador. Escherichia coli , Klebsiella pneumoniae, and clinically relevant antimicrobial resistance genes (ARGs) were detected across all age groups, but the highest abundance was found in children compared to mothers. In mothers, higher animal exposure trended towards a higher number of unique ARGs compared to low animal exposure (β= -5.58 [95% CI: -11.46, 0.29]) and was significantly associated with greater taxonomic diversity (β= -1.29 [-1.96, -0.63]). In addition, mothers with sewer systems or septic tanks and piped drinking water had fewer unique ARGs (β= -3.52 [-6.74, -0.30]) compared to those without, and mothers with longer duration of drinking water access had lower total ARG abundance (β= -0.05 [-0.1, -0.01]). In contrast, few associations were observed in children, likely due to the dynamic nature of the gut microbiome during early childhood. Improving WASH infrastructure and managing animal exposure may be important in reducing AMR but could also reduce taxonomic diversity in the gut.},
}

@article {pmid40475140,
year = {2025},
author = {Schott, EM and Charbonneau, M and Kiel, DP and Bukata, S and Zuscik, MJ and Rosen, C and Ballok, A and Toledo, GV and Steels, E and Huntress, H and Rao, A and Travison, TG and Soto-Giron, MJ and Wolff, I and Easson, DD and Engelke, K and Vitetta, L},
title = {A randomized, double-blind, placebo-controlled clinical study to evaluate the efficacy of the synbiotic medical food, SBD111, for the clinical dietary management of bone loss in menopausal women.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.20.25325893},
pmid = {40475140},
abstract = {SUMMARY: This 12-month study in 286 early postmenopausal women evaluated the efficacy and safety of SBD111, a synbiotic medical food, in reducing bone loss. SBD111 did not significantly reduce bone loss for the full cohort, but did produce evidence of reduced bone loss in women with osteopenia and BMI ≥ 30.

PURPOSE: To determine the efficacy of SBD111, a synbiotic medical food comprising probiotics and prebiotics, in reducing bone loss in women post-menopause, including prespecified subpopulations of women with osteopenia or elevated BMI.

METHODS: In this prospective, multicenter, double-blind, randomized, placebo-controlled clinical food trial (NCT05009875), 286 healthy, non-osteoporotic women between 1-6 years post-menopause were enrolled and consumed SBD111 (4.75×10 [10] colony forming units) or placebo (maltodextrin) capsules twice daily for 12-months. The primary endpoint was change in areal BMD at the lumbar spine (LS). Secondary endpoints included change in areal BMD at the femoral neck (FN) and total hip (TH), trabecular volumetric BMD at the LS, markers of bone turnover and inflammation, and safety. Changes in gut microbiome composition were exploratory. The hypotheses being tested were formulated before data collection.

RESULTS: 286 Women [age 55 ± 3 years (mean ± standard deviation)] were enrolled, with 221 (77%) completing the study. For the primary outcome, SBD111 administration was not associated with significantly less bone loss in the LS after 12-months [0.15% (-0.52%, 0.82%), mean effect size (95% CI) by linear mixed effects regression]. However, SBD111 was associated with reduced BMD loss in the TH for women with BMI ≥ 30 [0.97% (0.015%, 1.925%)] and modestly reduced BMD loss in the FN for women with osteopenia [0.89% (-0.277%, 2.051%)].

CONCLUSIONS: These findings indicate SBD111 did not significantly reduce BMD loss for the full cohort. However, the trial produced evidence that SBD111 reduced bone loss in women with osteopenia and BMI ≥ 30.},
}

@article {pmid40475064,
year = {2025},
author = {Liu, YY},
title = {Deep learning for microbiome-informed precision nutrition.},
journal = {National science review},
volume = {12},
number = {6},
pages = {nwaf148},
pmid = {40475064},
issn = {2053-714X},
}

@article {pmid40474970,
year = {2025},
author = {Vari, F and Serra, I and Friuli, M and Cavallo, V and Gammaldi, N and Vergara, D and Salzet, M and Giudetti, AM},
title = {Pharmacological potential of endocannabinoid and endocannabinoid-like compounds in protecting intestinal structure and metabolism under high-fat conditions.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1567543},
pmid = {40474970},
issn = {1663-9812},
abstract = {The intestine plays a crucial role in nutrient absorption, digestion, and regulation of metabolic processes. Intestinal structure and functions are influenced by several factors, with dietary composition being one of the most significant. Diets rich in various types of fats, including saturated, monounsaturated, and polyunsaturated fats, have distinct effects on intestinal cell metabolism and overall intestinal health. High consumption of saturated fats, frequently found in animal products, has been associated with inflammation, altered gut microbiota composition, and impaired intestinal barrier function, with potential consequences such as metabolic disorders, obesity, and insulin resistance. In contrast, monounsaturated fats, found in foods such as olive oil and avocado, promote intestinal cell integrity, reducing inflammation and supporting a healthier microbiome. Polyunsaturated fatty acids, especially omega-3 fatty acids, have shown anti-inflammatory effects and may improve the function and adaptability of intestinal cells, promoting better nutrient absorption and immune regulation. Recent evidence suggests that endocannabinoids and endocannabinoid-like compounds, such as oleoylethanolamide have a protective effect on the function and structure of the intestine. These endocannabinoid pathways modulating compounds can act on receptors in the intestinal epithelium, improving the intestinal barrier and counteracting inflammation, facilitating a more favorable environment for intestinal health. Understanding how different fats influence intestinal metabolism and the protective role of endocannabinoids and endocannabinoid-like compounds is essential to developing dietary strategies to improve intestinal health and prevent diet-related diseases. This review explores the impact of high fats on intestinal metabolism and the main role of endocannabinoids and endocannabinoid-like compounds on these effects.},
}

@article {pmid40474491,
year = {2025},
author = {Myint, SMMP and Lasher, AT and Liu, K and Geurts, AM and Austad, SN and Sun, LY},
title = {A Novel GH Deficient Rat Model Reveals Cross-Species Insights Into Aging.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e70126},
doi = {10.1111/acel.70126},
pmid = {40474491},
issn = {1474-9726},
support = {AG050225/AG/NIA NIH HHS/United States ; AG057734/AG/NIA NIH HHS/United States ; AG048264/AG/NIA NIH HHS/United States ; P30DK056336//the NIH Nutrition and Obesity Research Center/ ; P30DK079626//Diabetes Research Center/ ; P30AG050886A//the UAB Nathan Shock Center/ ; },
abstract = {Multiple studies in mice with genetically disrupted growth hormone (GH) signaling have demonstrated that such disruption results in reduced body size, robustly increased longevity (> 50% in some cases), and improvements across multiple health parameters. However, it remains unclear how generalizable these findings are across mammals. Evidence in rats is limited and inconsistent. These conflicting results highlight the need for further investigation into the role of GH signaling in longevity across species. To address this gap, we developed a novel GH-deficient rat model using CRISPR/Cas9 technology to introduce a 10 bp deletion in exon 3 of the gene encoding rat GH-releasing hormone (GHRH) yielding a non-functional GHRH product. Physiological characterization of GHRH knockout (KO) rats revealed that they were half the body weight of wild-type controls. Additionally, relative to controls, they displayed an increased percent body fat, enhanced insulin sensitivity, reduced circulating insulin-like growth factor I (IGF-I) concentration, and a decreased reliance on glucose oxidation for energy metabolism, as determined by indirect calorimetry. Analysis of the gut microbial community in adult GHRH-KO rats further revealed a less diverse male microbiome, but a more diverse female KO microbiome compared to controls. Collectively, these findings demonstrate that multiple aspects of the GH activity-deficient phenotype, well-documented in mice, are faithfully recapitulated in our rat model. Therefore, the GHRH-deficient rat model represents a valuable new tool for advancing our understanding of the role of GH signaling in aging processes.},
}

@article {pmid40474448,
year = {2025},
author = {Fan, H and Li, C and Zhang, Z and Hu, M and Liu, S and Wu, A and Wang, Y and Lei, Z and Guo, L and Hu, L},
title = {pH-Responsive Probiotic-Liposome Hybrid System Synergistically Treats Radiation-Induced Injury via Dual Mechanisms of Anti-Inflammatory and Microbiome Modulation.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e2501642},
doi = {10.1002/adhm.202501642},
pmid = {40474448},
issn = {2192-2659},
support = {12205215//National Natural Science Foundation of China/ ; //Key Laboratory of Radiation Damage and Treatment of Jiangsu Provincial Universities and Colleges/ ; SJC2023001//Suzhou Fundamental Research Project/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
abstract = {Radiation-induced intestinal injury poses significant clinical challenges in radiotherapy. This study develops an oral pH-responsive probiotic-liposome hybrid system (EcN[PIN]-L) by conjugating Escherichia coli Nissle 1917 (EcN) with pinocembrin (PIN)-loaded liposomes (B-Lip-PIN) via biotin-streptavidin binding and encapsulating them in Eudragit L100-55 (L100-55). The system resists gastric acid, releases bacteria in intestinal pH conditions, and combines PIN's anti-inflammatory properties with EcN's probiotic effects. In irradiated mice, EcN[PIN]-L demonstrates effective intestinal colonization and multiple therapeutic benefits: it reduces pro-inflammatory cytokines (TNF-α, IL-17A), enhances intestinal barrier function, and decreases epithelial apoptosis. 16S rRNA sequencing reveals improved microbiota homeostasis with increased beneficial bacteria and decreased harmful species. The system shows superior efficacy compared to individual components, addressing both inflammatory damage and microbial dysbiosis while maintaining biocompatibility. These results highlight EcN[PIN]-L as a promising dual-mechanism therapy for radiation-induced intestinal injury, offering targeted delivery and combined anti-inflammatory/microbiome-modulating action.},
}

@article {pmid40474319,
year = {2025},
author = {Hu, Z and Wu, L and Lv, Y and Ge, C and Luo, X and Zhan, S and Huang, W and Shen, X and Yu, D and Liu, B},
title = {Integrated analysis of microbiome and transcriptome reveals the mechanisms underlying the chlorogenic acid-mediated attenuation of oxidative stress and systemic inflammatory responses via gut-liver axis in post-peaking laying hens.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {82},
pmid = {40474319},
issn = {1674-9782},
support = {2024C02004//Key Research & Development Program of Zhejiang Province/ ; 2023ZDXT15//Collaborative Extension Program for Advancements in Agricultural Technologies of Zhejiang Province/ ; },
abstract = {BACKGROUND: Systemic inflammatory responses and oxidative stress occur in laying hens during the aging process, particularly during the post-peaking laying period, which generally result in multi-organ damages, leading to significant declines in egg performance and quality. Chlorogenic acid (CGA)-enriched extract from Eucommia ulmoides leaves has anti-inflammatory and antioxidant activities. However, the mechanisms underlying whether and how CGA alleviates systemic inflammatory responses and oxidative stress to improve egg performance and quality in post-peaking laying hens remain unclear. In this study, the potential regulatory mechanisms of CGA in alleviating inflammatory responses and oxidative stress along the gut-liver axis were investigated. A total of 360 55-week-old Hy-line white-laying hens were randomly selected and divided into four groups. The hens in the four groups were fed a basal diet (CON) or basal diets supplemented with 200, 400, and 800 mg/kg of CGA (CGA200, CGA400, and CGA800, respectively) for 10 weeks.

RESULTS: The results demonstrated that CGA significantly alleviated intestinal and hepatic damages resulting from systemic inflammatory responses and oxidative stress, thereby improving the laying performance and egg quality of post-peaking laying hens. CGA reduced systemic inflammation by improving intestinal barrier function and modulating inflammation-associated microbiota (Blautia and Megamonas), thus inhibiting endotoxin translocation. CGA can also reduce oxidative stress by upregulating the NRF-2 pathway-related genes and increasing antioxidant enzyme activities in the liver. The results of transcriptome sequencing revealed that CGA promoted lipid metabolism by regulating hepatic adipocytokine pathway-related genes/protein and reduced the inflammatory responses and apoptosis in liver by regulating PI3K/AKT pathway-related genes/proteins, which was also verified by qPCR and western blotting.

CONCLUSION: CGA alleviated multi-organ damages and dysfunction by suppressing the systemic inflammatory responses and oxidative stress in post-peaking laying hens, thereby improving egg performance and quality. The optimal dose of CGA is 400 mg/kg in this experiment. These results provide a sound theoretical basis for the application of CGA as an exogenous animal feed additive for laying hens.},
}

@article {pmid40474258,
year = {2025},
author = {Wang, L and Jiang, W and Yang, M and Danzeng, Q and Liu, S and Cui, M},
title = {Combination strategies of gut microbiota in cancer therapy through metabolic reprogramming and immune remodeling.},
journal = {Cell communication and signaling : CCS},
volume = {23},
number = {1},
pages = {270},
pmid = {40474258},
issn = {1478-811X},
support = {No. 82303116//Natural Science Foundation of China/ ; YDZJ202301ZYTS047//Natural Science Foundation of Jilin Province/ ; 2022JC069//Health Science and Technology Capacity improvement Project of Jilin Province/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Neoplasms/therapy/immunology/microbiology/metabolism ; Animals ; Tumor Microenvironment ; Metabolic Reprogramming ; },
abstract = {Over the past decade, there has been a qualitative improvement in the understanding of gut microbiota in cancer development and treatment. Gut microbiota regulates metabolic reprogramming that occurs in the competition between tumor cells and immune cells for essential nutrients in the tumor microenvironment (TME). Besides, gut microbiota dysbiosis is one of the key factors leading to the formation of aging environment, which has many similarities with the TME. Accumulating research findings have demonstrated that gut microbiota enhances the efficacy of cancer therapies by activating the immune system and facilitating the biotransformation of drugs. Other studies also have shown that specific microbial composition is the effective biomarker of drug resistance and toxicity for cancer treatment. Microbiota-directed therapies are being explored intensively for their potential in cancer prevention and treatment. In this review, we summarize the role of gut microbiota in metabolic reprogramming and immune remodeling; provide an overview of the relationship between gut microbiota and the efficacy, resistance, and toxicity of cancer treatment; propose a series of strategies to integrate gut microbiota into cancer treatment, optimizing antitumor effectiveness and reducing side effects.},
}

Humans
*Gastrointestinal Microbiome
*Neoplasms/therapy/immunology/microbiology/metabolism
Animals
Tumor Microenvironment
Metabolic Reprogramming

@article {pmid40474246,
year = {2025},
author = {Denison, ER and Pound, HL and Gann, ER and Gilbert, NE and Weston, DJ and Pelletier, DA and Wilhelm, SW},
title = {Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {62},
pmid = {40474246},
issn = {2524-6372},
support = {DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-AC05-00OR22725//U.S. Department of Energy/ ; DE-AC05-00OR22725//U.S. Department of Energy/ ; },
}

@article {pmid40474179,
year = {2025},
author = {Ho, TE and Yang, YM and Gu, WJ and Meng, W and Chen, XY and Wu, SC and Lo, ECM and Li, F and Lu, HX},
title = {Construction of an early childhood caries risk prediction model based on the oral microbiome: a nested case‒control study.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {923},
pmid = {40474179},
issn = {1472-6831},
support = {202240355//General Project of the Shanghai Municipal Health Committee/ ; 202240355//General Project of the Shanghai Municipal Health Committee/ ; 2022ZZ01017//Shanghai's Top Priority Research Center/ ; 2022ZZ01017//Shanghai's Top Priority Research Center/ ; 22410760200//Hong Kong Macao Taiwan Science and Technology Cooperation Project of the Shanghai Municipal Science and Technology Commission/ ; },
mesh = {Humans ; Case-Control Studies ; *Dental Caries/microbiology/epidemiology ; Child, Preschool ; *Microbiota ; Female ; Male ; Prospective Studies ; Risk Assessment ; *Mouth/microbiology ; Risk Factors ; Dental Plaque/microbiology ; Oral Hygiene ; Health Behavior ; },
abstract = {BACKGROUND: Research on dental caries risk prediction models that integrate socio-demographics, oral health behaviors, and oral microbiota remains insufficient. The present study aimed to compare differences in socio-demographics, oral health behaviors, and oral microbial diversity among preschoolers with different levels of ECC progression and to construct a caries risk prediction model to prevent the occurrence and development of ECC in young children.

METHODS: A nested case-control study was conducted in a prospective cohort study to follow up preschoolers from 36 months to 48 months of age. Dental caries status and supragingival plaque data were collected at each follow-up visit, and questionnaire surveys of their mothers were conducted to collect information on the socio-demographic backgrounds and oral health-related behaviors of the preschoolers. High-throughput 16 S rRNA gene sequencing technology was used to observe the oral microbial diversity in children, and an ECC risk prediction model was constructed using the random forest method.

RESULTS: There were 18 preschoolers each in the caries-free to caries-free group (H2H), caries-free to decayed group (H2C) and decayed to decayed group (C2C) according to ECC progression. The alpha diversity analysis showed statistically significant differences in the Simpson and Shannon indices between the H2H and H2C groups (P < 0.05), and the beta diversity analysis revealed statistically significant differences between the H2H group and the H2C and C2C groups. Therefore, an ECC risk prediction model was constructed based on the H2H and H2C groups. The results of risk prediction model showed that place of residence, maternal completion of oral hygiene, toothbrushing frequency and use of dental floss, and three oral microorganisms, including Selenomonas sp. oral taxon 137, Porphyromonas sp. oral taxon 278 str. W7784, and the human oral bacterium C73, were risk factors for ECC progression after one year, and the area under the curve of the model was 95.00% (95% CI, 86.50-100.00%).

CONCLUSION: The oral microbial diversity of consistently caries-free children differed considerably from that of children who eventually developed decay, and oral health behaviors such as toothbrushing frequency and some oral microorganisms had good ECC predictive ability.},
}

Humans
Case-Control Studies
*Dental Caries/microbiology/epidemiology
Child, Preschool
*Microbiota
Female
Male
Prospective Studies
Risk Assessment
*Mouth/microbiology
Risk Factors
Dental Plaque/microbiology
Oral Hygiene
Health Behavior

@article {pmid40474156,
year = {2025},
author = {Qiu, X and Xu, T and Huang, Y and Wei, C and Wang, L and Wu, B},
title = {Relationship between depression and oral microbiome diversity: analysis of NHANES data (2009-2012).},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {914},
pmid = {40474156},
issn = {1472-6831},
support = {72404193//National Natural Science Foundation of China (NSFC) Youth Fund/ ; 892003120//Guangdong Science and Technology Programs Youth Fund/ ; 20240813143325033//Shenzhen Natural Science Foundation General Program for Basic Research/ ; },
mesh = {Humans ; Male ; Female ; Cross-Sectional Studies ; Adult ; *Depression/microbiology ; *Microbiota ; *Mouth/microbiology ; Nutrition Surveys ; Middle Aged ; RNA, Ribosomal, 16S ; United States ; },
abstract = {BACKGROUND: While the association between the gut microbiome and depression is well studied, the association between the oral microbiome and depression is less well characterized.

METHODS: This cross-sectional study analyzed the association between depression and diversity of oral microbiome using data from the 2009-2012 National Health and Nutrition Examination Survey (NHANES). The gene sequencing of 16S ribosomal RNA was adopted for the profiling of oral microbiome. Alpha diversity, quantified by the observed number of amplicon sequence variants (ASVs), and beta diversity, assessed using Bray-Curtis dissimilarity, were evaluated to represent oral microbiome diversity. Depressive symptoms were measured by the Patient Health Questionnaire-9 (PHQ-9) scale, with alpha diversity as the primary predictor. Weighted logistic regression was employed to examine the relationship between depression and microbial alpha diversity. Threshold effect analysis was performed to explore potential nonlinear relationships between the observed ASVs and depression. Subgroup analysis indicated that smoke, excessive alcohol consumption, and oral treatment influenced the association between oral microbiology and depression, with interaction effects observed across gender and racial groups. Beta diversity differences were evaluated using Bray-Curtis dissimilarity and visualized via non-metric multidimensional scaling (NMDS).

RESULTS: A total of 15,018 participants were included, with an average age of 42.25 ± 15.2 years. In the fully adjusted model, the alpha diversity of oral microbiome was significantly negatively correlated with depression (OR = -0.51, 95% CI: -0.79--0.23, P = 0.003). Threshold analysis also revealed a nonlinear association in this relationship, with a significant inflection point as Log10ASVs of 2.32. Furthermore, beta diversity of the oral microbiome differed significantly between the normal and depression groups (p = 0.001). Sensitivity analyses showed that the relationship between depression and oral microbial diversity observed in this research was particularly pronounced among non-Hispanic Whites (OR = 0.16, 95% CI: 0.07-0.35) and men (OR = 0.14, 95% CI: 0.06-0.30). Additionally, significant differences in oral microbiome beta diversity were observed between the normal and depression groups (p = 0.001).

