@article {pmid41025644,
year = {2025},
author = {Saito, D and Saito, CPB and Cannavan, FDS and Tsai, SM},
title = {Draft genome sequences of six Rothia mucilaginosa strains assembled from the human oral microbiome.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0050825},
doi = {10.1128/mra.00508-25},
pmid = {41025644},
issn = {2576-098X},
abstract = {We report draft metagenome-assembled genomes (MAGs) of six Rothia mucilaginosa strains recovered from the oral microbiome of distinct human subjects. MAGs were retrieved according to a species-specific genome mapping approach, displaying high average nucleotide identities (≥95.85%) to R. mucilaginosa ATCC 25296's genome and minimal contamination levels (≤3.75%).},
}

@article {pmid41023926,
year = {2025},
author = {Chen, Y and Chen, Z and Xu, D and Li, S and Chen, F and Yu, X and Cai, S and Zeng, C and Ye, X and Yang, J and Liu, J and Lin, J and Xiao, S},
title = {Early prediction of bloodstream infections in ICU patients using machine learning methods based on routine laboratory parameters.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1196},
pmid = {41023926},
issn = {1471-2334},
abstract = {BACKGROUND: Bloodstream infections (BSIs) are a major cause of morbidity and mortality in Intensive Care Units (ICUs). Although blood cultures remain the diagnostic gold standard, their long turnaround time may hinder early risk warning. Early risk stratification using routinely available laboratory data may facilitate prompt clinical intervention. This study aimed to develop and validate machine learning (ML) models to predict the likelihood of BSIs in ICU patients based on laboratory tests obtained within the first 24 h of admission.

METHODS: This was a retrospective, two-center cohort study using data from the Sixth Affiliated Hospital of Sun Yat-sen University (SAH-SYSU) and the Medical Information Mart for Intensive Care IV (MIMIC, v3.0) database. Adult ICU patients (≥ 18 years) with available first-day laboratory results and blood culture data were included. Multiple ML algorithms, including random forest, XGBoost, GBM, LightGBM, and SVM, were trained and validated using tenfold cross-validation. Model performance was assessed via area under the receiver operating characteristic curve (AUROC), calibration curves, Brier score, and decision curve analysis (DCA). Feature selection was conducted using the Boruta algorithm to develop simplified models. External validation was performed across cohorts using shared features.

RESULTS: A total of 754 patients from SAH-SYSU (BSI prevalence: 27.7%) and 3,136 patients from MIMIC (BSI prevalence: 14.0%) were included. Tree-based models outperformed linear classifiers. In internal validation, XGBoost achieved the best performance (AUROC = 0.87 in MIMIC, 0.83 in SYSU). Simplified models using Boruta-selected features retained similar predictive performance (p > 0.05). Cross-cohort validation yielded AUROCs of 0.61 (MIMIC → SYSU) and 0.64 (SYSU → MIMIC). A compact four-feature model demonstrated moderate performance (AUROC up to 0.65), supporting feasibility in resource-limited settings.

CONCLUSIONS: ML-based models using only routine laboratory tests from the first ICU day can effectively identify patients at increased risk of BSIs. These models offer a rapid, interpretable, and generalizable tool for early clinical decision-making. Future studies should prospectively validate the model and explore its integration into electronic health records to support real-time risk stratification.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-025-11580-4.},
}

@article {pmid41023588,
year = {2025},
author = {Nascimento, T and Inácio, J and Guerreiro, D and Patrício, P and Proença, L and Toscano, C and Barroso, H},
title = {Exploring the skin mycobiome in intensive care patients: a pilot study on fungal diversity from axillary and groin swabs.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {589},
pmid = {41023588},
issn = {1471-2180},
support = {10.54499/UIDB/04585/2020//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {Humans ; Pilot Projects ; *Skin/microbiology ; *Mycobiome ; Male ; *Fungi/classification/isolation & purification/genetics ; Female ; Intensive Care Units ; Middle Aged ; Aged ; *Axilla/microbiology ; *Groin/microbiology ; DNA, Fungal/genetics ; Adult ; Critical Illness ; Biodiversity ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {The skin mycobiome is a largely unexplored component of the human microbiome, especially in critically ill patients. Fungal colonisation in the Intensive Care Unit (ICU) may be influenced by underlying comorbidities and hospital-related risk factors, potentially impacting patient outcomes. This pilot study aimed to characterize the diversity and abundance of skin fungi in ICU patients during their first week of hospitalization. A total of 35 ICU patients were recruited and divided into two groups: Group 1 (patients with 1-2 comorbidities and ICU risk factors) and Group 2 (patients with more than 2 comorbidities and ICU risk factors). Bilateral axillary-groin swabs were collected on admission day (D1) and after one week of ICU stay (D8) for fungal identification. Culture-based methods and MALDI-TOF MS were initially used, followed by Internal Transcribed Spacer 2 (ITS2) sequencing via the Illumina MiSeq platform for in-depth analysis of fungal communities. Fungal diversity and relative abundance were assessed using standard alpha and beta diversity metrics. Culture and MALDI-TOF MS identified only Candida spp., suggesting limited diversity. ITS2 sequencing revealed that Candida (69.3%) was the most prevalent genus, followed by Penicillium (10.3%) and Cladosporium (4.0%), with Malassezia being rare (0.7%). Diversity analysis indicated a relatively stable fungal community throughout the first week (ANOSIM, p = 0.499), with no significant changes in species richness or community structure. By Day 8, Candida spp. represented 79.9% and 78.9% of the mycobiome in Groups 1 and 2, respectively. Preliminary data suggest that the ICU skin mycobiome is dominated by Candida spp. and exhibits low fungal diversity. These findings provide foundational insight into the skin mycobiome of critically ill patients and underscore the need for further research to elucidate its clinical significance and potential role in patient management.},
}

Humans
Pilot Projects
*Skin/microbiology
*Mycobiome
Male
*Fungi/classification/isolation & purification/genetics
Female
Intensive Care Units
Middle Aged
Aged
*Axilla/microbiology
*Groin/microbiology
DNA, Fungal/genetics
Adult
Critical Illness
Biodiversity
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

@article {pmid41022221,
year = {2025},
author = {Delic, M and Butorova, I and Kuskov, A},
title = {Chitosan application in cosmetics and dermatology - Antimicrobial and prebiotic potential to control human microbiome.},
journal = {Journal of biotechnology},
volume = {408},
number = {},
pages = {217-231},
doi = {10.1016/j.jbiotec.2025.09.014},
pmid = {41022221},
issn = {1873-4863},
abstract = {The human microbiome has become a critically important field of study, with recent advances continuously revealing new aspects of its functional roles. A deeper understanding of the complex metabolic interactions between the microbiome, therapeutic agents, and the human host is now developing. A key challenge is the development of effective novel antimicrobial compounds, particularly those targeting biofilm-related infections implicated in a wide range of chronic diseases, to better control the human microbiota and treat typical skin diseases. Chitosan, a polysaccharide derived from various natural sources, possesses a unique set of biological properties, making it a promising base for numerous cosmetic and medicinal products aimed at managing dermatological diseases and modulating the microbiome. By altering its characteristics, chitosan's properties can be tuned to produce biomacromolecules with optimized activity beneficial to human microbiota. This review summarizes the sources and mechanisms underlying chitosan's antimicrobial activity, its immunomodulatory and anti-pathogenic effects, and critically evaluates its dual potential as both an antimicrobial and a prebiotic agent. Special emphasis is placed on chitosan-based formulations for treating skin diseases and promoting microbiome health - an emerging and promising area of research.},
}