CONCLUSIONS: The findings suggest that the diversity of oral microbiome is negatively correlated with depressive symptoms. Hence, oral dysbiosis may serve as a therapeutic target or biomarker of depression. However, the underlying mechanisms require further investigation.},
}

Humans
Male
Female
Cross-Sectional Studies
Adult
*Depression/microbiology
*Microbiota
*Mouth/microbiology
Nutrition Surveys
Middle Aged
RNA, Ribosomal, 16S
United States

@article {pmid40474070,
year = {2025},
author = {Boodaghidizaji, M and Jungles, T and Chen, T and Zhang, B and Yao, T and Landay, A and Keshavarzian, A and Hamaker, B and Ardekani, A},
title = {Machine learning based gut microbiota pattern and response to fiber as a diagnostic tool for chronic inflammatory diseases.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {353},
pmid = {40474070},
issn = {1471-2180},
mesh = {Humans ; *Machine Learning ; *Dietary Fiber ; *Gastrointestinal Microbiome ; Crohn Disease/diagnosis/microbiology ; Feces/microbiology ; Parkinson Disease/diagnosis/microbiology ; Colitis, Ulcerative/diagnosis/microbiology ; HIV Infections/diagnosis/microbiology ; Dysbiosis/microbiology/diagnosis ; Bacteria/classification/genetics/isolation & purification ; Algorithms ; Female ; Male ; *Inflammation/diagnosis/microbiology ; Chronic Disease ; },
abstract = {Gut microbiota has been implicated in the pathogenesis of multiple gastrointestinal (GI) and systemic metabolic and inflammatory disorders where disrupted gut microbiota composition and function (dysbiosis) has been found in multiple studies. Thus, human microbiome data holds significant potential as a source of information for diagnosing and characterizing diseases-such as phenotypes, disease course, and therapeutic response-associated with dysbiotic microbiota communities. However, multiple attempts to leverage gut microbiota taxonomic data for diagnostic and disease characterization have failed due to significant inter-individual variability of microbiota community and overlap of disrupted microbiota communities among multiple diseases. One potential approach is to look at the microbiota community pattern and response to microbiota modifiers like dietary fiber in different disease states. This approach has become feasible with the advent of machine learning, which can uncover hidden patterns in human microbiome data and enable disease prediction. Accordingly, the aim of our study was to test the hypothesis that machine learning algorithms can distinguish stool microbiota patterns-and their responses to fiber-across diseases with previously reported overlapping dysbiotic microbiota profiles. Here, we applied machine learning algorithms to distinguish between Parkinson's disease, Crohn's disease (CD), ulcerative colitis (UC), human immune deficiency virus (HIV), and healthy control (HC) subjects in the presence and absence of fiber treatments. We demonstrated that machine learning algorithms can classify diseases with accuracy as high as 95%. Furthermore, applying machine learning to microbiome data to distinguish UC from CD yielded a prediction accuracy of up to 90%.},
}

Humans
*Machine Learning
*Dietary Fiber
*Gastrointestinal Microbiome
Crohn Disease/diagnosis/microbiology
Feces/microbiology
Parkinson Disease/diagnosis/microbiology
Colitis, Ulcerative/diagnosis/microbiology
HIV Infections/diagnosis/microbiology
Dysbiosis/microbiology/diagnosis
Bacteria/classification/genetics/isolation & purification
Algorithms
Female
Male
*Inflammation/diagnosis/microbiology
Chronic Disease

@article {pmid40474023,
year = {2025},
author = {Kavitha, SA and Zainab, S and Muthyalaiah, YS and John, CM and Arockiasamy, S},
title = {Mechanism and implications of advanced glycation end products (AGE) and its receptor RAGE axis as crucial mediators linking inflammation and obesity.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {556},
pmid = {40474023},
issn = {1573-4978},
mesh = {Humans ; *Obesity/metabolism ; *Glycation End Products, Advanced/metabolism ; *Inflammation/metabolism ; *Receptor for Advanced Glycation End Products/metabolism ; Signal Transduction ; Oxidative Stress ; Animals ; Gastrointestinal Microbiome ; Insulin Resistance ; Metabolic Syndrome/metabolism ; Epigenesis, Genetic ; },
abstract = {Advanced glycation end products (AGEs) are heterogenous compounds that play a central role in various chronic diseases, such as diabetes, neurodegenerative disorders, cardiovascular diseases, and cancer. These are formed by non-enzymatic reaction between reducing sugar and amino group of proteins, lipids and nucleic acids. Elevated levels of AGEs are associated with obesity, which is linked to hyperglycemia, dyslipidemia and insulin resistance, contributing to metabolic syndrome and diabetes. Both dietary and endogenous AGEs contribute to persistent oxidative stress and inflammation directly through glycated biomolecules and indirectly through its receptor, receptor for advanced glycation end products, RAGE. In this context, inflammation is a sustained, systemic immune response with macrophage infiltration into adipose tissues, high pro- inflammatory cytokines leading to immune dysregulation, activation of key inflammatory pathways such as NF-kB and JNK signaling, increase oxidative stress, insulin resistance suggesting inflammation as both a cause and consequence of metabolic dysfunction. Persistent oxidative stress and inflammation accelerates AGEs formation, disrupt cellular signaling, alter extracellular matrix integrity, impair release of enzymes and hormones. Also, AGE-induced gut microbiome imbalance elicits conditions such as systemic inflammation, intestinal barrier dysfunction and metabolic imbalance, promoting obesity and its complications. This review explores the central role of AGEs in obesity-associated inflammation, emphasizing AGE-RAGE signaling, epigenetic regulation and gut microbiome dysfunction. Understanding this interplay mediated by AGEs is critical for identifying potential biomarkers of metabolic risk and strategize means to prevent AGEs formation, block AGE-RAGE interaction and signaling, thus mitigating the effects of obesity and its associated diseases.},
}

Humans
*Obesity/metabolism
*Glycation End Products, Advanced/metabolism
*Inflammation/metabolism
*Receptor for Advanced Glycation End Products/metabolism
Signal Transduction
Oxidative Stress
Animals
Gastrointestinal Microbiome
Insulin Resistance
Metabolic Syndrome/metabolism
Epigenesis, Genetic

@article {pmid40474000,
year = {2025},
author = {Cottam, DE and Cosgrove, DW and Megía-Palma, R and Žagar, A and Blázquez-Castro, S and Faria, JF and Turner, AE and Silva, DO and Pie, MR},
title = {Does the Gut Microbiome of the Insular Lizard Gallotia galloti Reflect Variation in Sex, Environment, and Population Genetic Differentiation?.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {61},
pmid = {40474000},
issn = {1432-184X},
mesh = {Animals ; *Lizards/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Spain ; *Bacteria/classification/genetics/isolation & purification ; Environment ; Genetic Variation ; Genetics, Population ; Sex Factors ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Despite their critical role in maintaining organismal health, the factors driving intraspecific variation in gut microbiotas in the wild are poorly understood. Gallotia galloti is a lizard endemic to the Canary Islands characterized by substantial phenotypic and genetic differentiation across populations, as well as by its ability to occur across considerably different environmental conditions. However, the extent to which such diversity is reflected in their gut microbiota is still unknown. Here, we use metabarcoding of fecal samples to explore how the gut microbiome of G. galloti reflects variation in sex, environment, human footprint, and subspecies identity. Fecal samples of 47 individuals were obtained across 13 locations to reflect the extent of intraspecific variation in the species. We found no evidence for consistent differences in microbiota richness across the studied groups, regardless of whether analyses were carried out at the genus, family, or phylum levels. Moreover, neither the richness nor composition of the microbiota was associated with variation in mean annual temperature, annual precipitation, and human footprint. Our results suggest that the generalist diet of G. galloti exposes them to a broad range of food items that provide a common template across the island, despite ecological and historical differences between populations.},
}

Animals
*Lizards/microbiology/genetics
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Male
Female
Spain
*Bacteria/classification/genetics/isolation & purification
Environment
Genetic Variation
Genetics, Population
Sex Factors
RNA, Ribosomal, 16S/genetics

@article {pmid40473637,
year = {2025},
author = {Bar, O and Vagios, S and Barkai, O and Elshirbini, J and Souter, I and Xu, J and James, K and Bormann, C and Mitsunami, M and Chavarro, JE and Foessleitner, P and Kwon, DS and Yassour, M and Mitchell, C},
title = {Harnessing vaginal inflammation and microbiome: a machine learning model for predicting IVF success.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {95},
pmid = {40473637},
issn = {2055-5008},
mesh = {Humans ; Female ; *Vagina/microbiology/immunology ; Pregnancy ; *Microbiota ; *Fertilization in Vitro ; Adult ; *Machine Learning ; Pilot Projects ; *Inflammation/microbiology ; Male ; Pregnancy Outcome ; },
abstract = {Humans are the only species with a commensal Lactobacillus-dominant vaginal microbiota. Reproductive tract microbes have been linked to fertility outcomes, as has intrauterine inflammation, suggesting immune response may mediate adverse outcomes. In this pilot study, we compared vaginal microbiota composition and immune marker concentrations between patients with unexplained or male factor infertility (MFI), as a control. We applied a supervised machine learning algorithm that integrated microbiome and inflammation data to predict pregnancy outcomes.Twenty-eight participants provided vaginal swabs at three IVF cycle time points; 18 achieved pregnancy. Pregnant participants had lower microbial diversity and inflammation. Among them, MFI cases had higher diversity but lower inflammation than those with unexplained infertility. Our model showed the highest prediction accuracy at time point 2 of the IVF cycle. These findings suggest that vaginal microbiota and inflammation jointly impact fertility and can inform predictive tools in reproductive medicine.},
}

Humans
Female
*Vagina/microbiology/immunology
Pregnancy
*Microbiota
*Fertilization in Vitro
Adult
*Machine Learning
Pilot Projects
*Inflammation/microbiology
Male
Pregnancy Outcome

@article {pmid40473402,
year = {2025},
author = {Barnich, N and Arthur, JC and Buisson, A and Campbell, BJ and Carbonnel, F and Chassaing, B and Coombes, BK and Denizot, J and Dogan, B and Faith, J and Kamada, N and Longman, RS and Martinez-Medina, M and O'Brien, CL and Sartor, RB and Zhang, S and , and Colombel, JF and Simpson, KW and , },
title = {Adherent-invasive Escherichia coli in Crohn's disease: the 25th anniversary.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335331},
pmid = {40473402},
issn = {1468-3288},
abstract = {In 1998, Arlette Darfeuille-Michaud, Christel Neut and Jean-Frederic Colombel discovered a novel pathovar of Escherichia coli, adherent and invasive Escherichia coli (AIEC), in the ileum of patients with Crohn's disease (CD), that was genetically distinct from diarrheagenic E. coli, could adhere to and invade intestinal epithelial cells and survive in macrophages. The consistent association between AIEC and CD (approximately 30% across the world), their ability to exploit CD-associated genetic traits, and virulence in preclinical colitis models but not healthy hosts spurred global research to elucidate their pathogenicity. Research focused on integrating AIEC with the microbiome, metabolome, metagenome, host response and the impact of diet and antimicrobials has linked the luminal microenvironment and AIEC metabolism to health and disease. This deeper understanding has led to therapeutic trials and precision medicine targeting AIEC-colonised patients. In November 2023, prominent members of the AIEC research community met to present and discuss the many facets of basic, translational and clinical AIEC fields at 'AIEC: past, present and future' in NYC. This review is a summary of this international meeting highlighting the history of AIEC, knowledge accumulated over the past 25 years about its pathogenic properties and proposes a standardised approach for screening patients for AIEC.},
}

@article {pmid40473400,
year = {2025},
author = {Szeto, CC and Ng, JKC},
title = {Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-microbiome study.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335600},
pmid = {40473400},
issn = {1468-3288},
}

@article {pmid40473134,
year = {2025},
author = {Sadeghi, S and Faramarzi, MA and Siroosi, M},
title = {Design of Novel Human Microbiome-Derived Peptides for Inhibition of OXA-48 Carbapenemase: An In-Silico and In-Vitro Approach.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107779},
doi = {10.1016/j.micpath.2025.107779},
pmid = {40473134},
issn = {1096-1208},
abstract = {Drug-resistant bacteria have become a global healthcare challenge, especially due to their acquisition of resistance to last-resort antibiotics. OXA-48 carbapenemase is one of the notorious enzymes that inactivates carbapenems through hydrolysis. The emergence of OXA-48 and OXA-48-like carbapenemases is a significant concern as they are responsible for many outbreaks of hospital-acquired infections in various countries, with limited treatment options available. Thus, targeting this enzyme and inhibiting its activity can be an attractive therapeutic strategy. In this study, a rational computer-aided approach was applied to design effective inhibitory peptides against OXA-48 carbapenemase. The primary library was constructed based on peptides derived from the Human Antimicrobial Peptide (HAMP) database. The binding of peptides to the enzyme was investigated through molecular docking studies using ClusPro. After each screening step, numerous targeted amino acid substitutions were performed to enhance the affinity and physicochemical properties of the selected peptides. The final selected peptides, in complex with the enzyme, were subjected to 200 ns Molecular Dynamics (MD) simulations using the GROMACS package, and MM/PBSA analysis was conducted to evaluate the binding free energy of the enzyme-peptide complexes. Finally, the inhibitory effects of the designed peptides were also computationally assessed on OXA-48-like carbapenemases. Homology modeling was used to generate 3D structures of the enzymes whose structures were not solved experimentally. Results indicated that the two final selected peptides effectively interacted with the important residues of OXA-48 carbapenemase and spatially blocked its active site. These peptides also demonstrated high binding affinity to the most common OXA-48-like carbapenemases in silico. In vitro studies on the efficacy of one of the designed peptides, M104, demonstrated that this peptide enhanced the activity of meropenem against a meropenem-resistant, clinical Klebsiella pneumoniae strain harboring the gene blaOXA48 by reducing its minimum inhibitory concentration (MIC) by 4-fold. In an era where effective inhibitors against OXA-48 carbapenemase are limited, present study addressed this urgent need by rationally designed novel peptides.},
}

@article {pmid40473131,
year = {2025},
author = {Gong, X and Zhu, Y and Ning, X and Zhang, K and Wang, T and Yin, S and Ji, J},
title = {Effect of Ichthyophthirius multifiliis infection on host immunity and microbiota shifts of Takifugu fasciatus.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107784},
doi = {10.1016/j.micpath.2025.107784},
pmid = {40473131},
issn = {1096-1208},
abstract = {Ichthyophthirius multifiliis (Ich) is a major pathogen responsible for high mortality rates in Takifugu fasciatus aquaculture. Despite its significance, the local and systemic immune responses of pufferfish to Ich infection remain poorly understood. Additionally, the interaction between ectoparasite infection and gut microbiota has not been thoroughly investigated. To address these gaps, we established an Ich infection model in pufferfish through bath administration. RT-PCR confirmed that Ich invades the skin, gill, and fin at 10 days post-infection (dpi) using 5,000 theronts per fish. RT-qPCR analysis revealed immune responses in the spleen, liver, gill, skin, and gut following infection, while H&E staining identified Ich intrusion into the epidermal layer of the skin. RNA-seq analysis showed that pathways such as Th1 and Th2 cell differentiation, legionellosis, and Chagas disease were significantly enriched in the spleen, whereas ECM-receptor interaction, calcium signaling, and PI3K-Akt signaling pathways were enriched in the skin, suggesting that Ich breaches local defenses and activates systemic immune responses. Furthermore, Ich infection reduced the alpha diversity of the gut microbiota, with notable compositional shifts, including a decrease in commensals such as Chryseobacterium and an increase in opportunistic bacteria like Elizabethkingia. These findings enhance our understanding of the intricate interactions between parasite, host, and gut microbiota, providing insights into the immune and microbiome dynamics of Ich infection in pufferfish.},
}

@article {pmid40473125,
year = {2025},
author = {Darwiche, S and Gacesa, R and Ferraro, RB and Alwan, W and Oben, JA and Rashidghamat, E and Long, PF},
title = {Prevalence of skin fungi markedly declines in the lesions of two patients with moderate Hidradenitis Suppurativa.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107778},
doi = {10.1016/j.micpath.2025.107778},
pmid = {40473125},
issn = {1096-1208},
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disorder affecting hair follicles in intertriginous regions, leading to painful nodules, sinus tracts, and scarring. The pathogenesis of HS is far from clear, but alterations in the bacterial community of the skin microbiome has been debated, yet the potential involvement of fungi - the mycobiome - has received almost no attention. Large areas of skin were sampled for amplicon metagenomics sequencing to negate the inference of low-sequence counts with the objective of examining the provenance of fungi between lesion and lesion-free skin from the same individuals. The DNA from skin swabs was isolated and the V4 region of the 18S rRNA gene was amplified and sequenced. Total fungal counts were inferred from taxonomic assignment of unique operational taxonomic units and absolute numbers then compared between skin sites. There were dramatically lower numbers of fungi in HS lesions with Malassezia dominance, as expected, across samples. This finding suggested, for the first time, that fungal depletion in lesions might be linked to HS pathology through disruption of normal skin barrier function and immunity, potentially due to reduced sebum production essential for fungal growth.},
}

@article {pmid40473107,
year = {2025},
author = {Mascaux, C and Sen, T and Sanchez-Cespedes, M and Ortiz-Cuaran, S and Bossé, Y and Dammeijer, F and Cavic, M and Barr, MP and Arulananda, S and Armisen, R and Berger, AH and Bianchi, F and Carbone, DP and Cerciello, F and Lockwood, WW and Mitsudomi, T and Ohara, S and Politi, K and Qin, S and Roisman, LC and Samstein, R and Skoulidis, F and Tan, AC and Thomas, A and Zhang, J and Wynes, MW and John, T and Tsao, MS and , },
title = {Advances in lung cancer basic and translational research in 2025 - Overview and perspectives focusing on non-small cell lung cancer.},
journal = {Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtho.2025.05.024},
pmid = {40473107},
issn = {1556-1380},
abstract = {Basic and translational research in lung cancer is a rapidly evolving field with transformational impact in early detection, diagnosis, therapeutic development and personalization of care. Recent advances have greatly increased our understanding in the molecular genomics, proteomics, pathogenesis and cellular biology of this deadly malignancy. The International Association for the Study of Lung Cancer (IASLC) recently formed a Basic and Translational Science (BaTS) Committee to further enhance the scientific leadership of IASLC in thoracic cancer research. This review by members of the committee highlights the breadth of current research in NSCLC, with a focus on molecular risk factors and processes in tumorigenesis, heterogeneity, phenotypic plasticity, metabolic reprograming, immunobiology, the immune microenvironment and microbiome. This review also identifies future research areas that may lead to further improvement in survival outcomes and curative therapies especially for patients with advanced NSCLC.},
}

@article {pmid40473000,
year = {2025},
author = {Carbone, E and Fabrizi, E and Rivabene, R and Cappella, M and Fortini, P and Conti, L and Locuratolo, N and Lorenzini, P and Lacorte, E and Piscopo, P},
title = {Human oral microbiome in aging: a systematic review.},
journal = {Mechanisms of ageing and development},
volume = {},
number = {},
pages = {112080},
doi = {10.1016/j.mad.2025.112080},
pmid = {40473000},
issn = {1872-6216},
abstract = {Studying aging and risk factors associated with chronic non-communicable diseases is increasingly relevant due to the progressive aging of the global population. Risk factors have focused on diet, physical exercise, cognitive activity, and lifestyle habits; however, recent research has begun to explore how the oral microbiome may influence health and contribute to chronic diseases. The aim of our systematic review is to evaluate the link between human oral microbiome and aging. This SR was carried out using PubMed, Cochrane Library, and Embase, identifying 3,490 records, of which 6 met our inclusion/exclusion criteria. These studies were qualitatively assessed using the Revised Risk of Bias Assessment Tool for Nonrandomized Studies of Interventions. Overall, the evidence suggests that while the bacterial and fungal communities remain similar across age groups, there is an increased presence of periodontal pathogens in older subjects. Moreover, bacterial species richness and alpha-diversity decrease with advancing age, though no clear age clustering was observed. Although the reviewed studies offer insights into the association between aging and changes in the oral microbiome, further research is required to address confounding factors, limitations in sample size, and gender differences, in order to better elucidate the role of microbiome alterations in general health.},
}