@article {pmid41015042,
year = {2025},
author = {Fang, S and Qin, Y and Lian, H and Zhong, Y and Yang, Y and Yu, XD and Yang, S and Liang, J and Xiao, W and Wen, S and Zhang, XM and Li, B and Huang, L},
title = {Reduced oxytocin signaling in the dBNST drives the transition from acute pain to persistent anxiety.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.09.012},
pmid = {41015042},
issn = {1879-0445},
abstract = {Transient sensory experiences can trigger sustained emotional disturbances, yet the underlying neural mechanisms remain unclear. Here, we show that acute pain induces persistent anxiety in male mice, independent of ongoing nociceptive input, through reduced oxytocin signaling in the dorsal bed nucleus of the stria terminalis (dBNST). Reactivating oxytocin receptors (Oxtrs) in the dBNST markedly alleviated anxiety-like behaviors following pain resolution. Mechanistically, chemogenetic inhibition of somatostatin-expressing (SST) neurons in the dBNST (dBNST[SST] neurons) abolished oxytocin's anxiolytic effects, while pharmacological blockade or selective knockdown of Oxtrs in these neurons increased anxiety-like behaviors. Transcriptomic and electrophysiological analyses further revealed that alterations in synaptic transmission and intrinsic excitability participate in this anxiety state. Together, these findings define a multilevel framework-spanning molecular, cellular, and circuit mechanisms-by which acute sensory input induces long-term emotional dysregulation. This study advances our understanding of pain-related affective disorders and highlights oxytocin signaling and dBNST[SST] neurons as promising therapeutic targets.},
}

@article {pmid41013188,
year = {2025},
author = {Xuan, P and Wang, R and Gu, J and Cui, H and Zhang, T},
title = {Structure-sensitive transformer and multi-view graph contrastive learning enhanced prediction of drug-related microbes.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {231},
pmid = {41013188},
issn = {1471-2105},
support = {2024A1515010176//Guangdong Basic and Applied Basic Research Foundation/ ; 62372282, 62172143//Natural Science Foundation of China/ ; 62372282, 62172143//Natural Science Foundation of China/ ; NTF22032//STU Scientific Research Initiation Grant/ ; },
mesh = {Humans ; *Machine Learning ; *Microbiota/drug effects ; *Computational Biology/methods ; Algorithms ; Semantics ; },
abstract = {BACKGROUND: The human microbiome plays a crucial role in regulating the efficacy and toxicity of drugs as well as in developing the drugs. Therefore, predicting the drug-related microbes is beneficial for analyzing the functional mechanisms of drugs. Recently, the graph learning based methods demonstrated their advantages in extracting the node features from the biological heterogeneous graphs. However, the previous methods failed to completely preserve the intrinsic structures of biological data and did not fully utilize the topological and positional information for predicting the drug-microbe associations.

RESULTS: We propose a new prediction model, structure-sensitive transformer and multi-view graph contrastive learning for microbe-drug association prediction (SMMDA), to encode and integrate the topological structures, semantics, and multiple-view embedding features of the drugs and microbes. Considering the sparsity of the original features of drugs and microbes, the learnable data augmentation strategy is designed to learn their global representations. Since similar drugs are more likely to associate with the similar microbes, a structure-sensitive transformer is proposed to integrate the topology structures composed of drugs (microbes) to form the multi-view embedding features. We design two contrastive learning strategies to exploit the complementary semantics across multiple views. As the embedding features from multiple views have various semantics, we design view-level attention to adaptively integrate these features.

CONCLUSIONS: The extensive experimental results show that SMMDA outperforms several state-of-the-art methods for predicting the drug-related candidate microbes. The ablation studies show the effectiveness of the major innovations which include the learnable data augmentation, structure-sensitive transformer-based node feature learning, and multi-view contrastive learning. The case studies on three drugs also demonstrate SMMDA's capability in retrieving the potential microbe candidates for the drugs.},
}

Humans
*Machine Learning
*Microbiota/drug effects
*Computational Biology/methods
Algorithms
Semantics