@article {pmid40472755,
year = {2025},
author = {Chen, M and Xing, L and Gao, S and Guo, Y and Qiu, T and Wang, X and Gao, M},
title = {Metagenomic analysis deciphers airborne pathogens with enhanced antimicrobial resistance and virulence factors in composting facilities.},
journal = {Environment international},
volume = {201},
number = {},
pages = {109569},
doi = {10.1016/j.envint.2025.109569},
pmid = {40472755},
issn = {1873-6750},
abstract = {The composting process has been shown to effectively reduce antimicrobial resistance (AMR) in animal manure, but its influence on surrounding airborne AMR remains unknown, particularly with regard to human-pathogenic antibiotic-resistant bacteria (HPARB). In this study, air and paired compost samples were collected from a full-scale composting facility, and the antibiotic resistome, microbiome, and HPARB were systematically analyzed in both two habitats using metagenomic analysis. Current result uncovered the profiles of HPARB in air, showing that significantly more airborne HPARB were assembled than that in compost samples. Airborne pathogens harboredan increased abundance and diversity of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in comparison with compost-borne HPARB. The core antibiotic resistome represents 18.58% of overall ARG subtypes, contributing to 86.31% of ARG abundance. A higher number of enriched core ARGs (2.16- to 13.36-times higher), including mexF, tetW, and vanS, were observed in air samples compared to compost samples. As an important human pathogen, Mycobacterium tuberculosis was prevalent in the air and carried more ARG (6) and VFG (130) subtypes than those in compost. A significantly higher risk score was detected for airborne AMR in the composting facility compared to that in hospital and urban environments. This study revealed the enhanced airborne HPARB through comparative experiments between air and composting habitats. It highlighted the unrecognized AMR risks associated with air in composting site and provided a scientific basis for accurately assessing health outcomes caused by occupational exposure.},
}

@article {pmid40472699,
year = {2025},
author = {Yang, Q and Cao, X and Li, S and Yang, X and Bai, P and Yan, Y and Qi, C and Deng, Z and Wu, B and Song, B},
title = {Chronic ozone exposure induces hippocampal microglia activation by microbial dysbiosis in rat lungs.},
journal = {Ecotoxicology and environmental safety},
volume = {300},
number = {},
pages = {118393},
doi = {10.1016/j.ecoenv.2025.118393},
pmid = {40472699},
issn = {1090-2414},
abstract = {Ozone (O3) pollution has become a significant international public health issue with adverse effects on human health. Recent studies have confirmed that O3 exposure induces neuroinflammation and cognitive dysfunction. It is hypothesized that O3 exposure affects the pulmonary microbiome, triggering inflammatory responses that subsequently contribute to neuroinflammation. After 40 days of O3 exposure in rats, distinct changes in the microbial community were identified using 16S rRNA gene sequencing. This was followed by an assessment of the impact of pulmonary microbiota on serum NETs (neutrophil extracellular traps). Additionally, changes in the hippocampal P2X4R/NLRP3 signaling pathway were investigated following O3 exposure. In vitro experiments were conducted to evaluate the effects of O3 on BV-2 cells. In vivo results indicated that O3 exposure led to an increased abundance of Pseudomonas aeruginosa within the pulmonary microbiota and significantly increased NET levels in rat serum. O3 exposure caused a loose arrangement of hippocampal neurons in rats, resulting in cell atrophy and even death. Compared to controls, O3 exposure significantly upregulated the expression of P2X4R/NLRP3 and pro-inflammatory factors. Similarly, BV-2 cells treated with serum from 1.0 ppm O3-exposed rats exhibited comparable changes. Treatment with a P2X4R inhibitor significantly reduced pathway protein and pro-inflammatory factors expression compared to O3 serum intervention alone. In conclusion, O3 exposure significantly alters the pulmonary microbiome, induces hippocampal damage, and NETs may act as a mediator between the lung and brain axes.},
}

@article {pmid40472561,
year = {2025},
author = {Lin, Z and Qiao, Y and Xu, K and Lu, L and Shu, QY and Tian, S},
title = {The endophytic fungus Serendipita indica reshapes rhizosphere soil microbiota to improve Salix suchowensis growth and phytoremediation.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138620},
doi = {10.1016/j.jhazmat.2025.138620},
pmid = {40472561},
issn = {1873-3336},
abstract = {Soil cadmium (Cd) contamination, a global issue threatening human health, can be mitigated through phytoremediation using plant growth-promoting microorganisms (PGPMs), which enhance heavy metal extraction. Endophyte Serendipita indica promotes plant growth and alleviates abiotic/biotic stress, but its role in reshaping rhizosphere microecology remains unclear. We combined in situ zymography, diffusive equilibration in thin films (DET), and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) to explore Cd rhizosphere processes. S. indica inoculation significantly increased stems and leaves biomass by 36.52 % and 31.63 %, respectively, and Cd accumulation by 44.30 % in stems and 33.17 % in leaves. DET and zymography mapping showed that S. indica inoculation reduced pH and enhanced enzyme activity in the rhizosphere. LA-ICP-MS mappings revealed that S. indica increased Cd concentration in the root-soil interface and enhanced Cd and phosphorus (P) bioavailability, promoting root uptake and transport to shoots. S. indica inoculation recruited a more complex and stable network, supporting willow growth and Cd absorption. Key strains like Gemmatimonas, Subgroup_10, and Sandaracinus facilitated organic matter degradation, releasing bioavailable P and Cd, thus enhancing the phytoremediation efficiency. In summary, a mutualistic system between S. indica and willow was established, enhancing Cd phytoremediation efficiency by altering rhizosphere microenvironment and microbiome.},
}

@article {pmid40472289,
year = {2025},
author = {Lim, LWZ and Toh, KY and Cook, AR and Lee, JWJ and Lim, JFY},
title = {Public knowledge, awareness and perception of gut microbiome and faecal microbiota transplantation in Singapore: a survey study.},
journal = {Singapore medical journal},
volume = {},
number = {},
pages = {},
pmid = {40472289},
issn = {2737-5935},
abstract = {INTRODUCTION: Despite the exponential increase in microbiome research, knowledge and beliefs about the gut microbiome and faecal microbiota transplantation (FMT) remain unclear. The aim of this study was to identify the extent of knowledge, awareness and perception among the general public regarding the gut microbiome and FMT.

METHODS: An online questionnaire on knowledge and beliefs about the gut microbiome and FMT was administered to 1831 participants. Data analysis software was used to generate descriptive statistics and explore associations between knowledge and sociodemographic variables.

RESULTS: Even though only 33% of participants had heard of the gut microbiome, more than 92% had consumed probiotic drinks or supplements. While 85% had not heard of the FMT procedure, 72% of respondents would consider having FMT to treat Clostridioides difficile infection (CDI). Willingness to receive FMT depended mainly on recommendation from healthcare providers (77%). Knowledge and awareness regarding the gut microbiome and FMT were relatively low, despite most participants having prior gut health-related behaviours.

CONCLUSION: This study identified the public's perceptions of FMT and the potential barriers to its uptake. Insights from the study highlight the need for health education to enhance acceptance of FMT and the importance of using information supported by medical professionals to immunise the public against poorly validated science.},
}

@article {pmid40472245,
year = {2025},
author = {Baeringsdottir, B and Haraldsson, A and Hrafnkelsson, B and Thors, V},
title = {Infant Antibiotic Exposure Is Associated With Increased Risk of Later Childhood Infections, Antibiotic Use and Asthma.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000004867},
pmid = {40472245},
issn = {1532-0987},
abstract = {BACKGROUND: Antimicrobials have saved millions of lives. Antibiotics are essential in treating infant infections, but may disrupt the gut microbiome and have adverse effects on later health.

METHODS: This population-based birth cohort study included full-term children born in Iceland from 2010 to 2019 with follow-up for 2-12 years. The cohort was divided into 4 groups according to antibiotic exposure; I: elective cesarean section, II: vaginal birth and maternal intrapartum antibiotics, III: vaginal birth and infants received antibiotics during the first week of life for >48 hours and IV: vaginal birth without antibiotic exposure. Rates of infections, antibiotic use and the risk of asthma later in childhood were calculated.

RESULTS: Of 43,600 children born in Iceland from 2010 to 2019, 22,393 were included. Group I had 1496 children, group II 3413, group III 356 and group IV 17,128 children. For all antibiotic exposure groups, the risk of infections and antibiotic use was significantly higher (20%-100%), with the largest effect observed for infants treated with antibiotics. This group also had a 2-fold risk of asthma diagnosis when compared with controls (odds ratio: 1.91, P < 0.05).

CONCLUSIONS: In this cohort study, children with early antibiotic exposure had higher rates of infections and antibiotic use later in childhood compared with controls. Diagnoses of asthma were significantly more common in children with early antibiotic exposure and this effect was most evident after the age of 8 years. The observed late side-effects of antibiotic use, possibly mediated through a disrupted microbiome, should promote a conservative approach to antibiotic treatment in young infants.},
}

@article {pmid40472200,
year = {2025},
author = {Hatch-McChesney, A and Suther, C and Thompson, LA and Radcliffe, PN and Cherian, RV and Liechty, ZS and Stamps, BW and Krieger, S and Nelman-Gonzalez, M and Crucian, B and Diak, D and Mehta, S and Goodson, MS and Barringer, N and Smith, TJ and Karl, JP},
title = {Sex Differences in Immune and Gut Microbiota Responses to Military Training.},
journal = {Medicine and science in sports and exercise},
volume = {},
number = {},
pages = {},
doi = {10.1249/MSS.0000000000003772},
pmid = {40472200},
issn = {1530-0315},
abstract = {PURPOSE: Military training includes multiple stressors that together may increase risk for illness by degrading immune function and altering gut microbiota. However, whether sex differences exist in those responses is undetermined. This study aimed to determine immune and gut microbiota responses during military training and identify sex differences in those responses.

METHODS: Seventy-two military cadets (33% female) participated in an arduous 17-day training event. Blood, saliva and stool were collected upon beginning (PRE) and completing (POST) training. Immune function was assessed by salivary secretory IgA (SIgA), latent virus reactivation, peripheral leukocyte distribution, circulating cytokines and mitogen-stimulated cytokine profiles. Gut microbiota composition was assessed by 16S rRNA amplicon sequencing.

RESULTS: Participants experienced a ~ 4% body weight loss and sex-independent increases in concentrations of cortisol, myoglobin, catecholamines and multiple cytokines. The granulocyte-to-lymphocyte ratio increased and SIgA decreased PRE to POST in males but not females (Pinteraction ≤ 0.02). Mitogen-stimulated cytokine profiles were generally reduced at POST versus PRE independent of sex. No differences in virus reactivation were observed. Sex differences in gut microbiota responses were limited to Bifidobacterium and Ruminococcus, which increased in males relative to females (log2 fold change (FC) = 2.0-2.4; qinteraction = 0.19). Independent of sex, 24 genera differed at POST versus PRE with Lactobacillus demonstrating the largest decrease (log2FC = -0.90; qtime = 0.02) and Veillonella the largest increase (log2FC = 1.09; qtime = 0.03). Multiple correlations between markers of stress, immune function and gut microbiota composition were observed (q ≤ 0.15).

CONCLUSIONS: Immune redistribution, leukocyte compromise and interrelated changes in gut microbiota composition were evident within this training environment. Those responses demonstrated associations with markers of stress severity but also sex differences suggesting a more pronounced depression of immune function in males.},
}

@article {pmid40472034,
year = {2025},
author = {Noack, C and Jenderny, S and Giez, C and Merza, O and Hofacker, LM and Wittlieb, J and Repnik, U and Bramkamp, M and Ochs, K and Bosch, TCG},
title = {Assembly of a functional neuronal circuit in embryos of an ancestral metazoan is influenced by temperature and the microbiome.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {23},
pages = {e2501225122},
doi = {10.1073/pnas.2501225122},
pmid = {40472034},
issn = {1091-6490},
support = {CRC 1182 C1; CRC 1461 A1//Deutsche Forschungsgemeinschaft (DFG)/ ; HMB//Canadian Institute for Advanced Research (ICRA)/ ; CRC 1461 A1//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {Animals ; *Microbiota/physiology ; *Hydra/embryology/microbiology/physiology ; *Neurons/physiology ; Temperature ; *Nerve Net/physiology/embryology ; Biological Evolution ; Embryo, Nonmammalian/physiology ; Gap Junctions/physiology ; },
abstract = {Understanding how neural populations emerge to give rise to behavior is a major goal in neuroscience. Here, we explore the self-assembly of neural circuits in Hydra, an organism with a simple nervous system but no centralized information processing, to enhance the understanding of nervous system evolution. We define self-assembly as spontaneous organization of neurons into functional circuits without requiring a prespecified structural template. In this context, the N4 neuronal circuit, which we have previously found to be particularly important in the feeding of the animal, develops in embryos through activity-driven self-assembly, a process in which intrinsic calcium activity drives connectivity and synchronization among spatially distributed neurons over time. Gap junctions and vesicle-mediated communication between neuronal and non-neuronal cells drive rapid assembly, with the embryo's prospective oral region exhibiting the highest neuronal density. An artificial electrical circuit-based model as a biophysically inspired simulation demonstrates dynamic increases in synchronization over time, along with predictions for selective dynamic adaptions of connections. Environmental factors, like temperature and an absent microbiome, modify neural architecture, suggesting the existence of a certain adaptability during neural development. We propose that these fundamental features originated in the last common bilaterian ancestor, supporting the hypothesis that the basic architecture of the nervous system is universal. Since in the natural habitat of Hydra both temperature fluctuations and changes in the microbiome can occur, our work not only illuminates a fundamental developmental process but also may guide environmental and evolutionary studies by explaining how organisms adapt to environmental variations.},
}

Animals
*Microbiota/physiology
*Hydra/embryology/microbiology/physiology
*Neurons/physiology
Temperature
*Nerve Net/physiology/embryology
Biological Evolution
Embryo, Nonmammalian/physiology
Gap Junctions/physiology

@article {pmid40472016,
year = {2025},
author = {MacIntosh, GH and Nuyens, AC and Vickery, JL and Berthold, A and Lloyd, VK},
title = {Epigenetic responses in Borrelia-infected Ixodes scapularis ticks: Over-expression of euchromatic histone lysine methyltransferase 2 and no change in DNA methylation.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0324546},
doi = {10.1371/journal.pone.0324546},
pmid = {40472016},
issn = {1932-6203},
mesh = {Animals ; *Ixodes/microbiology/genetics ; *DNA Methylation ; *Epigenesis, Genetic ; *Borrelia burgdorferi/physiology ; *Histone-Lysine N-Methyltransferase/genetics/metabolism ; Lyme Disease/microbiology ; },
abstract = {Borrelia burgdorferi, a tick-vectored spirochete bacteria best known for causing Lyme disease, has been found to induce physiological and behavioural changes in its tick vector that can increase tick fitness and its ability to transmit the bacteria. The mechanism by which this bacterium modulates these changes remains unknown. Epigenetics plays a central role in transducing external and internal microbiome environmental influences to the organism, so we investigated DNA methylation and the expression of a key histone modification enzyme in Borrelia-infected and uninfected Ixodes scapularis ticks. DNA methylation of the pericentromeric tandem repeats family, Ixodes scapularis Repeats (ISR), were assessed by methylated-DNA immunoprecipitation (MeDIP) followed by qPCR of the ISR regions. DNA methylation of the ISR sequences was found. The different repeats had different levels of DNA methylation, however, these levels were not significantly affected by the presence or absence of B. burgdorferi. The epigenetic regulator euchromatic histone lysine methyltransferase 2 (EHMT2) is recognized as having a key role in modulating the organismal stress response to infections. To assess EHMT2 transcription in Borrelia-infected and uninfected ticks, real-time reverse transcriptase PCR was performed. Uninfected ticks had over 800X lower EHMT2 expression than infected ticks. This study is among the first to identify a gene that may be involved in producing epigenetic differences in ticks depending on infection status and lays the groundwork for future epigenetic studies of I. scapularis in response to B. burgdorferi as well as other pathogens that these ticks transmit.},
}

Animals
*Ixodes/microbiology/genetics
*DNA Methylation
*Epigenesis, Genetic
*Borrelia burgdorferi/physiology
*Histone-Lysine N-Methyltransferase/genetics/metabolism
Lyme Disease/microbiology

@article {pmid40471941,
year = {2025},
author = {Ritz, T and Rosenkranz, MA and Celedón, JC and Davenport, PW and Djukanovic, R and Feldman, JM and Forsythe, P and Jajour, NN and Vercelli, D and von Leupoldt, A and Wright, RJ},
title = {Asthma: Biomedical and Psychobiological Perspectives for the Disease of the Year 2023.},
journal = {Biopsychosocial science and medicine},
volume = {},
number = {},
pages = {},
doi = {10.1097/PSY.0000000000001410},
pmid = {40471941},
issn = {2998-8756},
abstract = {Substantial knowledge about asthma has accumulated in past decades from biomedical and psychobiological research. This white paper reports on synergistic perspectives for these fields discussed at the first Annual Disease-A-Year Symposium of the American Psychosomatic Society. Progress has been made in identifying mechanical, cellular and molecular mechanisms of asthma and influences of psychosocial factors on development, pathophysiology, and management have been demonstrated. However, much remains to be learned about mechanisms of asthma development, in particular the role of genes and the microbiome, and their interaction with psychosocial factors. Additional psychobiological analysis of immunobiological pathways and pathophysiological features is also needed, as well as integration with asthma phenotypes. Although traditionally viewed as a peripheral disease of the airways, its effect on the central nervous system and cognition have begun to garner attention due to neuroscientific and technological advances. Brain-body interaction are also the focus of airway interoception research, with practical consequences for management of over- and underperception of airway obstruction. An integrative perspective on asthma recognizes societal factors that worsen and consolidate disparities in asthma outcomes and explores mechanisms of building resilience in patients from disadvantages communities. Biomedical treatment with novel monoclonal antibodies promises a personalized medicine approach, while improvements to asthma management trainings have increased disease control and quality of life. Psychobiological and mind-body interventions, such as exercise, breathing training, cognitive behavioral therapy, or meditation techniques, require further exploration in large-scale multicenter trials. Close interdisciplinary collaboration will bring the field closer to the ideal of a holistic biopsychosocial treatment of asthma.},
}

@article {pmid40471835,
year = {2025},
author = {Robinson, LA and Pascual, V},
title = {Recent insights into the role of innate immunity in lupus.},
journal = {Human molecular genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/hmg/ddaf066},
pmid = {40471835},
issn = {1460-2083},
support = {CORT P50AR070594/AR/NIAMS NIH HHS/United States ; //Center for Lupus Research (VP)/ ; U19 AI082715/AI/NIAID NIH HHS/United States ; },
abstract = {Systemic Lupus Erythematosus (SLE) is a complex autoimmune disorder characterized by loss of self-tolerance to nucleic acids, resulting in multisystem inflammation and organ damage. The genetic underpinning of SLE spans from common risk variants with modest effect sizes to rare monogenic mutations with high penetrance. Recent advances in next-generation sequencing and transcriptomic profiling have illuminated the central role of innate immune pathways in disease pathogenesis. This review synthesizes emerging evidence regarding innate immunity in SLE, with emphasis on toll-like receptor (TLR) signaling and regulatory mechanisms, NLRP3 inflammasome activation, myeloid cell dysregulation, and microbiome-immune interactions. Understanding these pathways provides a foundation for developing targeted therapeutics that may offer precision medicine approaches for this heterogeneous disease.},
}

@article {pmid40471540,
year = {2025},
author = {Zhang, Y and Zhang, K and Song, D and Yan, T and Ma, S and Liu, R and Jin, Y and Gong, H and Yang, L and Wang, X and Liu, S and Wang, C and Zhao, M},
title = {Combination of Rare Sugars L-arabinose, D-mannose, D-xylose, D-allulose, and D-tagatose Alleviates Cognitive Impairment in Mice with Type 2 Diabetes Mellitus.},
journal = {Molecular neurobiology},
volume = {},
number = {},
pages = {},
pmid = {40471540},
issn = {1559-1182},
support = {82071515//National Natural Science Foundation of China/ ; },
abstract = {Herein, the study was conducted to elucidate the impact of a rare sugar complex (RSC) containing L-arabinose, D-mannose, D-xylose, D-allulose, and D-tagatose on cognitive impairment in a Type 2 diabetes mellitus (T2DM) mouse model. Specifically, a diabetes model was established by administering a high-fat diet (HFD) followed by streptozotocin injection. Behavioral performance in T2DM mice was assessed using multiple behavioral tests, including the Morris water maze, Y maze, novel object recognition test, and novel location recognition test. Neuronal damage in the hippocampal region was detected through hematoxylin and eosin staining. Superoxide dismutase (SOD) and malondialdehyde (MDA) constituted key biomarkers for assessing oxidative stress, with SOD indicating antioxidant capacity and MDA reflecting lipid peroxidation. Both were quantified via enzyme-linked immunosorbent assay. Additionally, the types and richness of microorganisms in the feces of each group of mice were analyzed through 16S sequencing of gut microbiota. Behavioral assays demonstrated that T2DM mice exhibited learning and memory impairments, which were notably mitigated by the administration of RSC. SOD activity decreased significantly, whereas MDA levels increased substantially. HE staining revealed that RSC effectively suppressed hippocampal cell apoptosis in T2DM mice. Furthermore, RSC treatment restored the diversity and abundance of gut microbiota in T2DM mice. Collectively, these findings suggest that RSC alleviates cognitive impairment in T2DM mice by reducing cerebral oxidative stress and modulating the intestinal microbiome composition.},
}

@article {pmid40471453,
year = {2025},
author = {Birkeland, E and Bamigbetan, WA and Molven, KD and Thorsby, PM and Gulseth, HL and Aas, AM and Dahl, C},
title = {Can supplements with prebiotic fibres positively influence bone health in type 2 diabetes? Insights from a randomised controlled crossover trial.},
journal = {Archives of osteoporosis},
volume = {20},
number = {1},
pages = {71},
pmid = {40471453},
issn = {1862-3514},
support = {2013-2-267//The DAM Foundation/ ; 36660//Diabetesforbundet/ ; 36660//Mills DA/ ; },
mesh = {Humans ; *Prebiotics/administration & dosage ; *Diabetes Mellitus, Type 2/blood/physiopathology ; Cross-Over Studies ; Male ; Female ; Middle Aged ; Aged ; Double-Blind Method ; *Dietary Supplements ; Calcium/blood ; Vitamin D/blood/analogs & derivatives ; Magnesium/blood ; Bone Remodeling/drug effects ; Biomarkers/blood ; Inulin/administration & dosage ; Gastrointestinal Microbiome ; Fructans ; Collagen Type I/blood ; Procollagen/blood ; Peptides/blood ; Peptide Fragments/blood ; },
abstract = {UNLABELLED: Inulin-type fructans did not significantly improve serum levels of calcium, magnesium, vitamin D, or bone turnover markers in people with type 2 diabetes (T2D). However, interactions between gut microbiota and bone health were suggested, indicating the need for further research in this population.

BACKGROUND: Evidence suggests that a healthy gut microbiome benefits bone health, especially in immunocompromised populations like the elderly and people with T2D.

OBJECTIVE: We investigated the effect of prebiotics (inulin-type fructans) on serum concentrations of calcium, magnesium, 25(OH) vitamin D, and the bone turnover markers N-terminal propeptide of type 1 collagen (P1NP), and C-terminal telopeptide of type 1 collagen (CTX-1) in people with T2D.

DESIGN: Participants (29) were treated for 6 weeks with 16 g inulin-type fructans and 16 g control supplement (maltodextrin) in randomised and double-blind crossover design, with a 4-week washout between treatments.

RESULTS: Compared to the control, inulin-type fructans did not significantly affect serum concentrations (mean ± SEM) of calcium (0.05 ± 0.02 mmol/L vs. 0.02 ± 0.03 mmol/L, p = 0.324), magnesium (0.02 ± 0.01 mmol/L vs. 0.00 ± 0.01 mmol/L, p = 0.352), 25(OH) vitamin D (-3.60 ± 1.94 nmol/L vs. -2.00 ± 1.97 nmol/L, P = 0.564), P1NP (0.81 ± 0.95 ug/L vs. -0.89 ± 0.97 ug/L, p = 0.210), or CTX-1 (-0.01 ± 0.01 ug/L vs. 0.00 ± 0.01 ug/L, p = 0.438). However, post hoc analyses of correlations between changes support that cross-talk between the human host and gut microbiota may influence bone health in this population.

CONCLUSION: This study does not support that inulin-type fructans may improve serum levels of calcium, magnesium, or 25(OH) vitamin D, nor that they affect bone turnover markers in people with T2D over 6 weeks. Interactions between microbiota and bone health in this population warrants further investigations. The trial is registered at clinicaltrials.gov (NCT02569684).},
}

Humans
*Prebiotics/administration & dosage
*Diabetes Mellitus, Type 2/blood/physiopathology
Cross-Over Studies
Male
Female
Middle Aged
Aged
Double-Blind Method
*Dietary Supplements
Calcium/blood
Vitamin D/blood/analogs & derivatives
Magnesium/blood
Bone Remodeling/drug effects
Biomarkers/blood
Inulin/administration & dosage
Gastrointestinal Microbiome
Fructans
Collagen Type I/blood
Procollagen/blood
Peptides/blood
Peptide Fragments/blood

@article {pmid40471139,
year = {2025},
author = {Gawish, R and Varada, R and Deckert, F and Hladik, A and Steinbichl, L and Cimatti, L and Milanovic, K and Jain, M and Torgasheva, N and Tanzer, A and De Paepe, K and Van de Wiele, T and Hausmann, B and Lang, M and Pechhacker, M and Ibrahim, N and De Vries, I and Brostjan, C and Sixt, M and Gasche, C and Boon, L and Berry, D and Jantsch, MF and Pereira, FC and Vesely, C},
title = {Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis.},
journal = {The Journal of experimental medicine},
volume = {222},
number = {9},
pages = {},
doi = {10.1084/jem.20240109},
pmid = {40471139},
issn = {1540-9538},
support = {57-B28//Austrian Science Fund/ ; V 1025-B//Austrian Science Fund/ ; DOC32-B28//Austrian Science Fund/ ; F8007//Austrian Science Fund/ ; P32678//Austrian Science Fund/ ; //Medical University of Vienna/ ; },
mesh = {*Filamins/genetics/metabolism ; Animals ; *Myeloid Cells/metabolism/pathology ; Humans ; *Colitis/genetics/pathology/prevention & control ; *Inflammation/pathology/genetics ; Mice ; Mice, Inbred C57BL ; Neutrophils/metabolism ; *RNA Editing ; Macrophages/metabolism ; Male ; },
abstract = {Patho-mechanistic origins of ulcerative colitis are still poorly understood. The actin cross-linker filamin A (FLNA) impacts cellular responses through interaction with cytosolic proteins. Posttranscriptional A-to-I editing generates two forms of FLNA: genome-encoded FLNAQ and FLNAR. FLNA is edited in colon fibroblasts, smooth muscle cells, and endothelial cells. We found that the FLNA editing status determines colitis severity. Editing was highest in healthy colons and reduced during murine and human colitis. Mice that exclusively express FLNAR were highly resistant to DSS-induced colitis, whereas fully FLNAQ animals developed severe inflammation. While the genetic induction of FLNA editing influenced transcriptional states of structural cells and microbiome composition, we found that FLNAR exerts protection specifically via myeloid cells, which are physiologically unedited. Introducing fixed FLNAR did not hamper cell migration but reduced macrophage inflammation and rendered neutrophils less prone to NETosis. Thus, loss of FLNA editing correlates with colitis severity, and targeted editing of myeloid cells serves as a novel therapeutic approach in intestinal inflammation.},
}

*Filamins/genetics/metabolism
Animals
*Myeloid Cells/metabolism/pathology
Humans
*Colitis/genetics/pathology/prevention & control
*Inflammation/pathology/genetics
Mice
Mice, Inbred C57BL
Neutrophils/metabolism
*RNA Editing
Macrophages/metabolism
Male

@article {pmid40470946,
year = {2025},
author = {Wei, Y and Jia, W and Sun, Y and Zhang, T and Miao, H and Wu, Z and Dong, R and Ning, F and Kim, WJ},
title = {Investigating the immunomodulatory effects of honeybee venom peptide apamin in Drosophila platforms.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0013125},
doi = {10.1128/iai.00131-25},
pmid = {40470946},
issn = {1098-5522},
abstract = {Apamin, an 18-amino-acid honeybee venom peptide, although traditionally recognized for its neurotoxic effects, demonstrates potent antimicrobial properties in our research when genetically expressed in Drosophila. This antimicrobial efficacy is independent of its disulfide bonds and is enhanced when the peptide is membrane-tethered. Apamin selectively inhibits pathogenic bacteria, such as Pseudomonas aeruginosa, Enterococcus faecalis, and Escherichia coli, while promoting beneficial bacteria like Lactobacillus plantarum, thereby improving the gut microbiome. This gut-localized antimicrobial activity is associated with increased intestinal stem cell proliferation, midgut acidification, and enteroendocrine cell calcium signaling. Furthermore, apamin's antimicrobial function relies on specific peptidoglycan recognition proteins, particularly PGRP-LA and PGRP-SCs. Apamin expression alone is sufficient to restore the integrity of the gut barrier compromised by stressful conditions. Ultimately, apamin supplementation enhances honeybee gut health in the presence of ingested bacteria. The expression of other honeybee antimicrobial peptides also significantly reduces bacterial infection in flies. Overall, our study provides a comprehensive understanding of honeybee venom peptides and antimicrobial peptides functions, utilizing the Drosophila model system to unravel their mechanisms of action and therapeutic potential.},
}

@article {pmid40470930,
year = {2025},
author = {Ekregbesi, P and Seibert, B and Parish, MA and Flores-Garcia, Y and Creisher, PS and Hoffmann, JP and Liu, JA and Brayton, C and Zavala, F and Klein, SL},
title = {Multi-system dysregulation in placental malaria contributes to adverse perinatal outcomes in mice.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0002125},
doi = {10.1128/iai.00021-25},
pmid = {40470930},
issn = {1098-5522},
abstract = {Sequestration of Plasmodium parasites in the placental vasculature contributes to increased morbidity and mortality in pregnant compared to non-pregnant patients in malaria-endemic regions. In this study, outbred pregnant CD1 mice with semi-allogeneic fetuses were infected with transgenic Plasmodium berghei or mock inoculated by mosquito bite at either embryonic day (E)6 (first trimester-equivalent) or 10 (second trimester-equivalent) and were compared to non-pregnant females. P. berghei-infected mosquitoes had greater biting avidity for E10 dams than uninfected mosquitoes, which was not apparent for E6 dams nor non-pregnant females. Infected E10 dams had greater numbers of parasites than E6 dams in the uterus and spleen, but not in the blood or liver. While parasites were found in placentas, no parasites were present in fetuses. Maternal infection at E6 caused greater maternal morbidity, with greater rates of fetal reabsorption and stillbirths than at E10. Infection at E10 caused adverse offspring outcomes, including growth restriction. To identify possible mechanisms of adverse offspring outcomes, E10 dams were euthanized during peak parasitemia (8 days postinfection [dpi]), and outcomes were compared to mock-infected dams. P. berghei caused significant systemic maternal immune activation with elevated circulating lymphocytes, eosinophils, and neutrophils and splenic cytokine concentrations. P. berghei infection at E10 increased corticosterone and decreased progesterone concentrations, which could contribute to adverse perinatal outcomes through immunomodulation. There were limited changes in the maternal fecal microbiome after P. berghei infection. Mosquito bite infection of outbred dams with P. berghei causes placental malaria and provides a novel, tractable model to investigate therapeutic treatments.},
}

@article {pmid40470429,
year = {2025},
author = {Ahmad, OM and Rukh, S and Dos Santos Pereira, S and Saran, A and Chandran, VI and Muneeb, A and Banderas Echeverry, WM and Shoyoye, M and Akintunde, DM and Hassan, D and Morani, Z and Masood, L},
title = {A Comprehensive Review of the Role of Virulence Factors in Enteropathogenic Escherichia coli-Induced Intestinal Injury.},
journal = {Cureus},
volume = {17},
number = {5},
pages = {e83475},
pmid = {40470429},
issn = {2168-8184},
abstract = {Escherichia coli (E. coli) is a rod-shaped gram-negative bacterium that includes the diarrheagenic strains, an identical group of intestinal pathogens.E. coli diarrhea is transmitted through the feco-oral route, through contaminated food and water. Enteropathogenic E. coli (EPEC) is one of the leading causes of diarrhea in the pediatric age group in developing and developed countries. Depending on the absence or presence of E. coli adherence factor plasmids, they are classified as typical or atypical isolates. The distinguishing feature of EPEC's pathology is the attaching and effacing lesions, which facilitate localized damage by tightly adhering to intestinal epithelial cells, disarranging their surfaces, and effacing microvilli. Typical EPEC possess the locus of enterocyte effacement (LEE), a pathogenicity island, encoding adherence factors, including the Type III Secretion System (T3SS), a needle-like structure injecting effector proteins into host cells. EPEC also have other effector genes like cif or nleC encoded by non-LEE pathogenicity islands, which enable destruction of tight junctions in the host cell. Another key virulence factor is bundle-forming pili (BFP), which aids in the first attachment to enterocytes. Methods like quantitative PCR exist to diagnose EPEC accurately. As of today, no licensed vaccine exists to prevent EPEC infections. Virulence factors for attachment, such as bfpA and intimin, and immunogenic carriers can be potential candidates for vaccine development. Moreover, studies are required to better understand the interaction of EPECwith the intestinal microbiome and immune evasion strategies. This article is aimed at providing a comprehensive review of the epidemiology, transmission, virulence factors, challenges in studying EPEC virulence factors, pathogenesis, host-pathogen interaction, mechanism of intestinal injury, diagnosis, treatment, antibiotic resistance, and vaccination strategy for EPEC, and future research implications. We conducted a comprehensive literature search using credible sources such as PubMed, Google Scholar, and Scopus. We refined our keywords, applied database filters, and assessed citations in the included studies. No meta-analysis, statistical aggregation, or formal evaluation of risk bias was carried out as this review consolidates the literature narratively. High-quality English articles published in reputable peer-reviewed journals from 2010 to 2025 were analyzed, and their findings have been summarized in this comprehensive review.},
}

@article {pmid40470262,
year = {2025},
author = {Fu, F and Yu, Y and Wang, B and Zhao, X and Wang, N and Yin, J and Wu, K and Zhou, Q},
title = {Prostate and urinary microbiomes in prostate cancer development: focus on Cutibacterium acnes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1562729},
pmid = {40470262},
issn = {2235-2988},
mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/pathology ; *Microbiota ; *Prostate/microbiology/pathology ; *Propionibacteriaceae/isolation & purification ; *Urine/microbiology ; },
abstract = {Prostate cancer (PCa) is one of the most prevalent malignancies among men, with its incidence steadily increasing worldwide. Recent advances in microbiome research have opened new avenues for understanding and treating PCa; however, studies focusing specifically on the prostate tissue microbiome remain limited. Evidence suggests that the microbial communities within PCa tissues exhibit significant diversity and regional variability, with certain bacteria potentially contributing to PCa initiation and progression through chronic inflammation. The prostate microbiome comprises not only bacteria but also viruses, fungi, and parasites, and its diversity is influenced by a complex interplay of genetic, environmental, and lifestyle factors. Methodological limitations and sample contamination further complicate the interpretation of microbiome data. The urinary microbiome is similarly diverse and shaped by multiple overlapping influences. Although urine, prostatic fluid, and prostate tissue are anatomically and functionally connected, whether urine and prostatic fluid can accurately reflect the prostate tissue microbiome remains to be conclusively determined. Among the microorganisms detected, Cutibacterium acnes is frequently identified in prostate tissue, urine, and prostatic fluid from PCa patients. This bacterium is known to elicit inflammatory responses through various pathways, potentially impacting tumorigenesis and cancer progression. Nevertheless, findings across studies remain inconsistent. Further research is necessary to elucidate the underlying mechanisms by which the microbiome influences PCa. Such efforts may offer novel insights and strategies for the diagnosis, treatment, and prevention of this disease.},
}

Humans
Male
*Prostatic Neoplasms/microbiology/pathology
*Microbiota
*Prostate/microbiology/pathology
*Propionibacteriaceae/isolation & purification
*Urine/microbiology

@article {pmid40470258,
year = {2025},
author = {Demirci, M and Gadhave, K},
title = {Editorial: Human microbiome and COVID-19.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1613825},
pmid = {40470258},
issn = {2235-2988},
}

@article {pmid40470050,
year = {2025},
author = {Issilbayeva, A and Sergazy, S and Zhashkeyev, A and Gulyayev, A and Kozhakhmetov, S and Shulgau, Z and Nurgaziyev, M and Nurgaziyeva, A and Zhetkenev, S and Mukhanbetzhanov, N and Jarmukhanov, Z and Mukhanbetzhanova, Z and Vinogradova, E and Zhumadilov, Z and Kushugulova, A and Aljofan, M},
title = {Polyphenol-mediated microbiome modulation in STEMI patients: a pilot study.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1522373},
pmid = {40470050},
issn = {2296-858X},
abstract = {INTRODUCTION: This study investigates the effects of polyphenol supplementation on gut microbiome composition and cardiovascular health in patients with ST-segment elevation myocardial infarction (STEMI).

METHODS: Double-blind randomized control trial where participants received either polyphenol supplementation or placebo for 3 months, after which composition of the gut microbiome; clinical and laboratory parameters, including TMAO levels and oxidative stress levels, were assessed.

RESULTS: The stable TMAO levels (from 0.5 [0.2-0.9] to 0.4 [0.3-0.9] μmol, p > 0.05) were observed in the polyphenol group, compared to the increase observed in the placebo group (from 0.5 [0.3-0.6] to 0.7 [0.5-1.4] μmol, p < 0.001). Polyphenol supplementation significantly decreased the Firmicutes/Bacteroidetes ratio (p = 0.04) and increased beneficial bacteria such as Roseburia (p = 0.01), Agathobaculum sp. (p = 0.004), Alistipes finegoldii (p = 0.04) and Sellimonas (p = 0.002). Predicted metabolic pathways analysis supports potential mechanisms linking polyphenol intake to microbiome modulation and TMAO regulation.

CONCLUSION: Our findings demonstrate that polyphenol supplementation maintains stable TMAO levels by restructuring gut microbiome composition in STEMI patients, evidenced by a more focused microbiome with a significant increase in beneficial butyrate-producing bacteria (Roseburia, Agathobaculum sp., Alistipes finegoldii, and Sellimonas) and a decreased Firmicutes/Bacteroidetes ratio, suggesting microbiome-mediated cardioprotective effects. While promising,l our preliminary findings require further studies with larger cohorts and more advanced sequencing methods to establish their significance for cardiovascular health.

CLINICAL TRIAL REGISTRATION: ClinicalTrial.gov, identfier: NCT06573892.},
}

@article {pmid40469771,
year = {2025},
author = {Muthumula, CMR and Yanamadala, Y and Gokulan, K and Karn, K and Cunny, H and Sutherland, V and Santos, JH and Khare, S},
title = {Effect of in utero and lactational exposure to antiretroviral therapy on the gut microbial composition and metabolic function in aged rat offspring.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {250},
number = {},
pages = {10468},
pmid = {40469771},
issn = {1535-3699},
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/drug effects ; Pregnancy ; Male ; *Prenatal Exposure Delayed Effects/microbiology ; *Lactation/drug effects ; Rats ; Fatty Acids, Volatile/metabolism ; *Anti-Retroviral Agents/adverse effects/pharmacology ; Feces/microbiology ; },
abstract = {Despite the highly effective impact of antiretroviral therapy (ART) in reducing mother-to-child transmission of human immunodeficiency virus (HIV), there are concerns of long-term impacts of ART on the health of the offspring. The implications of perinatal exposure to antiviral drugs on the gut bacterial population and metabolic function in the offspring is unclear but may influence health outcomes given the various reported effects of the microbiome in human health. This study aims to gain insight into the potential effect of in utero and lactational exposure to ART on gut microbiota populations and short-chain fatty acids (SCFAs) production in aged rat offspring. Pregnant rats were administered a combination of antiretroviral drugs (abacavir/dolutegravir/lamivudine) at two different dose levels during gestation and throughout lactation, and the fecal bacterial abundance and SCFA levels of the offspring were analyzed when they reached 12 months of age. Our results showed dose-dependent and sex-based differences in fecal microbial abundance at various taxonomic levels. Specifically, we found a decline in Firmicutes in males, and an increase in Actinobacteria among males and females. Furthermore, a sex-specific distribution reorganization of Lactobacillus, Bifidobacterium, and Akkermansia was identified. No significant difference in the concentration of prominent SCFAs and IgA levels were identified. These findings provide preliminary information indicating the need to evaluate perinatal effects of ART more comprehensively on the gut bacterial and metabolic function in future studies, and their potential role in offspring health outcomes.},
}

Animals
Female
*Gastrointestinal Microbiome/drug effects
Pregnancy
Male
*Prenatal Exposure Delayed Effects/microbiology
*Lactation/drug effects
Rats
Fatty Acids, Volatile/metabolism
*Anti-Retroviral Agents/adverse effects/pharmacology
Feces/microbiology

@article {pmid40469741,
year = {2025},
author = {Qi, JQ and Yuan, HY and Sun, SC and Zama, EF and Tao, BX and Liu, J and Zhang, BH},
title = {Biochar amendment alters rare microbial taxa and enhances wheat growth in alkaline farmland: insights into soil microbiome dynamics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1563712},
pmid = {40469741},
issn = {1664-302X},
abstract = {INTRODUCTION: Biochar is recognized as a promising soil amendment for maintaining soil fertility and improving soil conditions. Alkaline farmland is widely distributed globally. Soil microbial taxa, including rare, intermediate, and abundant bacteria, fungi, protists, and phoD-harboring microbes, play essential roles in carbon, nitrogen, and phosphorus cycling. However, the impacts of biochar on the community composition of these taxa in alkaline farmland are not well understood. Gaining insights into how the soil microbiome responds to biochar application and its association with crop biomass is crucial for sustainable agriculture. In particular, the responses of rare microbial communities, such as rare protists and phoD-harboring microbial taxa, to biochar and their relationship with crop biomass remain largely unexplored.