@article {pmid41011478,
year = {2025},
author = {Cortés, M and Olate, P and Rodriguez, R and Diaz, R and Martínez, A and Hernández, G and Sepulveda, N and Paz, EA and Quiñones, J},
title = {Human Microbiome as an Immunoregulatory Axis: Mechanisms, Dysbiosis, and Therapeutic Modulation.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092147},
pmid = {41011478},
issn = {2076-2607},
support = {N° 21231033//Agencia Nacional de Investigación y Desarrollo/ ; },
abstract = {The human microbiome plays a central role in modulating the immune system and maintaining immunophysiological homeostasis, contributing to the prevention of immune-mediated diseases. In particular, the gut microbiota is a key ecosystem for immune system maturation, especially in early life. This review aimed to analyze the molecular and cellular mechanisms linking the microbiome to immune and neuronal functions, as well as the impact of dysbiosis and emerging therapeutic strategies targeting the microbiome. The analysis was based on scientific databases, prioritizing studies published since 2000, with special emphasis on the past decade. The microbiome influences immune signaling through microorganism-associated molecular patterns (MAMPs) and pattern recognition receptors (PRRs), including Toll-like receptors (TLRs). Additionally, microbial metabolites-such as short-chain fatty acids (SCFAs), tryptophan derivatives, and secondary bile acids-exert significant immunomodulatory effects. The intestinal epithelial barrier is also described as an active immunological interface contributing to systemic regulation. The literature highlights innovative therapies, including fecal microbiota transplantation (FMT), probiotics, and microbiome editing with CRISPR-Cas technologies. These strategies aim to restore microbial balance and improve immune outcomes. The growing body of evidence positions the microbiome as a valuable clinical and diagnostic target, with significant potential for application in personalized medicine.},
}

@article {pmid41011312,
year = {2025},
author = {Corona-Angeles, JA and Martínez-Pulido, RL and Oregon-Romero, E and Palafox-Sánchez, CA},
title = {Role of the Microbiome and Its Metabolites in Primary Sjögren's Syndrome.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13091979},
pmid = {41011312},
issn = {2076-2607},
abstract = {Primary Sjögren's syndrome (pSS) is a chronic, autoimmune rheumatic disease characterized by progressive lymphocytic infiltration of the exocrine glands, leading to inflammation and subsequent tissue damage. As a multifactorial disease, its etiology is complex, making it difficult to predict disease progression. Among the environmental factors implicated in pSS, the involvement of microorganisms has gained increasing attention. Since the launch of the Human Microbiome Project, growing evidence has highlighted the role of dysbiosis in the pathogenesis of various autoimmune diseases, including pSS. Shifts in the abundance of specific bacterial phyla can lead to corresponding changes in the levels of key microbial metabolites involved in tissue homeostasis and immune regulation-such as short-chain fatty acids (SCFAs), choline, taurine, serine, lactate, and tryptophan and their metabolites. Understanding the mechanisms by which these metabolites influence immune processes may provide deeper insights into the progression of the disease. Therefore, this review aims to explore the mechanisms through which microbiota-derived metabolites contribute to the pathophysiology of primary Sjögren's syndrome.},
}

@article {pmid41009770,
year = {2025},
author = {Pita-Galeana, MA and Ruhle, M and López-Vázquez, L and de Anda-Jáuregui, G and Hernández-Lemus, E},
title = {Computational Metagenomics: State of the Art.},
journal = {International journal of molecular sciences},
volume = {26},
number = {18},
pages = {},
doi = {10.3390/ijms26189206},
pmid = {41009770},
issn = {1422-0067},
mesh = {*Metagenomics/methods ; Humans ; *Microbiota/genetics ; *Computational Biology/methods ; Machine Learning ; Metagenome ; },
abstract = {Computational metagenomics has revolutionized our understanding of the human microbiome, enabling the characterization of microbial diversity, the prediction of functional capabilities, and the identification of associations with human health outcomes. This review provides a concise yet comprehensive overview of state-of-the-art computational approaches in metagenomics, alongside widely used methods and tools employed in amplicon-based metagenomics. It is intended as an introductory resource for new researchers, outlining key methodologies, challenges, and future directions in the field. We discuss recent advances in bioinformatics pipelines, machine learning (ML) models, and integrative frameworks that are transforming our understanding of the microbiome's role in health and disease. By addressing current limitations and proposing innovative solutions, this review aims to outline a roadmap for future research and clinical translation in computational metagenomics.},
}