METHODS: In this study, topsoil (0-10 cm) samples were collected from a three-year field experiment in a wheat (Triticum aestivum cv. Jimai 22)-maize (Zea mays cv. Jiyuan 169) rotational cropping system. The experiment included treatments with and without biochar application (CK). Gene abundance of bacterial 16S rRNA and phoD, a gene encoding an alkaline phosphatase involved in phosphorus cycling, was quantified using quantitative polymerase chain reaction (qPCR). The compositions and diversities of bacterial, fungal, protistan, and phoD-harboring microbial communities were analyzed by Illumina MiSeq sequencing.

RESULTS: Biochar application significantly reduced soil total phosphorus (TP) and ammonium nitrogen (NH4 [+]-N) contents. It increased soil N:P ratios by 19.63%, 2.80%, 23.36%, and 27.10% in B0.5, B1.0, B1.5, and B2.0 treatments, respectively. Soil dissolved organic carbon (DOC) positively correlated with bacterial 16S rRNA gene abundance, while total nitrogen (TN) linked to the ratio of phoD to bacterial 16S rRNA gene abundance and rare protistan taxa. In terms of crop yield, the B1.5 treatment (3.42 t ha[-1]) increased wheat yield by 35% compared to the CK treatment. Mantel test and random forest analyses indicated that rare phoD-harboring, protistan, and fungal communities significantly contributed to wheat growth.

DISCUSSION: This study offers valuable insights into the effects of biochar on soil microbiomes, especially the responses of abundant, intermediate, and rare taxa. The changes in soil nutrient contents and the correlations between soil properties and microbial communities suggest that biochar can modify the soil environment and microbial structure. The significant contribution of rare microbial communities to wheat growth emphasizes their importance in maintaining agricultural ecosystem health and ensuring sustainable ecosystem services. These findings can guide the rational application of biochar in alkaline farmland to promote sustainable agriculture.},
}

@article {pmid40469735,
year = {2025},
author = {Heisel, T and Gonia, S and Dillon, A and Hoops, SL and Al-Ghalith, GA and Gohl, D and Mukhopadhyay, S and Puopolo, K and Kennedy, P and Sadowsky, MJ and Knights, D and Johnson, AJ and Gerber, JS and Gale, CA},
title = {Gut mycobiome maturation and its determinants during early childhood: a comparison of ITS2 amplicon and shotgun metagenomic sequencing approaches.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1539750},
pmid = {40469735},
issn = {1664-302X},
abstract = {INTRODUCTION: Microbial colonization of the gut in early life is important for the development of metabolism, immunity, and the brain. Fungi and bacteria both colonize the human infant gut. The relatively smaller contribution of fungi to the gut microbiome, as compared to bacteria, has posed technical challenges for the precise characterization of fungal communities (mycobiomes) and limited the ability to longitudinally examine mycobiome development.

BACKGROUND: The aims of this study were to (1) characterize mycobiome maturation and identify clinical determinants of mycobiome compositional variation during the first 2 years of life and (2) compare two sequencing approaches (ITS2 amplicon and whole genome metagenomics) for characterizing mycobiome maturational features. Longitudinal fecal samples and associated clinical metadata were obtained from subjects enrolled as part of the MAGIC (Microbiome, Antibiotics and Growth Infant Cohort) study.

RESULTS: Overall, fungal richness increased and mycobiome composition changed in a similar ordered pattern during the first 2 years of life utilizing either amplicon or metagenomic sequencing approaches. Less resolution of taxa to species and genera levels was observed for the metagenomic dataset. The predominant taxa identified by both sequencing approaches, Candida albicans, Saccharomyces/S. cerevisiae, and Malassezia restricta, each exhibited similar dynamics in abundances and prevalences over the first 2 years of life, irrespective of sequencing approach. Antibiotic exposure and breastfeeding status contributed to time-specific mycobiome compositional variation, results that were consistent for both types of sequence datasets. Candida albicans exhibited altered abundance dynamics in association with perinatal antibiotic exposure and birth mode for both sequencing approaches. Post hoc analyses suggested that the birth mode association could be driven by exposure to perinatal antibiotics in children delivered by cesarean section rather than by birth mode itself.

DISCUSSION: In summary, amplicon and metagenomic sequencing approaches provide generally similar results with respect to mycobiome maturational dynamics and the contribution of clinical variables to variation. Differences in taxa identification by the two approaches likely due to sequence database differences, primer/genome sequence variation, and/or sequencing depth should be taken into consideration.},
}

@article {pmid40469729,
year = {2025},
author = {Sakha, M and Gweyi-Onyango, JP and Masso, C and Baijukya, FP},
title = {Diversity, characteristics, and abundance of native arbuscular mycorrhizal fungi in the semi-arid lands of Eastern Kenya.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1582476},
pmid = {40469729},
issn = {1664-302X},
abstract = {Elucidating the diversity of native arbuscular mycorrhizal (AM) fungi is essential for the sustainable management of semi-arid land ecosystems. This is because they significantly improve plant nutrient uptake and decrease the stress caused by biotic and abiotic factors. In this study, we examined the AM fungal communities and the key drivers influencing their diversity and occurrence in the smallholder farming systems of Eastern Kenya. Soils samples were collected from 34 diverse agricultural fields and AM fungal spores were extracted using wet-sieving and decantation techniques. The spores were quantified, and AM fungal communities were identified based on their morphological characteristics. Statistical data analyses, including relative abundance, the Shannon-Wiener index, analysis of variance (ANOVA), and principal component analysis (PCA), were performed using R software 4.4.0. The results revealed that two AM fungal families dominated the agricultural fields, namely Gigasporaceae (61.0%) and Acaulosporaceae (39.0%). These fungal families comprised a total of five genera, with the following relative abundances: Acaulospora (39.0%), Gigaspora (35.05%), Scutellospora (23.92%), Dentiscutata (1.32%), and Rococetra (0.72%). The AM fungal morpho-species were ranked from 1 to 26 across the five genera. Acaulospora denticulata ranked the highest, with a proportion of 25.19%. The Shannon-Wiener diversity index revealed a higher diversity of AM fungi in agricultural fields with greater spore richness. The PCA showed that the composition of AM fungal communities was strongly related to soil physiochemical characteristics. Dryland farming systems also played a role in AM fungal composition. Overall, the distribution of AM fungal communities across the agricultural fields was lower, implying the need to adopt sustainable dryland farming systems to enhance native AM fungal communities and support the development of context-specific biofertilizers.},
}

@article {pmid40469726,
year = {2025},
author = {Wang, N and Li, X and Weng, H and Zhang, Y and Li, Q and Luo, X and Chen, Y and Dong, Y},
title = {A bibliometric study of global trends in diabetic nephropathy and intestinal flora research.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1577703},
pmid = {40469726},
issn = {1664-302X},
abstract = {BACKGROUND: Diabetic nephropathy is chronic kidney damage caused by diabetes and is one of the most common microvascular complications of diabetes. In diabetic patients, prolonged hyperglycemia leads to progressive damage to kidney structure and function. With the increasing incidence of diabetes, the number of patients with Diabetic Nephropathy is also increasing year by year. At present, there is no drug to cure Diabetic Nephropathy. More and more evidence shows that the development of Diabetic Nephropathy is inseparable from the intestinal axis, and the disorder of intestinal flora is related to the progress of diabetes. Maybe we can explore the pathogenesis of Diabetic Nephropathy from the intestinal flora and find new methods to treat Diabetic Nephropathy.

METHODS: This article uses CiteSpace VOSviewer and Bibliometrix statistical software explore research hotspots and trends of intestinal flora and Diabetic Nephropathy. The Web of Science Core Collection (WoSCC) was searched for literature from database establishment to December 4, 2024, and ultimately 238 articles were included for quantitative analysis.

RESULTS: The number of publications has been increasing year by year, reaching its peak in 2024. The high-yield institution is Beijing University of Chinese Medicine, and the most productive country is China. Zhang Yi ranks first in the number of publications by the author. After removing the theme word, inflammation appears the most frequently, followed by oxidative stress. The outbreak hotspots are mainly concentrated in uremic toxin, short chain fatty acid, soy milk, aryl hydrocarbon receptor.

CONCLUSION: The exploration of the mechanism of action and therapeutic or adjuvant therapeutic targets of the gut microbiome and its metabolites in DN patients may become a research hotspot in the future direction of DN and gut microbiome. Inflammation, oxidative stress, and the production of urinary toxins in DN patients are the directions for researchers to explore the mechanisms related to DN patients and gut microbiome. Aryl hydrocarbon receptor (AhR), Short-chain fatty acids (SCFAs), Traditional Chinese medicine and soy milk provide researchers with treatment ideas for diabetic nephropathy. Exploring the specific mechanisms and therapeutic effects of DN and gut microbiome requires cohort studies and clinical trials for validation.},
}

@article {pmid40469724,
year = {2025},
author = {Zhu, G and Song, H and Duan, M and Wang, J and Luo, J and Yang, S and Wu, F and Jiang, J and Chen, J and Tang, W},
title = {Dietary preferences affect the gut microbiota of three snake species (Squamata: Colubridae).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1559646},
pmid = {40469724},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut microbiota is an emerging frontier in animal research, and researchers are increasingly transparent about its importance to animal health. Reptiles, particularly snakes, have not received the same attention given to other vertebrates, and the composition of their wild gut microbiome remains understudied.

METHODS: In this study, the HiSeq high-throughput sequencing platform was used to sequence and analyze the 16S rRNA V4 region of the gut microbiota of three species (Gonyosoma coeruleum, Rhabdophis pentasupralabralis, Rhabdophis tigrinus).

RESULTS: This study investigated alpha diversity analysis and showed that the gut microbiota richness of RP was significantly higher than that of the other two snakes. The dominant genus of Gonyosoma coeruleum (GC) and Rhabdophis tigrinus (RT) is Cetobacterium, while Enterobacteriaceae; g_uncultured is the dominant genus of Rhabdophis pentasupralabralis (RP). Tree clustering based on Bray-Curtis distances and Jaccard similarity coefficients indicated that the gut microbiota composition of RP and RT was more similar. The unique diet of RP promotes a diverse, competitive gut microbiota, while GC and RT displayed more stable networks linked to shared dietary habits. The functional heat map showed that the predicted functions of the gut microbes of the three snake species were different. These findings suggest that dietary preferences exert a stronger influence on gut microbial composition and function than host genetic background, and distantly related species with similar diets exhibit convergent gut microbiota characteristics.},
}

@article {pmid40469670,
year = {2025},
author = {Lopez Leyva, L and Gonzalez, E and Maurice, CF and Koski, KG},
title = {Milk mineral composition is strongly associated with the human milk microbiome.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1550292},
pmid = {40469670},
issn = {2296-861X},
abstract = {INTRODUCTION: Associations between maternal mineral intake, human milk mineral concentrations, and their interactions with the milk microbiota remain understudied, especially in low- and middle-income countries. To understand potential interactions and gain insight into milk composition dynamics, we explored associations of milk mineral concentrations with maternal mineral intakes and the human milk microbiome in an indigenous Guatemalan community.

METHODS: In this cross-sectional study, milk samples were collected from 77 Mam-Mayan mothers and classified into early and established lactation. Concentrations of 9 milk minerals were analyzed, and maternal dietary intake was obtained from two 24-h recalls. Microbiome diversity was assessed by 16S rRNA gene sequencing (V5-V6 region). DESeq2 was used for differential abundance analysis. PCA and Spearman's rank correlation explored relationships among milk minerals, maternal mineral intake, and differentially abundant microbial taxa; results with FDR-adjusted p-values < 0.1 were retained.

RESULTS: Our multifactorial analysis revealed strong associations between milk minerals and the milk microbiome and weak associations with maternal intake. Several maternal intakes (Ca, Se, K, Fe, Mn) and milk mineral concentrations (Ca, Se, K, Mg, Na) were below reference values. In early lactation, milk Fe, Mn, Se, and Cu correlated with differentially abundant taxa, while in established lactation, Fe, Mn, Se, Ca, and Na were correlated. Fe and Mn accounted for 64% of bacterial associations in early lactation and 75% in established lactation. These minerals were correlated with Pseudomonadota (early), Actinomycetota (established), and Bacillota (both), but all species were unique to each stage.

CONCLUSION: Our findings reveal a complex interplay between milk minerals and the microbiome. Iron, manganese, and selenium were consistently associated with milk bacteria across lactation stages. These correlations may reflect microbial responses to mineral availability. Further longitudinal studies with larger samples are needed to clarify how this interaction influences mineral bioavailability and infant growth.},
}

@article {pmid40469523,
year = {2025},
author = {Wang, YC and Wang, S and Lv, YH and Wang, C},
title = {QSCNAS: A platform for quorum sensing and quenching bacteria analysis in global wastewater treatment plants.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70026},
pmid = {40469523},
issn = {2770-596X},
abstract = {This study identifies the potential quorum sensing (QS) bacteria in wastewater treatment plants (WWTPs) and constructs a QS communication network through the establishment of a local QS bacterial database with six languages and the analysis of over 1000 activated sludge microbiome samples collected from 269 WWTPs. The results not only advance the understanding of bacterial communication in WWTPs but also provide a valuable tool for developing regulatory strategies to optimize the functionality of these vital ecosystems.},
}

@article {pmid40469522,
year = {2025},
author = {Wen, T and Liu, YX and Liu, L and Niu, G and Ding, Z and Teng, X and Ma, J and Liu, Y and Yang, S and Xie, P and Zhang, T and Wang, L and Lu, Z and Shen, Q and Yuan, J},
title = {ggClusterNet 2: An R package for microbial co-occurrence networks and associated indicator correlation patterns.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70041},
pmid = {40469522},
issn = {2770-596X},
abstract = {Since its initial release in 2022, ggClusterNet has become a vital tool for microbiome research, enabling microbial co-occurrence network analysis and visualization in over 300 studies. To address emerging challenges, including multi-factor experimental designs, multi-treatment conditions, and multi-omics data, we present a comprehensive upgrade with four key components: (1) A microbial co-occurrence network pipeline integrating network computation (Pearson/Spearman/SparCC correlations), visualization, topological characterization of network and node properties, multi-network comparison with statistical testing, network stability (robustness) analysis, and module identification and analysis; (2) Network mining functions for multi-factor, multi-treatment, and spatiotemporal-scale analysis, including Facet.Network() and module.compare.m.ts(); (3) Transkingdom network construction using microbiota, multi-omics, and other relevant data, with diverse visualization layouts such as MatCorPlot2() and cor_link3(); and (4) Transkingdom and multi-omics network analysis, including corBionetwork.st() and visualization algorithms tailored for complex network exploration, including model_maptree2(), model_Gephi.3(), and cir.squ(). The updates in ggClusterNet 2 enable researchers to explore complex network interactions, offering a robust, efficient, user-friendly, reproducible, and visually versatile tool for microbial co-occurrence networks and indicator correlation patterns. The ggClusterNet 2R package is open-source and available on GitHub (https://github.com/taowenmicro/ggClusterNet).},
}

@article {pmid40469520,
year = {2025},
author = {Yu, L and Chen, Z and Yin, S and Guo, Q and Chen, Y and Li, J and Wang, Y and Liu, X and Xu, Z and Zhang, Y and Zhang, Y and Zheng, Z and Chen, K and Ding, Y and Fan, H and Liu, Z and Ding, Y},
title = {Gut-derived Lactobacillus from exceptional responders mitigates chemoradiotherapy-induced intestinal injury through methionine-driven epigenetic modulation.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70043},
pmid = {40469520},
issn = {2770-596X},
abstract = {Acute chemoradiotherapy-induced intestinal injury (ACRIII) is a common and debilitating complication in patients with colorectal cancer, significantly impairing both quality of life and treatment outcomes. This study aimed to investigate the role of the gut microbiome in mitigating ACRIII. Through bioinformatics analysis of clinical fecal samples and fecal microbiota transplantation (FMT) experiments in mice, we identified a strong association between a high abundance of Lactobacillus species and the absence of ACRIII. From the fecal samples of rectal cancer patients who achieved complete remission without experiencing ACRIII during chemoradiotherapy, 10 novel Lactobacillus strains were isolated and characterized. Among these, Lacticaseibacillus rhamnosus DY801 exhibited a robust capacity to synthesize methionine through metB. This microbial methionine production modulated methionine metabolism in host gut lymphoid tissue inducer (Lti) cells, without diminishing the therapeutic efficacy of chemoradiotherapy. Supplementation with methionine increased intracellular levels of S-adenosylmethionine and enhanced histone H3 lysine 4 trimethylation (H3K4me3) in Lti cells. These epigenetic modifications led to the suppression of pro-inflammatory cytokines interleukin-17A (IL-17A) and interleukin-22 (IL-22), ultimately reducing ACRIII severity. Our findings suggest that specific Lactobacillus strains derived from patients with exceptional treatment responses may offer a novel therapeutic avenue for preventing or alleviating ACRIII. This microbiome-based approach holds significant potential for improving patient outcomes and enhancing the tolerability of chemoradiotherapy in colorectal cancer.},
}

@article {pmid40469508,
year = {2025},
author = {Zhao, S and Zhong, H and He, Y and Li, X and Zhu, L and Xiong, Z and Zhang, X and Zheng, N and Morgavi, DP and Wang, J},
title = {Leveraging core enzyme structures for microbiota targeted functional regulation: Urease as an example.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70032},
pmid = {40469508},
issn = {2770-596X},
abstract = {Microbial communities play critical roles in various ecosystems. Despite extensive research on the taxonomic and functional diversity of microbial communities, effective approaches to regulate targeted microbial functions remain limited. Here, we present an innovative methodology that integrates core enzyme identification, protein structural characterization, regulator virtual screening, and functional validation to achieve precise microbiome functional regulation. As a proof of concept, we focused on the regulation of urea decomposition by the rumen microbiota in ruminants. Through metagenomic analysis, we identified the core urease gene and its corresponding microbial genome (MAG257) affiliated with the unclassified Succinivibrionaceae, and reconstructed its complete gene cluster. Structural analysis of the urease catalytic subunit (UreC) via cryo-electron microscopy (cryo-EM) revealed detailed features of its active site, guiding molecular docking studies that identified epiberberine, a natural compound with potent urease inhibitory activity. Validation in a rumen simulation system demonstrated that epiberberine significantly reduced urea decomposition and enhanced nitrogen utilization. This study establishes a robust framework that combines structural biology and computational screening to achieve targeted microbiome functional regulation, offering a promising tool for microbiome engineering and broader applications in animal productivity, human health, environmental improvement, and biotechnology.},
}

@article {pmid40469507,
year = {2025},
author = {Shen, Y and Qu, W and Song, M and Zhang, T and Liu, C and Shi, X and Xu, X and Jiang, J and Ding, L and Mo, F and Mao, Z and Huang, M and Xu, Z and Chen, J and Shen, E and Ruan, J and Liu, J and Timko, MP and Chen, Y and Fan, L and Zheng, S and Wang, Y},
title = {Single-microbe RNA sequencing uncovers unexplored specialized metabolic functions of keystone species in the human gut.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70035},
pmid = {40469507},
issn = {2770-596X},
abstract = {The human body is inhabited by trillions of microorganisms that play a crucial role in health and diseases. Our understanding of the species and functional composition of the human gut microbiome is rapidly expanding, but it is still mainly based on taxonomic profiles or gene abundance measurements. As such, little is known about the species-function heterogeneity and dynamic activities in human microecosystem niches. By applying a novel gut-specific single-microbe ribonucleic acid (RNA) sequencing and analytical framework on three healthy donors with distinct enterotypes, we created a comprehensive transcriptional landscape of the human gut microbiome and dissected functional specialization in 38,922 single microbes across 198 species. We investigated the functional redundancy and complementarity involved in short-chain fatty acids related central carbon metabolism and studied the heterogeneity and covariation of single-microbe metabolic capacity. Comparing the human gut microbiome at different times throughout the day, we were able to map diurnal dynamic activities of the gut microbiome and discovered its association with sub-population functional heterogeneous. Remarkably, using single-microbe RNA sequencing, we systematically dissected the metabolic function heterogeneity of Megamonas funiformis, a keystone species in Asian populations. Together with in vitro and in vivo experimental validations, we proved M. funiformis can effectively improve mineral absorption through exogenous phytic acid degradation, which could potentially serve as a probiotic that reduces malnutrition caused by deficiency of mineral elements. Our results indicated that species-function heterogeneity widely exists and plays important roles in the human gut microbiome, and through single-microbe RNA sequencing, we have been able to capture the transcriptional activity variances and identify keystone species with specialized metabolic functions of possible biological and clinical importance.},
}

@article {pmid40469504,
year = {2025},
author = {Van Den Bossche, T and Armengaud, J and Benndorf, D and Blakeley-Ruiz, JA and Brauer, M and Cheng, K and Creskey, M and Figeys, D and Grenga, L and Griffin, TJ and Henry, C and Hettich, RL and Holstein, T and Jagtap, PD and Jehmlich, N and Kim, J and Kleiner, M and Kunath, BJ and Malliet, X and Martens, L and Mehta, S and Mesuere, B and Ning, Z and Tanca, A and Uzzau, S and Verschaffelt, P and Wang, J and Wilmes, P and Zhang, X and Zhang, X and Li, L and , },
title = {The microbiologist's guide to metaproteomics.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70031},
pmid = {40469504},
issn = {2770-596X},
abstract = {Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state-of-the-art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.},
}

@article {pmid40469040,
year = {2025},
author = {Vogel, SC and Murgueitio, N and Huth, N and Sem, K and Knickmeyer, RC and Short, SJ and Mills-Koonce, R and Propper, C and Wagner, NJ},
title = {Longitudinal associations between the infant gut microbiome and negative affect in toddlerhood.},
journal = {Development and psychopathology},
volume = {},
number = {},
pages = {1-13},
doi = {10.1017/S0954579425100229},
pmid = {40469040},
issn = {1469-2198},
abstract = {The role of the gut microbiome in infant development has gained increasing interest in recent years. Most research on this topic has focused on the first three to four years of life because this is a critical period for developing gut-brain connections. Prior studies have identified associations between the composition and diversity of the gut microbiome in infancy and markers of temperament, including negative affect. However, the specific microbes affected, and the directionality of these associations have differed between studies, likely due to differences in the developmental period of focus and assessment approaches. In the current preregistered study, we examined connections between the gut microbiome, assessed at two time points in infancy (2 weeks and 18 months), and negative affect measured at 30 months of age in a longitudinal study of infants and their caregivers. We found that infants with higher gut microbiome diversity at 2 weeks showed more observed negative affect during a study visit at 30 months. We also found evidence for associations between specific genera of bacteria in infancy and negative affect. These results suggest associations between specific features of the gut microbiome and child behavior may differ based on timing of gut microbiome measurement.},
}

@article {pmid40468884,
year = {2025},
author = {Lee, Y and Ko, YM and Kwak, YS},
title = {Genetic and Nutritional Dynamics of SynCom in Suppressing Apple Fire Blight.},
journal = {The plant pathology journal},
volume = {41},
number = {3},
pages = {380-391},
doi = {10.5423/PPJ.OA.03.2025.0040},
pmid = {40468884},
issn = {1598-2254},
support = {RS-2020-RD009282//Rural Development Administration/ ; RS-2025-00516084//National Research Foundation of Korea/ ; },
abstract = {Fire blight disease, caused by Erwinia amylovora, occurs in apples and other Rosaceae plants and is known to cause significant economic damage. The pathogen usually infects flowers during the reproductive growth period of plants, colonizes, and penetrates by producing exopolysaccharides in the stigma. A synthetic microbial community (SynCom) is an artificial community of microorganisms designed to enhance host viability. To construct SynCom, we attempted to identify and utilize the microbial characteristics of apple trees that are not infected with the pathogen compared to those that are infected. In our previous study, we composed SynCom with strains expected to reduce the density of fire blight pathogens through microbiome analysis, strain isolation, and continuous replacement culture. We are able to observe the disease control effect of the constructed SynCom. However, no study has been conducted to clearly determine the genetic mechanism underlying this effect of the SynCom. Here, we present that potential secondary metabolite candidates and nutritional competition with the pathogen were confirmed as biochemical mechanisms through whole genome analysis of SynCom strains. Additionally, by co-cultivating SynCom with the pathogen in limited nutrient conditions, such as apple blossom extracts, which are susceptible to the pathogen, we confirmed the potential of SynCom treatment to reduce the pathogen densities. This study demonstrates that genetic selection using metagenomics can effectively identify microorganisms with potential functional capabilities.},
}

@article {pmid40468702,
year = {2025},
author = {Yoon, SJ and Han, SK and Kim, TS and Suk, KT and Choi, DH and Kim, YD and Kim, MY and Cheon, GJ and Baik, SK and Kim, DJ},
title = {The crosstalk between gut microbiota and microbiota-derived metabolites in hepatocellular carcinoma.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/1040841X.2025.2501590},
pmid = {40468702},
issn = {1549-7828},
abstract = {Hepatocellular carcinoma (HCC), one of the leading causes of death worldwide, is a consequence of persistent liver injury, inflammation, and fibrosis. Recent research has demonstrated that the gut-liver axis plays a crucial role in the pathological mechanisms of HCC development. Given the overall paucity of data available, we examined both clinical and animal studies investigating the influence of gut microbiota and their metabolites on the development of HCC in light of current scientific understanding. In this review, we concentrate on the mechanism by which intestinal dysbiosis facilitates the hepatocarcinogenesis pathway and offer a detailed account of the specific pathways involved in the promotion of HCC by the microbiome and its metabolites. Based on this, researchers might extrapolate which strains would be beneficial or harmful to restore gut homeostasis by targeting gut-liver axis in the pathogenesis of HCC.},
}

@article {pmid40468659,
year = {2025},
author = {Hossain, MS and Seo, H and Lee, KA and Ul-Haq, A and Kim, S and Jo, S and Rahim, MA and Tajdozian, H and Ghorbanian, F and Yoon, Y and Barman, I and Shuvo, MSH and Kim, HS and Song, HY},
title = {Microbiome therapeutic PMC72 through reverse translational research in gout.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {5},
pages = {e2501002},
doi = {10.71150/jm.2501002},
pmid = {40468659},
issn = {1976-3794},
support = {RS-202300219563//National Research Foundation of Korea/ ; //Ministry of Science and ICT/ ; 2020R1I1A-3072680//Ministry of Education/ ; //Soonchunhyang University Research Fund/ ; },
mesh = {Animals ; *Gout/therapy/microbiology/chemically induced ; Humans ; Mice ; *Gastrointestinal Microbiome/drug effects ; Hyperuricemia/chemically induced/therapy ; Uric Acid/blood/metabolism ; Disease Models, Animal ; Translational Research, Biomedical ; Dysbiosis ; Male ; Feces/microbiology ; Febuxostat/therapeutic use ; Oxonic Acid ; Oxidative Stress ; },
abstract = {Gout is an inflammatory arthritis resulting from the deposition of monosodium urate crystals. Urate-lowering therapies for gout have limitations, including side effects and limited efficacy, highlighting the need for novel therapeutic approaches to improve patient outcomes. In this context, our research team conducted a microbiome analysis of fecal samples from healthy individuals and gout patients, identifying Bifidobacterium as a key biomarker. Subsequently, we isolated and identified this strain, B. longum PMC72, and demonstrated its efficacy in a gout mouse model. In potassium oxonate (PO)-induced hyperuricemia mice, PMC72 significantly alleviated nausea, gait disturbances, ankle inflammation, and improved renal health. These effects were associated with marked reductions in oxidative stress markers, including serum uric acid, blood urea nitrogen, hepatic xanthine oxidase, and malondialdehyde (MDA) levels in serum, liver, and joint samples, as well as the downregulation of inflammation and uric acid transport-related gene expression in kidney samples. These benefits were comparable to those treated with Febuxostat, a standard urate-lowering therapy for gout. Furthermore, gut microbiome analysis revealed that PMC72 restored dysbiosis induced by hyperuricemia, contrasting with the reduced microbial diversity observed with febuxostat alone, and showed a complete recovery to eubiosis when combined with Febuxostat. These findings position PMC72 as a promising microbial therapeutic candidate for gout management, demonstrating significant development potential and serving as a benchmark for reverse translational microbiome-based therapeutic research.},
}

Animals
*Gout/therapy/microbiology/chemically induced
Humans
Mice
*Gastrointestinal Microbiome/drug effects
Hyperuricemia/chemically induced/therapy
Uric Acid/blood/metabolism
Disease Models, Animal
Translational Research, Biomedical
Dysbiosis
Male
Feces/microbiology
Febuxostat/therapeutic use
Oxonic Acid
Oxidative Stress

@article {pmid40468650,
year = {2025},
author = {Cha, RR and Sonu, I},
title = {Fecal microbiota transplantation: present and future.},
journal = {Clinical endoscopy},
volume = {58},
number = {3},
pages = {352-359},
doi = {10.5946/ce.2024.270},
pmid = {40468650},
issn = {2234-2400},
support = {//Gyeongsang National University Fund/ ; },
abstract = {Fecal microbiota transplantation (FMT) involves transplanting fecal matter from healthy donors into patients with gut dysbiosis to restore microbial balance. It has been proven to be highly effective in treating recurrent Clostridioides difficile infection (CDI), and United States Food and Drug Administration-approved microbiome-based therapies, such as REBYOTA (fecal microbiota live-jslm) and VOWST (fecal microbiota spores live-brpk), offer promising treatment options. Although FMT is widely used to treat recurrent CDI, its use in gastrointestinal and metabolic diseases remains limited. Future research directions include optimizing donor selection, understanding microbial mechanisms, and exploring the potential of FMT for treating other diseases. Ongoing research not only aims to broaden its indications but also improves its safety and efficacy. Emerging therapies such as VE303 (Vedanta) are being studied to refine treatment approaches and expand the use of microbiota-based therapies. Further studies are needed to standardize guidelines, improve patient outcomes, and better define the role of FMT in the treatment of diseases beyond recurrent CDI.},
}

@article {pmid40468453,
year = {2025},
author = {Hu, F and Gebeyew, K and Wu, Z and Chen, B and Jiao, J and Tan, Z and Tian, D and He, Z},
title = {Fat-rich diet promotes microbiome-dependent ATP synthesis in sheep model.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {81},
pmid = {40468453},
issn = {1674-9782},
support = {XDA26040304//Strategic Priority Research Program/ ; XDA26050102//Strategic Priority Research Program/ ; 32072760//National Natural Science Foundation of China/ ; 2022JJ10054//Natural Science Foundation of Hunan Province of China/ ; },
abstract = {BACKGROUND: The ketogenic diet that forces adenosine triphosphate (ATP) production by beta-oxidation of fatty acids instead of carbohydrate glycolysis, has gained consensus on host metabolism. However, the mechanisms how a ketogenic diet alters gastrointestinal microbiome and its downstream consequences on microbial nutrient availability and energy metabolism remain to be elucidated. Here, we used the sheep model fed with fat-rich diet to evaluate the symbiotic microbiome across three regions of the gastrointestinal tract (rumen, ileum, and colon) to gain a comprehensive understanding of the microbial energy metabolism and microbe-mediated ATP biosynthesis.

RESULTS: Results showed that sheep fed a fat-rich diet had a greater ADG and increased reliance on fat oxidation for fuel utilization. Metagenomics analysis showed the loss of the specialized fiber-degrading bacteria (genus_Fibrobacter) in the rumen and enrichment of genera RUG420 and Eubacterium, which are involved in lipid metabolism and bile acid processing, in the ileum. A significant functional shift related to energy metabolism was shared across three regions of the gastrointestinal microbiomes. These shifts were dominated by glycolysis/gluconeogenesis and TCA cycle in the rumen and by fatty acid degradation and bile acid transformation in the ileum, indicating adaptation to nutrient availability and energy acquisition. Notably, the abundance of substrate-level phosphorylation (SLP) enzymes was significantly increased in the rumen, ileum and colon, while the ATP-producing capacity through electron transport phosphorylation (ETP) by family_Bacteroidaceae in rumen and Acutalibacteraceae in ileum of sheep with fat-rich diet.

CONCLUSIONS: Altogether, the ATP-related microbiome encoding SLP and ETP in rumen, ileum, and colon contributed 36.95% to the host's weight variation. Our study is the first one demonstrating the microbial potential in the ATP synthesis under the shift in dietary energy source, providing a new perspective on the energy metabolism and precise human macronutrients nutrition.},
}

@article {pmid40468444,
year = {2025},
author = {Tang, Q and Yin, X and Wen, G and Luo, Z and Zhang, L and Tan, S},
title = {Unraveling the composition and function of pig gut microbiome from metagenomics.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {60},
pmid = {40468444},
issn = {2524-4671},
support = {No. [2023] 211//2022 Hunan Province Vocational Education "Chuyi" Action High Level Teacher Team Construction Project/ ; No. [2023] 211//2022 Hunan Province Vocational Education "Chuyi" Action High Level Teacher Team Construction Project/ ; },
abstract = {The gut microbiome plays a crucial role in intestinal maturation, metabolism, and immunoregulation, significantly influencing the host's health and growth performance. This review highlights the use of metagenomic techniques to the composition, function, and dynamic changes of the pig gut microbiota. Research has revealed that environmental and host factors, particularly diet, drive significant variations in microbial composition, which in turn shape host epigenetics through microbial components and metabolites. Furthermore, the strong correlation between the gut microbiota and host health presents opportunities for improving growth performance in the livestock industry.},
}

@article {pmid40468436,
year = {2025},
author = {Kilama, J and Islam, MS and Amat, S},
title = {Bovine ocular microbiome: the next frontier in managing Pinkeye in cattle.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {58},
pmid = {40468436},
issn = {2524-4671},
abstract = {Infectious bovine keratoconjunctivitis (IBK), or pinkeye, represents a significant economic challenge to dairy and beef cattle industries resulting in decreased productivity and increased treatment costs. The current IBK prevention and control strategies in cattle face challenges owing to the multifactorial nature of the disease, the rise of antibiotic resistance in IBK pathogens, and inconsistent efficacy of IBK vaccines. Recent efforts in metagenomic characterization of the eye microbiome in humans and animals, including cattle, have revealed that the ocular surface is colonized by relatively diverse and dynamic microbial community that is essential for maintaining ocular health and can be leveraged to enhance resistance against infectious ocular diseases. In this narrative review, we provide comprehensive insights into the ocular microbiota by summarizing the amplicon and metagenomic sequencing- and culture-based studies conducted in cattle, and by reviewing relevant findings from humans and other animal species. We also explore the potential of the ocular microbiome as a new frontier in managing IBK. Finally, we examine the gut-eye-microbiome axis and discuss its potential contribution in improving the resistance of cattle against IBK.},
}

@article {pmid40468269,
year = {2025},
author = {Li, B and Yang, Y and Xu, B and Song, P and Jiang, F and Gao, H and Cai, Z and Gu, H and Zhang, T},
title = {Comparative macrogenomics reveal plateau adaptation of gut microbiome in cervids.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {154},
pmid = {40468269},
issn = {1741-7007},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Deer/microbiology/genetics ; Phylogeny ; Metagenome ; Metagenomics ; *Adaptation, Physiological/genetics ; Energy Metabolism ; Biological Evolution ; },
abstract = {BACKGROUND: Diverse gut microbiota in animals significantly influences host physiology, ecological adaptation, and evolution. However, the specific functional roles of gut microbiota in facilitating host adaptation, as well as the coevolutionary dynamics between microbiota and their hosts, remain largely understudied.

RESULTS: A total of 41,847 metagenome-assembled genomes and 3193 high-quality species-level genome bins were generated, establishing a comprehensive gut microbiome catalog for cervids in this study. Phylogenetic analysis revealed a coevolutionary relationship between cervids and their gut microbiota. Comparative metagenomic analyses further indicated that the gut microbiota of plateau cervids have undergone genome-level adaptations related to energy metabolism. At the genus level, species-level genome bins from the genera Alistipes and Faecousia in plateau cervids exhibit enhanced energy metabolism capabilities. Structural variations analysis revealed that the insertion and duplications structural variations in the gut microbiota of plateau cervids were significantly enriched in energy metabolism pathways. In contrast, the deletions and contractions in structural variations were predominantly enriched with metabolic pathways involved in the biosynthesis of diverse biochemical molecules.

CONCLUSIONS: Our study provides a comprehensive gut microbiome catalog of the cervid gut microbiota, revealing the coevolutionary relationship between cervid gut microbiota and hosts. These findings highlight the adaptive genomic evolution of the gut microbiota in contributing to the plateau adaptability of cervids and offer new insights into the mechanisms by which the gut microbiota help hosts adapt to extreme environments.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Deer/microbiology/genetics
Phylogeny
Metagenome
Metagenomics
*Adaptation, Physiological/genetics
Energy Metabolism
Biological Evolution

@article {pmid40468214,
year = {2025},
author = {Yang, X and Chen, H and Wu, L and Guo, X and Xue, D},
title = {Diversity and correlation analysis of microbiomes and metabolites of Sphagnum palustre in various microhabitats.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {761},
pmid = {40468214},
issn = {1471-2229},
support = {2019QZKK0304//Second Tibetan Plateau Scientific Expedition/ ; QNTS202201//Youth Innovation Program of CIB/ ; 2022376//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 2021JDTD011//Youth Science and Technology Innovation Team Program of Sichuan Province of China/ ; },
mesh = {*Microbiota ; *Sphagnopsida/microbiology/metabolism ; Ecosystem ; Soil Microbiology ; Bacteria/genetics/metabolism ; },
abstract = {BACKGROUND: Sphagnum peat mosses are crucial contributors to global carbon sequestration and are a dominant presence in many northern peatland environments. These mosses host a wide variety of microorganisms, which reside within their tissues and on their surfaces. Despite this close association, the connection between these microorganisms and the production of metabolites across different parts of Sphagnum remains unclear.

RESULTS: This research explored the connection between microbial diversity and metabolite production in various microhabitats of Sphagnum palustre by employing metagenomic and metabolomic techniques. Our results indicate that the S. palustre microbiome composition is more strongly influenced by microhabitat than by geographic location. Microbiome diversity microbiomes related to S. palustre showed a steady decrease from soil to near soil, from X to CAP, and from belowground to aboveground habitats. In contrast, network complexity increased. Species abundance analysis indicated that Proteobacteria was the most prevalent bacterial phylum across CAP, S, Z, and X. Additionally, Ascomycota emerged as the predominant fungal phylum. There were significant differences in nitrogen fixation activity, methane oxidation activity, total nitrogen, and total carbon among different microhabitats. The FAPROTAX analysis revealed differences in the metabolic potential of the carbon (C) and nitrogen (N) cycles across the four microhabitats. LC-MS/MS technology was employed to quantitatively assess metabolites across various S. palustre microhabitats. A total of 3,822 metabolites and 353 differential metabolites were detected, predominantly including lipids, organic acids, and carboxylic acids. The majority of these differential metabolites were associated with metabolic pathways such as carotenoid biosynthesis, steroid biosynthesis, secondary bile acid biosynthesis, as well as the biosynthesis of neomycin, kanamycin, and gentamicin. Correlation analysis revealed both positive and negative relationships between microorganisms and differential metabolites. Methylocystis, which was significantly enriched in X and T, showed a strong positive correlation with differential metabolites in S vs T and Z vs X, but a negative correlation with those in X vs T (p < 0.05).

CONCLUSION: In summary, our study demonstrates that Sphagnum palustre microbiomes are primarily influenced by microhabitats rather than specific environmental conditions at different sites. We identified significant variations in microbial community diversity across various S. palustre microhabitats. Correlation analysis revealed links between microorganisms and differential metabolic processes. This comprehensive investigation of aboveground and belowground microbiomes and metabolites in S. palustre provides new insights into the distribution of microbial communities and metabolites across different microhabitats.},
}

*Microbiota
*Sphagnopsida/microbiology/metabolism
Ecosystem
Soil Microbiology
Bacteria/genetics/metabolism

@article {pmid40468177,
year = {2025},
author = {Yang, B and Yue, C and Guo, C and Zheng, M and Yao, X and Xu, J and Huang, S and Yang, M},
title = {Disease-resistant watermelon variety against Fusarium wilt by remodeling rhizosphere soil microenvironment.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {350},
pmid = {40468177},
issn = {1471-2180},
support = {112024AS0100//Natural Science Foundation of Henan Province/ ; },
mesh = {*Rhizosphere ; *Citrullus/microbiology/genetics ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Fusarium/physiology/pathogenicity ; *Disease Resistance ; Soil/chemistry ; Bacteria/classification/genetics/isolation & purification ; Microbiota ; Fungi/classification/genetics/isolation & purification ; Transcriptome ; },
abstract = {BACKGROUND: Rhizosphere microorganisms and their interactions play a critical role in enhancing plant disease resistance. Here, we found that the disease severity of the resistant variety LW025 showed a decreasing trend with the increase in continuous cropping cycles. However, the mechanisms underlying the reduction in disease severity during the continuous cropping of the resistant watermelon variety LW025, particularly its relationship with the rhizosphere microbiome, remain unclear.

RESULTS: In this study, the transcriptome of different watermelon varieties after continuous planting in pathogen-containing and pathogen-free soils was analyzed. The results showed that only two genes expression showed significant differences in disease-resistant variety between healthy and diseased soils. Subsequently, we analyzed the differences of rhizosphere soil microbial communities after planting different watermelon varieties for three consecutive seasons, as well as the relationship between differential microorganisms and soil physiochemical properties and soil enzyme activity. The results demonstrated continuous cropping of the disease-resistant variety LW025 formed a rhizosphere microbiome different from the initial soil and susceptible variety. Specifically, fungal changes were primarily observed in Ascomycota and Chytridiomycota, while bacterial changes were mainly observed in Cyanobacteria and Gemmatimonadetes. The bacterial functions enriched in the rhizosphere of the resistant variety LW025 after continuous cropping were primarily associated with soil nitrogen cycling. Furthermore, the plant disease index showed a significant positive correlation with the available phosphorus and potassium content in the soil, while exhibiting a significant negative correlation with soil pH and catalase activity.

CONCLUSIONS: Overall, the reduction in disease severity associated with continuous cropping of the disease-resistant variety LW025 was more closely related to changes in the rhizosphere microecological environment. This study explained the mechanism of the resistant variety LW025 against Fusarium infection, and provided new prospects for the development of technologies based on rhizosphere microecological environment modification to improve the resistance of watermelon to Fusarium wilt.},
}

*Rhizosphere
*Citrullus/microbiology/genetics
*Soil Microbiology
*Plant Diseases/microbiology
*Fusarium/physiology/pathogenicity
*Disease Resistance
Soil/chemistry
Bacteria/classification/genetics/isolation & purification
Microbiota
Fungi/classification/genetics/isolation & purification
Transcriptome

@article {pmid40468006,
year = {2025},
author = {Sanz, Y and Cryan, JF and Deschasaux-Tanguy, M and Elinav, E and Lambrecht, R and Veiga, P},
title = {The gut microbiome connects nutrition and human health.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {40468006},
issn = {1759-5053},
abstract = {The gut microbiome has an undeniable role in mediating the health effects of the diet, given its ability to co-digest nutrients and influence nutrient signalling to multiple organ systems. As a suboptimal diet is a major risk factor for and contributor to disease, understanding the multidirectional interactions between the food we eat, the gut microbiome and the different body organ systems is crucial from a public health perspective. Indeed, this research area is leading to the refinement of nutritional concepts and strategies to optimize health through diet. In this Review, we provide an update on how dietary patterns and food intake shape gut microbiome features, the mode of action of diet-microorganism interactions on the immune, nervous and cardiometabolic systems and how this knowledge could explain the heterogeneity of dietary responses, and support food-based dietary guidelines and medical and precision nutrition. Finally, we discuss the knowledge gaps and research efforts needed to progress towards the integration of microbiome science with more precise dietary advice to leverage the role of nutrition in human health.},
}

@article {pmid40467971,
year = {2025},
author = {Smoliński, J and Czyż, K and Kleszcz, A and Trusz, A and Wyrostek, A and Zajfert, K},
title = {A preliminary study on farmed and free-ranging mouflons core microbiome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19555},
pmid = {40467971},
issn = {2045-2322},
mesh = {Animals ; Feces/microbiology ; *Gastrointestinal Microbiome ; Bacteroidetes/genetics/isolation & purification ; *Microbiota ; Firmicutes/genetics/isolation & purification ; Bacteria/genetics/classification ; },
abstract = {The digestive tract of ruminants is populated by a diverse microbiome and is also known as a specific ecosystem. The close relationship between the microbiota and the host digestive system influences development and proper health. The rich microflora of ruminants is often altered by the influence of the environment, diet or individual factors, which in turn affects production rates. The most extensive part of the gastrointestinal tract in terms of microbiology is the large intestine, where bacterial levels increase in the caudal direction. The purpose of this study was to compare the core microbiomes of the feces of farmed and free-ranging mouflons, taking into account differences in housing conditions, as well as their diet and individual variability. The most characteristic clusters for ruminants were studied: Firmicutes and Bacteroidetes, as well as the families Lactobacillaceae and Clostridiaceae. The material for the study consisted of feces collected from 10 farmed and 10 free-ranging mouflons. The experiment was based on demonstrating changes in the levels of the bacteria tested by means of DNA isolation from feces and real-time PCR analysis, taking into account dietary and environmental differences. The results showed that the levels of the Lactobacillaceae and Clostridiaceae families were significantly higher in free-ranging individuals than in farmed ones (p < 0.01). For the Firmicutes and Bacteroidetes phyla, no statistically significant differences were shown. In addition, each mouflon was characterized by an individual composition of the microbiome, which changed through environmental, individual and dietary factors.},
}

Animals
Feces/microbiology
*Gastrointestinal Microbiome
Bacteroidetes/genetics/isolation & purification
*Microbiota
Firmicutes/genetics/isolation & purification
Bacteria/genetics/classification

@article {pmid40467897,
year = {2025},
author = {Wu, Y and Ehlert, B and Metwally, AA and Perelman, D and Park, H and Brooks, AW and Abbasi, F and Michael, B and Celli, A and Bejikian, C and Ayhan, E and Lu, Y and Lancaster, SM and Hornburg, D and Ramirez, L and Bogumil, D and Pollock, S and Wong, F and Bradley, D and Gutjahr, G and Rangan, ES and Wang, T and McGuire, L and Venkat Rangan, P and Ræder, H and Shipony, Z and Lipson, D and McLaughlin, T and Snyder, MP},
title = {Individual variations in glycemic responses to carbohydrates and underlying metabolic physiology.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40467897},
issn = {1546-170X},
support = {R01 DK110186-01//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; P30DK116074//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; F32DK126287//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01 DK110186-01//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; P30DK116074//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; 11-23-PDF-76//American Diabetes Association (ADA)/ ; 2T15LM007033//U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; },
abstract = {Elevated postprandial glycemic responses (PPGRs) are associated with type 2 diabetes and cardiovascular disease. PPGRs to the same foods have been shown to vary between individuals, but systematic characterization of the underlying physiologic and molecular basis is lacking. We measured PPGRs using continuous glucose monitoring in 55 well-phenotyped participants challenged with seven different standard carbohydrate meals administered in replicate. We also examined whether preloading a rice meal with fiber, protein or fat ('mitigators') altered PPGRs. We performed gold-standard metabolic tests and multi-omics profiling to examine the physiologic and molecular basis for interindividual PPGR differences. Overall, rice was the most glucose-elevating carbohydrate meal, but there was considerable interindividual variability. Individuals with the highest PPGR to potatoes (potato-spikers) were more insulin resistant and had lower beta cell function, whereas grape-spikers were more insulin sensitive. Rice-spikers were more likely to be Asian individuals, and bread-spikers had higher blood pressure. Mitigators were less effective in reducing PPGRs in insulin-resistant as compared to insulin-sensitive participants. Multi-omics signatures of PPGR and metabolic phenotypes were discovered, including insulin-resistance-associated triglycerides, hypertension-associated metabolites and PPGR-associated microbiome pathways. These results demonstrate interindividual variability in PPGRs to carbohydrate meals and mitigators and their association with metabolic and molecular profiles.},
}

@article {pmid40467859,
year = {2025},
author = {Ferretti, P and Johnson, K and Priya, S and Blekhman, R},
title = {Genomics of host-microbiome interactions in humans.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {40467859},
issn = {1471-0064},
abstract = {The human microbiome is a complex ecosystem of microorganisms that inhabit the human body and have a crucial role in human health. Microbiome composition is shaped by its interaction with many factors, including human genetics. Advances in genomic technologies are improving the ability to quantify the effect of human genetics on the microbiome through improved heritability studies and microbiome genome-wide association studies (GWAS). Complementary studies using transcriptomic analyses are providing a more comprehensive view of the bidirectional relationship between host gene expression and the microbiome. The resulting insights into the genetic mechanisms driving host-microbiome interactions will ultimately contribute to the development of personalized medicine and targeted therapies.},
}

@article {pmid40467839,
year = {2025},
author = {Chen, YA and Kawashima, H and Park, J and Mohsen, A and Hosomi, K and Nakagata, T and Murakami, H and Nanri, H and Miyachi, M and Kunisawa, J and Mizuguchi, K},
title = {NIBN Japan Microbiome Database, a database for exploring the correlations between human microbiome and health.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19640},
pmid = {40467839},
issn = {2045-2322},
support = {22AC5002//Ministry of Health, Labour and Welfare/ ; 22AC5002//Ministry of Health, Labour and Welfare/ ; 20AC5004//Ministry of Health, Labour and Welfare/ ; 20AC5004//Ministry of Health, Labour and Welfare/ ; },
mesh = {Humans ; Japan ; *Databases, Factual ; *Gastrointestinal Microbiome ; *Microbiota ; Metadata ; },
abstract = {Recent research has highlighted the substantial impact of gut microbiome on various aspects of human health, such as obesity, inflammation, infectious diseases, and cancer. As a result, gut microbiota composition is increasingly recognized as a potential health indicator and biomarker for disease. Numerous factors, including lifestyle, diet, and physical fitness, are known to shape the composition of the human microbiome. However, a significant challenge in elucidating the relationships between these factors and the gut microbiome lies in needing a comprehensive database that integrates diverse human microbiome profiles with extensive sample metadata. To address this issue, we developed an extensive human microbiome database for healthy individuals. This initiative led to the establishment of the NIBN Japan Microbiome Database (NIBN JMD), one of the largest resources of its kind, encompassing up to 1,000 metadata points and more than 2,000 microbiome samples, including data from longitudinal studies. In this article, we describe the creation and features of NIBN JMD, detailing the data collection, processing, and database implementation. NIBN JMD is publicly accessible at https://jmd.nibn.go.jp/ .},
}

Humans
Japan
*Databases, Factual
*Gastrointestinal Microbiome
*Microbiota
Metadata

@article {pmid40467588,
year = {2025},
author = {Tajadura-Ortega, V and Chai, W and Roberts, LA and Zhang, Y and Di Maio, A and Decout, AC and Pinheiro, BA and Palma, AS and De Nicola, G and Riaposova, L and Gimeno-Molina, B and Lee, YS and Cao, H and Piskarev, V and Akune, Y and Costa, TRD and Amin, H and Sykes, L and Bennett, PR and Marchesi, JR and Feizi, T and Liu, Y and MacIntyre, DA},
title = {Identification and characterisation of vaginal bacteria-glycan interactions implicated in reproductive tract health and pregnancy outcomes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5207},
pmid = {40467588},
issn = {2041-1723},
mesh = {Female ; Humans ; *Vagina/microbiology/metabolism ; Pregnancy ; *Polysaccharides/metabolism ; Bacterial Adhesion/physiology ; Pregnancy Outcome ; *Reproductive Health ; Chondroitin Sulfates/metabolism ; Escherichia coli/metabolism ; Microbiota ; *Bacteria/metabolism ; Lactobacillus/metabolism ; Streptococcus agalactiae/metabolism ; Epithelial Cells/microbiology/metabolism ; },
abstract = {Lactobacillus displacement from the vaginal microbiome associates with adverse health outcomes and is linked to increased risk of preterm birth. Glycans mediate bacterial adhesion events involved in colonisation and infection. Using customised glycan microarrays, we establish glycan interaction profiles of vaginal bacteria implicated in reproductive health. Glycan binding signatures of the opportunistic pathogens Escherichia coli, Fusobacterium nucleatum and Streptococcus agalactiae to oligomannose N-glycans, galactose-terminating glycans and hyaluronic acid, respectively are highly distinct from Lactobacillus commensals. Binding to sulphated glycosaminoglycans by vaginal bacteria is pH dependent, as is binding to neutral and sialic acid-terminating glycans by F. nucleatum. Adhesion of Lactobacillus crispatus, Lactobacillus iners, Gardnerella vaginalis, S. agalactiae and F. nucleatum to vaginal epithelial cells is partially mediated by chondroitin sulphate. S. agalactiae binding to chondroitin sulphate C oligosaccharides is inhibited by L. crispatus. This study highlights glycans as mediators of vaginal bacterial binding events involved in reproductive health and disease.},
}

Female
Humans
*Vagina/microbiology/metabolism
Pregnancy
*Polysaccharides/metabolism
Bacterial Adhesion/physiology
Pregnancy Outcome
*Reproductive Health
Chondroitin Sulfates/metabolism
Escherichia coli/metabolism
Microbiota
*Bacteria/metabolism
Lactobacillus/metabolism
Streptococcus agalactiae/metabolism
Epithelial Cells/microbiology/metabolism

@article {pmid40467587,
year = {2025},
author = {Xiong, S and Xie, B and Yin, N and Zhu, H and Gao, H and Xu, X and Xiao, K and Cai, X and Sun, G and Sun, X and Cui, Y and Van de Wiele, T and Zhu, Y},
title = {Prenatal exposure to trace elements impacts mother-infant gut microbiome, metabolome and resistome during the first year of life.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5186},
pmid = {40467587},
issn = {2041-1723},
support = {No. L232076//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Pregnancy ; Infant ; *Trace Elements/adverse effects ; *Metabolome/drug effects ; Feces/microbiology ; *Prenatal Exposure Delayed Effects/microbiology/metabolism ; Adult ; Male ; Metagenomics ; Hair/chemistry ; *Maternal Exposure/adverse effects ; Infant, Newborn ; Bacteria/genetics/classification/drug effects ; Copper ; },
abstract = {Infancy is a critical window for the colonization of gut microbiome. However, xenobiotic impacts on gut microbiome development in early life remain poorly understood. Here, we recruit 146 mother-infant pairs and collect stool samples at 3, 6, and 12 months after delivery for amplicon sequencing (N = 353), metagenomics (N = 65), and metabolomics (N = 198). Trace elements in maternal hair samples (N = 119) affect diversity and composition of the infant gut microbiome. Shannon diversity in 3 month-old infants is correlated positively with selenium and negatively with copper, and relative abundance of Bifidobacterium increases under high exposure to aluminum and manganese. During the first year of life, infants and their paired mothers have distinct microbial diversity and composition, and their bacterial community structures gradually approach. here are 56 differential metabolites between the first and second visit and 515 differential metabolites between the second and third visit. The typical profile of antibiotic resistance genes (ARGs) significantly differs between infants and their mothers. High levels of copper and arsenic exposure may induce the enrichment of ARGs in the infant gut. Our findings highlight the dynamics of the gut microbiome, metabolites, and ARG profiles of mother-infant pairs after delivery, associated with prenatal exposure to trace elements.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
Female
Pregnancy
Infant
*Trace Elements/adverse effects
*Metabolome/drug effects
Feces/microbiology
*Prenatal Exposure Delayed Effects/microbiology/metabolism
Adult
Male
Metagenomics
Hair/chemistry
*Maternal Exposure/adverse effects
Infant, Newborn
Bacteria/genetics/classification/drug effects
Copper

@article {pmid40345399,
year = {2025},
author = {Livingston, DBH and Sweet, A and Chowdary, M and Samuel Demissie, M and Rodrigue, A and Pillagawa Gedara, K and Kishore, L and Mahmoodianfard, S and Power, KA},
title = {Diet alters the effects of lipopolysaccharide on intestinal health and cecal microbiota composition in C57Bl/6 male mice.},
journal = {The Journal of nutritional biochemistry},
volume = {144},
number = {},
pages = {109951},
doi = {10.1016/j.jnutbio.2025.109951},
pmid = {40345399},
issn = {1873-4847},
abstract = {Lipopolysaccharide (LPS), a component of the gram-negative bacteria, induces an inflammatory cascade in mice, negatively impacting aspects of the microbiota gut-brain axis (mGBA). Flaxseed (FS), an oilseed enriched in dietary fiber and n3 poly-unsaturated fatty acids, has been shown to partially attenuate LPS-induced systemic and neuroinflammation. In this study, we investigated the impact of FS and FS oil (FO) diets on microbial dysbiosis, biomarkers of intestinal health, hepatic inflammation and oxidative stress, and metabolic homeostasis in male mice, 24-hours post LPS-exposure. Compared to saline-treated mice, LPS mice showed diet-dependent shifts in the cecal microbiome. Most notably, LPS-treated basal diet (BD)-fed mice had reduced Muribaculaceae and Lachnospiraceae, FS-LPS mice had elevated Akkermansia and Enterobacteriaceae, and both the FS-LPS and FO-LPS mice had increased Bacteroides. LPS increased cecal short-chain fatty acid concentrations, the highest of which were found in FS-fed mice. Intestinal health biomarkers were modulated by LPS in a diet-specific manner such that ileal mucous content was elevated in FS- and FO-fed mice, while LPS-induced inflammation (IL-1β) was attenuated in FS-fed mice. On the other hand, LPS-induced hepatic inflammation and oxidative stress, which were not attenuated by FS or FO diets. Bacteroides abundance and serum Il-10 levels, and cecal butyrate concentrations and hippocampal IL-6 mRNA, were negatively correlated in FS-fed mice only, suggesting a potential role of the microbiome in the anti-inflammatory effects of FS post-LPS treatment. Collectively, LPS exposure negatively impacted the cecal microbiome and markers of intestinal, hepatic, and metabolic health, the former being beneficially altered by FS diet.},
}

@article {pmid40467492,
year = {2025},
author = {Tonomura, S and Hattori, Y and Ishibashi, T and Ikeda, S and Noda, K and Chiba, T and Kato, Y and Asano, R and Fukuma, K and Edamoto-Taira, Y and Motooka, D and Inagaki, T and Okazawa, M and Nakamura, S and Koga, M and Toyoda, K and Nomura, R and Nakano, K and Friedland, RP and Takeda, K and Takahashi, R and Ihara, M and Nakaoka, Y},
title = {Oral Pathobiont Streptococcus Anginosus Is Enriched in the Gut of Stroke Patients and Predicts 2-Year Cardiovascular Outcome.},
journal = {Circulation journal : official journal of the Japanese Circulation Society},
volume = {},
number = {},
pages = {},
doi = {10.1253/circj.CJ-24-0872},
pmid = {40467492},
issn = {1347-4820},
abstract = {BACKGROUND: Several cross-sectional studies have implicated gut dysbiosis caused by an abundance of oral commensals in stroke, but the effect on long-term prognosis is still unknown. Therefore, we longitudinally investigated oral pathobionts in the gut and their clinical relevance to stroke.

METHODS AND RESULTS: We analyzed the salivary and gut microbiomes collected from 189 acute stroke and 55 non-stroke subjects, and found that Streptococcus anginosus was significantly more abundant in both the saliva (median [IQR], 0.01 [0.00-0.14] vs. 0.00 [0.00-0.03], P=0.02) and gut (0.09 [0.00-0.28] vs. 0.00 [0.00-0.02], P<0.001) of the stroke patients compared with their non-stroke counterparts. Network analysis revealed S. anginosus as a central hub in gut dysbiosis. After adjusting for vascular risks, S. anginosus (odds ratio 1.20, 95% confidence interval 1.06-1.36, P<0.01), Anaerostipes hadrus (0.82, [0.73-0.93], P<0.01), and Bacteroides plebeius (0.86, [0.86-0.93], P=0.01) in the gut were independent predictors of stroke. Longitudinally, S. anginosus in the gut was significantly associated with increased rates of death and major cardiovascular events (P=0.04; log-rank test), whereas A. hadrus and B. plebeius were not (P=0.45 and P=0.19). After adjusting for vascular risks, S. anginosus in the gut was a residual risk for increased rates of death and major cardiovascular events (hazard ratio 4.78, 95% confidence interval 1.08-21.18, P=0.04)Conclusions: S. anginosus in the gut may increase the risk of stroke and a poor prognosis.},
}

@article {pmid40467356,
year = {2025},
author = {Messadi, A and Sayhi, S and Ghedira, K and Zaouaoui, C and Arfaoui, B and Khouikhi, S and Rebai, M and Guediche, NEH and Abdelhafidh, N and Louzir, B and Faida, A},
title = {Microbial diversity investigation using 16S metagenomics in Tunisian patients with systemic lupus erythematosus.},
journal = {Revista Argentina de microbiologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ram.2025.04.002},
pmid = {40467356},
issn = {0325-7541},
abstract = {Systemic lupus erythematosus (SLE) is a multisystemic autoimmune disease associated with significant morbidity and mortality. It is characterized by a loss of self-immune tolerance and autoantibody production, leading to multiple organ damage. Emerging investigations have confirmed the role of gut microbiota dysbiosis in patients with SLE, although the underlying mechanisms remain unclear to date. In this study, we aim to investigate the bacterial profile of SLE including phylum/class/genus relative abundance and diversity, to compare them with healthy controls and to study the correlation of relative abundance of different patterns with clinical/biological parameters. In this case-control study, the bacterial profile was investigated in 7 SLE patients and 7 healthy controls using 16S metagenomics clustering. The present study reported a low abundance of the class Bacilli (0.58% in SLE vs 1.26% in the controls), the genus Lactobacillus (0.43% vs 0.74%), as well as a higher abundance of the genera Gammaproteobacteria (2.37% vs 0.77%) and Escherichia-Shigella (2.04% vs 0.51%) in SLE samples compared to the controls (p<0.05). We also found an association between the class Betaproteobacteria (4.42% vs 1.57%) and the genus Faecalibacterium (11.34% vs 3.35%) and renal manifestations (p<0.05). The phylum Actinobacteria (0.21% vs 3.8%, p=0.036) and the genus Bifidobacterium levels were lower in active SLE compared to the healthy controls. This study is the first report on the gut microbiota of SLE and the first case-control study in Tunisia and North Africa. We obtained a particular profile of bacterial gut microbiota for the SLE group. We found a specific clustering when compared to the healthy controls.},
}

@article {pmid40467241,
year = {2025},
author = {Alegbeleye, O and Boas, DMV and Sant'Ana, AS},
title = {Harnessing the microbiota of vegetables and ready-to-eat (RTE) vegetables for quality and safety.},
journal = {Food research international (Ottawa, Ont.)},
volume = {214},
number = {},
pages = {116667},
doi = {10.1016/j.foodres.2025.116667},
pmid = {40467241},
issn = {1873-7145},
mesh = {*Vegetables/microbiology/virology ; *Food Microbiology ; *Microbiota ; *Food Safety ; *Fast Foods/microbiology ; Humans ; Bacteria/classification/isolation & purification ; Salads/microbiology ; *Food Quality ; },
abstract = {The microbiota of vegetables and Ready-to-Eat (RTE) vegetable salads can have significant implications for quality and safety. Some microbial groups occurring on vegetables can cause foodborne illnesses, while others can potentially influence the shelf life of vegetables and vegetable salad products. The comprehensive assessment of the microbial structure and diversity of vegetables requires sensitive detection and characterization techniques, and this review discusses some of the strengths and limitations of conventional culture dependent approaches and the promise of some contemporary microbial detection/characterization approaches. Some bacterial groups recovered from vegetables have exhibited resistance to important antibiotics and without adequate safeguards, consumption of vegetables and salad products can potentially contribute to the spread and burden of antibiotic resistance. Studies summarised herein indicate that bacterial groups including Pseudomonas, Erwinia, and Lactic Acid Bacteria which contain common spoilage species are predominant in vegetables. Some possible sources of these bacteria to vegetables include agricultural input and post-harvest handling. Viruses and fungi contribute significantly to shaping microbiota of vegetables but also contain some species that are relevant for public health safety and vegetable shelf-life. Inspite of the relevance of these groups on the phylloshpere of vegetables, there is a comparative dearth of data on the incidence and prevalence of fungal and viral groups on vegetablesComprehensive understanding of the microbial profile of vegetables offers a more accurate assessment of potential food safety, and spoilage risks, and studies should aim to assess the total microbiome of vegetables and vegetable salads.},
}

*Vegetables/microbiology/virology
*Food Microbiology
*Microbiota
*Food Safety
*Fast Foods/microbiology
Humans
Bacteria/classification/isolation & purification
Salads/microbiology
*Food Quality

@article {pmid40467108,
year = {2025},
author = {Ghensi, P and Heidrich, V and Bazzani, D and Asnicar, F and Armanini, F and Bertelle, A and Dell'Acqua, F and Dellasega, E and Waldner, R and Vicentini, D and Bolzan, M and Trevisiol, L and Tomasi, C and Pasolli, E and Segata, N},
title = {Shotgun Metagenomics Identifies in a Cross-Sectional Setting Improved Plaque Microbiome Biomarkers for Peri-Implant Diseases.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.14121},
pmid = {40467108},
issn = {1600-051X},
support = {//Italian Society of Periodontology and Implantology (SIdP)/ ; //Eklund Foundation/ ; //International Team for Implantology (ITI)/ ; /ERC_/European Research Council/International ; //CLC Scientific S.r.l./ ; //PreBiomics S.r.l./ ; },
abstract = {AIM: This observational study aimed to verify and improve the predictive value of plaque microbiome of patients with dental implant for peri-implant diseases.

MATERIALS AND METHODS: Patients were included in one of the following study groups according to the health status of their dental implants: (a) healthy, (b) affected by mucositis and (c) affected by peri-implantitis. From each patient, submucosal plaque microbiome samples were collected from the considered dental implant and from a contralateral healthy implant/tooth. After shotgun metagenomic sequencing, the plaque microbiome was profiled taxonomically and functionally with MetaPhlAn 4 and HUMAnN 3, respectively. Taxonomic and functional profiles were fed into machine-learning models, which were then evaluated with cross-validation to assess the extent to which the plaque microbiome could be used to pinpoint peri-implant diseases.

RESULTS: Shotgun metagenomics sequencing was performed for a total of 158 samples spanning 102 individuals. Four-hundred and forty-seven prokaryotic species were identified as part of the peri-implant microbiome, 34% of which were currently uncharacterized species. At the community level, the peri-implant microbiome differed according to the health status of the implant (p ≤ 0.006 for all pairwise comparisons) but this was site-specific, as healthy contralateral sites showed no discriminating microbiome features. Peri-implantitis microbiomes further showed lower inter-subject variability than healthy plaque microbiomes (p < 0.001), while mucositis-associated microbiomes were in the middle of the continuum between health and peri-implantitis. Each health condition was associated with a strong signature of taxonomic and functional microbiome biomarkers (log10 LDA score ≥ 2.5), 30% and 13% of which represented uncharacterized microbial functions and unknown species, respectively. Distinct Fusobacterium nucleatum clades were associated with implant status, highlighting the subspecies F. nucleatum's functional and phenotypic diversity. Machine-learning models trained on taxonomic or functional plaque microbiome profiles were highly accurate in differentiating clinical groups (AUC = 0.78-0.96) and highlighted the extent to which the peri-implant microbiome is associated with peri-implant clinical parameters (AUC = 0.79-0.87).

CONCLUSIONS: Plaque microbiome profiling with shotgun metagenomics revealed consistent associations between microbiome composition and peri-implant diseases. In addition to pointing to peri-implant-associated microbes, warranting further mechanistic studies, we showed high-resolution plaque microbiome evaluation via metagenomics as an effective tool. Its utility within protocols for clinical management of peri-implant diseases should be explored in the future.},
}

@article {pmid40467103,
year = {2025},
author = {Phi Dang, C and Croitoru, K and Turpin, W},
title = {DUOX2-mediated gut barrier dysfunction: a preclinical mechanism in IBD pathogenesis?.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335565},
pmid = {40467103},
issn = {1468-3288},
}

@article {pmid40466870,
year = {2025},
author = {Gurjar, S and Taliyan, R and Kumari, S and Kesharwani, P},
title = {The interplay of triphala and its constituents with respect to metabolic disorders and gut-microbiome.},
journal = {Fitoterapia},
volume = {},
number = {},
pages = {106642},
doi = {10.1016/j.fitote.2025.106642},
pmid = {40466870},
issn = {1873-6971},
abstract = {Ayurveda is based on natural therapeutic methods that focuses on eliminating toxins from the body and enhancing both physical and mental regeneration using herbal remedies. Medicinal plants have significant elemental and therapeutic value. Triphala (TLP) is a highly potent polyherbal Ayurvedic remedy that is widely regarded as one of the most crucial ayurvedic supplements. This study aims to analyze and comprehend the effectiveness and therapeutic value of TLP and its components by summarizing the pertinent literature based on a selection of publications obtained through a focused search of reliable academic resources. The review primarily emphasizes on the ethnomedical and pharmacological effects of TLP, while also providing a probable explanation of the underlying molecular mechanism. TLP is recognized for its antioxidant, anti-inflammatory, immunomodulatory, antibacterial, antimutagenic, hypoglycemic, antineoplastic, chemoprotective, and radioprotective properties. It is also effective against parasitic infections, and other infectious disorders. Although, the mechanisms are not well explored but these activities are also ascribed to alter the gut microbiota composition. Therefore, it is imperative to undertake rigorous systematic study for TLP in order to identify and assess the chemical ingredients which bring about the change either in gut microbiome composition or increase the number of beneficial gut-microbiota. Hence, this review thoroughly examines the pharmacological advantages of Triphala with special emphasis on molecular mechanisms altering the gut-microbiota prior to its potential utilization in clinical environments.},
}

@article {pmid40466780,
year = {2025},
author = {Yang, Y and Abdelfattah, A and Jia, H and Kumar, V and Jiang, Y and Cheng, L},
title = {Enhanced nitrogen removal by Comamonas 110 colonization and bioaugmentation in sequencing batch activated sludge bioreactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132759},
doi = {10.1016/j.biortech.2025.132759},
pmid = {40466780},
issn = {1873-2976},
abstract = {While pure functional strains demonstrate high pollutant removal efficiency, their environmental persistence remains challenging. This study optimized Comamonas 110 inoculation strategies in activated sludge systems, enhancing nitrogen removal efficiency (44 % of nitrogen removal at day 180) and achieving stable colonization (15.22 % abundance at day 180) through 30 % initial dosage combined with operational parameter regulation. Monod modeling and 16S rRNA sequencing revealed Comamonas 110 suppressed Nitrite-Oxidizing Bacteria (NOB) while boosting Ammonia-Oxidizing Bacteria (AOB). Denitrifying enzymes (NAR and NIR) increased significantly in inoculated reactors, attributing to the substantial presence of Comamonas 110. Metagenomics revealed upregulated (tricarboxylic acid) TCA cycle genes and nitrogen metabolism pathways, optimizing electron transfer for denitrification. Concurrently, Extracellular Polymeric Substance (EPS) synthesis-related genes were activated, promoting co-aggregation with native EPS-producing microbes. This study provides new insights into colonization dynamics of bioaugmentation strains through microbiome-environment interplay.},
}

@article {pmid40466732,
year = {2025},
author = {Markey, W and Srinath, H},
title = {The alarming rise of early-onset colorectal cancer.},
journal = {Australian journal of general practice},
volume = {54},
number = {6},
pages = {392-399},
pmid = {40466732},
issn = {2208-7958},
mesh = {Humans ; *Colorectal Neoplasms/epidemiology/diagnosis ; Australia/epidemiology ; Risk Factors ; Incidence ; Age of Onset ; Early Detection of Cancer/methods/trends/statistics & numerical data ; Female ; Mass Screening/methods/trends/statistics & numerical data ; Male ; Middle Aged ; Adult ; },
abstract = {BACKGROUND: Over the past 20 years of the Australian National Bowel Cancer Screening Program, there has been a reduction in Australia's overall rates of colorectal cancer. However, during this same period, there has been a steady rise in the incidence of early-onset colorectal cancer (EOCRC), presenting a new public health issue.

OBJECTIVE: The aim of this study was to evaluate the literature regarding the rising incidence of EOCRC, highlight the importance of the recent reduction in screening age and document what might be done in a primary healthcare setting.

DISCUSSION: The increasing incidence of EOCRC has been largely attributed to risk factors including a Western diet, obesity, tobacco use and alcohol intake, which contribute to microbiome dysgenesis and chronic inflammation from an early age. In response, the initial screening age for colorectal cancer was lowered to 45 years from July 2024 via an opt-in system; however, there is evidence to support a further reduction in screening age to 40 years.},
}

Humans
*Colorectal Neoplasms/epidemiology/diagnosis
Australia/epidemiology
Risk Factors
Incidence
Age of Onset
Early Detection of Cancer/methods/trends/statistics & numerical data
Female
Mass Screening/methods/trends/statistics & numerical data
Male
Middle Aged
Adult

@article {pmid40466498,
year = {2025},
author = {Egea, LG and Jiménez-Ramos, R},
title = {Antibiotic pollution alters the microbiome and reduces primary production and growth in the seagrass Cymodocea nodosa (Ucria) Ascherson.},
journal = {Marine environmental research},
volume = {210},
number = {},
pages = {107242},
doi = {10.1016/j.marenvres.2025.107242},
pmid = {40466498},
issn = {1879-0291},
abstract = {Antibiotics are considered a contaminant of emerging concern that can affect marine plants and their associated microbiome. To date, limited information is available about the effects of antibiotic pollution on seagrasses. Here, we conducted a seven-day mesocosm experiment in which we exposed the seagrass Cymodocea nodosa to a cocktail of ampicillin, streptomycin, and amoxicillin (with two total concentration exposure levels of 20 and 200 μg L[-1]). At the end of the incubation, we assessed phyllosphere and rhizosphere microbiome composition, plant growth, and carbon metabolism. We found that the seagrass community switched from a highly autotrophic in control (19.41 mmol C m[-2] d[-1]) to a moderately heterotrophic in the high-exposure treatment (-2.74 mmol C m[-2] d[-1]). This decrease in net community production was attributed to (i) a reduction in photosynthetic pigments (from 20 % to 41 %) due to antibiotic-induced oxidative stress in the seagrass chloroplasts and (ii) a change in the phyllosphere that showed lower species richness and abundance (from x0.3 to x0.7-fold lower) in exposure treatments compared to control. Although most bacterial families showed a reduced relative abundance under antibiotic stress, some taxa, including Pseudoalteromonadaceae, Halomonadaceae, and Cellvibrionaceae, were markedly enriched in the phyllosphere. Our results show that phyllosphere bacterial community is more sensitive to antibiotic pollution in the seawater column than rhizosphere community. Long-term antibiotic stress may also promote the development of seagrass diseases. Overall, our results suggest that antibiotic exposure may reduce seagrass growth and health and may compromise their function as a blue carbon sink.},
}

@article {pmid40466388,
year = {2025},
author = {Memariani, H and Memariani, M and Eskandari, SE and Ghasemian, A and Nour Neamatollahi, A},
title = {The potential role of probiotics and their bioactive compounds in the management of pulmonary tuberculosis.},
journal = {Journal of infection and public health},
volume = {18},
number = {9},
pages = {102840},
doi = {10.1016/j.jiph.2025.102840},
pmid = {40466388},
issn = {1876-035X},
abstract = {The significance of gut microbiota in human health is well recognized, yet its effects on pulmonary infectious diseases like tuberculosis (TB) are not thoroughly comprehended. While anti-TB drugs and preventive strategies are indispensable, the incorporation of adjunct therapies, including probiotics and their bioactive compounds, could provide potential biotherapeutic benefits. This review strives to collate the recent experimental and clinical investigations into the manipulation of the gut microbiome through probiotics, exploring their potential to sustain eubiosis, enhance recovery from TB, and mitigate the adverse effects of anti-TB therapies. The multi-pronged mechanisms by which probiotics act against M. tuberculosis include their immunomodulatory properties, the promotion of autophagy, direct inhibition of the pathogen growth via bacteriocin production, the reduction of adverse effects from anti-TB drugs, and a diminished risk of comorbidities. Future research should prioritize high-quality randomized controlled trials that integrate omics with personalized microbiome-based therapeutic approaches to combat TB.},
}

@article {pmid40466265,
year = {2025},
author = {Chang, S and Song, M and Lee, J and Kim, S and Song, D and Jeon, K and Kim, H and Yang, J and Kim, H and Cho, J},
title = {Stimbiotics help improve intestinal immunity and positively modulate the gut microbiome in broilers with necrotic enteritis.},
journal = {Poultry science},
volume = {104},
number = {8},
pages = {105315},
doi = {10.1016/j.psj.2025.105315},
pmid = {40466265},
issn = {1525-3171},
abstract = {This experiment was conducted to investigate the effect of stimbiotic (STB) in broilers with necrotic enteritis (NE) on nutrient digestibility and gut health. A total of 200 one-day-old Arbor Acres (initial body weight of 44.03 ± 0.28 g) were used in this experiment for 28 days. All broilers were randomly allocated into four treatments, and each experimental group had 10 replicate cages with five broilers per cage. The experiment was conducted in a 2 × 2 factorial designs consisting of two levels of challenge (challenge and non-challenge) and two levels of STB (0 and 0.05 %). All broilers in challenged groups were orally challenged by overdosing with coccidia vaccines (× 10 recommended doses; Livacox® Q). The NE challenge significantly decreased (P < 0.05) nutrient digestibility, interferon-γ, heterophil levels in blood, and villus height:crypt depth (VH:CD) compared to the non-challenge group. Also, the NE challenge significantly lower (P < 0.05) ZO-1 and higher MUC2 gene expression than the non-challenge group. Supplementation of 0.05 % STB with NE challenge significantly increased (P < 0.05) gross energy digestibility and decreased (P < 0.05) the number of oocysts per gram of feces compared to the NE-challenged group. Supplementation of 0.05 % STB significantly increased (P < 0.05) the VH:CD in ileum compared to the non-supplementation group. Also, supplementation of 0.05 % STB is significantly lower (P < 0.05) MUC2 and TLR4 gene expression in ileum than the non-supplementation group. At the genus level, the supplementation of 0.05 % STB with NE challenge significantly decreased (P < 0.05) the abundance of Muribaculaceae compared to the NE-challenged group on d 21. In conclusion, supplementation of 0.05 % STB in a diet could positively regulate the cecal microflora and gene expression of tight junction protein and alleviate the decline in nutrient digestibility caused by NE.},
}

@article {pmid40466051,
year = {2025},
author = {Montgomery, ST and Carr, PG and Caparrós-Martín, JA},
title = {Optimisation of DNA Extraction from Nasal Lining Fluid to Assess the Nasal Microbiome Using Third-Generation Sequencing.},
journal = {American journal of respiratory cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1165/rcmb.2025-0046MA},
pmid = {40466051},
issn = {1535-4989},
abstract = {Sampling nasal lining fluid (NLF) via nasosorption is minimally invasive and well tolerated, but the feasibility of assessing the nasal microbiome using these samples is unknown. However, low biomass makes airway samples particularly susceptible to issues related to contaminant DNA. For this study, we collected nasal swabs and NLF from adult volunteers. DNA was extracted from a mock microbial community and NLF using a column-based kit (ZymoBIOMICS), a precipitation-based kit (Qiagen), or a previously published precipitation-based method. Quality and quantity of DNA was assessed and short-read 16S rRNA sequencing performed to assess feasibility and extraction bias. An optimised methodology was used to extract DNA from NLF and nasal swabs, and long-read 16S rRNA sequencing performed to compare microbial profiles between NLF and nasal swabs. All extraction methods recovered DNA from the mock community, but only precipitation-based methods yielded sufficient DNA from NLF. Extraction methodologies significantly affected microbial profiles, with mechanical lysis needed to minimize bias. Profiles obtained from NLF and swabs were comparable with long-read sequencing. Our findings demonstrate the feasibility of profiling the nasal microbiome using NLF and validated two extraction methodologies as suitable for full-length 16S rRNA sequencing of low-biomass respiratory samples. Our data demonstrate the importance of unbiased DNA extraction methodologies in low-biomass respiratory samples. Additionally, we demonstrated NLF may be an appropriate surrogate for swabs to assess the nasal microbiome.},
}

@article {pmid40465720,
year = {2025},
author = {de Porto, AP and Dylla, NP and Stutz, M and Lin, H and Khalid, M and Mullowney, MW and Little, J and Rose, A and Moran, D and McMillin, M and Burgo, V and Smith, R and Woodson, C and Metcalfe, C and Ramaswamy, R and Lehmann, C and Odenwald, M and Bandealy, N and Zhao, J and Kim, M and Adler, E and Sundararajan, A and Sidebottom, A and Kress, JP and Wolfe, KS and Pamer, EG and Patel, BK},
title = {Fecal metabolite profiling identifies critically ill patients with increased 30-day mortality.},
journal = {Science advances},
volume = {11},
number = {23},
pages = {eadt1466},
doi = {10.1126/sciadv.adt1466},
pmid = {40465720},
issn = {2375-2548},
mesh = {Humans ; *Critical Illness/mortality ; *Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Intensive Care Units ; *Metabolome ; Dysbiosis/mortality/microbiology ; Metabolomics/methods ; Prospective Studies ; },
abstract = {Critically ill patients admitted to the medical intensive care unit (MICU) have reduced intestinal microbiota diversity and altered microbiome-associated metabolite concentrations. Metabolites produced by the gut microbiota have been associated with survival of patients receiving complex medical treatments and thus might represent a treatable trait to improve clinical outcomes. We prospectively collected fecal specimens, defined microbiome compositions by shotgun metagenomic sequencing, and quantified microbiota-derived fecal metabolites by mass spectrometry from 196 critically ill patients admitted to the MICU for non-COVID-19 respiratory failure or shock to correlate microbiota features and metabolites with 30-day mortality. Microbiota compositions of the first fecal sample after MICU admission did not independently associate with 30-day mortality. We developed a metabolic dysbiosis score (MDS) that uses fecal concentrations of 13 microbiota-derived metabolites, which predicted 30-day mortality independent of known confounders. The MDS complements existing tools to identify patients at high risk of mortality by incorporating potentially modifiable, microbiome-related, independent contributors to host resilience.},
}

Humans
*Critical Illness/mortality
*Feces/microbiology/chemistry
Male
Female
Middle Aged
*Gastrointestinal Microbiome
Aged
Intensive Care Units
*Metabolome
Dysbiosis/mortality/microbiology
Metabolomics/methods
Prospective Studies