*Metagenomics/methods
Humans
*Microbiota/genetics
*Computational Biology/methods
Machine Learning
Metagenome

@article {pmid41000747,
year = {2025},
author = {Tripp, AD and Qu, EB and Balogun, I and Brodsky, J and Baker, JS and Mancuso, CP and Roux, S and Hussain, FA and Lieberman, TD},
title = {Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.09.675206},
pmid = {41000747},
issn = {2692-8205},
abstract = {Despite Cutibacterium acnes being the most abundant and prevalent bacteria on human skin, only a single type of phage has been identified that infects this host. Here, we leverage this one-to-one system to systematically characterize how the phage-bacteria arms race shapes C. acnes evolution and community composition on individual people. Our analysis reveals a surprising lack of phage-mediated selection despite global prevalence of C. acnes phages. Analysis of anti-phage defense systems across 3,205 bacterial genomes revealed a limited, phylogenetically restricted defense repertoire under weak selective pressure to diversify or be maintained. Functional assays did not reveal alternative phage resistance mechanisms or fitness costs associated with defense gene carriage that could explain this limited immune arsenal. This lack of pressure to maintain phage resistance could not be explained by lack of phage colonization, as examination of 471 global human facial skin metagenomes demonstrated that even in samples with high virus-to-microbe ratio, phage-sensitive clades dominate on-person populations. Together, these findings indicate that phage pressure, while present, does not play a critical role in determining strain fitness and success within C. acnes populations on human skin. We propose that this observed weak phage-mediated selective pressure can be explained by the anatomy of skin: C. acnes growth is thought to occur at the bottom of pores, where exposure to phage may be limited by physical barriers. Together, this portrait of a static arms race provides a strong contrast with other microbial species in different ecosystems and expands understanding of phage-bacteria interactions in the human microbiome.},
}

@article {pmid40999889,
year = {2025},
author = {Tu, Z and Lin, J and Li, Z and Zhu, Y and Xu, C and Qiu, Z and Wang, Q and Ye, Y and Wen, Y and Li, J and Leong, KW and Wen, W},
title = {Tackling Allergic Airway Inflammation with Organic Sheet-Like Nanoplatforms by Targeted Elimination of Epithelial Small Extracellular Vesicles.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04197},
doi = {10.1002/advs.202504197},
pmid = {40999889},
issn = {2198-3844},
support = {82271188//National Natural Science Foundation of China/ ; 82020108009//National Natural Science Foundation of China/ ; 81900918//National Natural Science Foundation of China/ ; 2022QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; 2025A04J7163//Funding by Science and Technology Projects in Guangzhou/ ; 2023P-ZD06//Key Clinical Technique of Guangzhou/ ; 2023B1111040004//Guangdong Natural Science Foundation of China/ ; 2022A1515010002//Guangdong Natural Science Foundation of China/ ; 2022A1515010506//Guangdong Natural Science Foundation of China/ ; },
abstract = {Allergic airway inflammatory disorders, such as allergic rhinitis (AR) and asthma, affect the health of more than one billion people worldwide, yet therapeutic outcomes remain unsatisfactory. 2D nanomaterials are extensively adopted in biomedical research, but their inorganic components often limit clinical applications. To address these challenges, functionalized "inorganic-free" nanosheets PNSE are developed as a potential strategy for alleviating allergic inflammation via targeted elimination of epithelial small extracellular vesicles (sEVs). PNSE are prepared using template-based synthesis technology and modified with epidermal growth factor receptor aptamers, which exhibit low cytotoxicity, mild protein adsorption, and potent epithelial sEVs binding efficacy. PNSE suppresses sEVs-triggered stimulator of interferon genes activation, alleviating the dendritic cell maturation and eosinophil extracellular trap formation in vitro. In addition, PNSE displays exceptional biocompatibility, preferential airway localization, and robust modulation for allergic airway inflammation in vivo. Transcriptome analysis and multi-channel flow cytometry of airway tissues further confirm the alleviation of dysregulated airway inflammation in house dust mite-stimulated animal models. These results highlight the pivotal feature of the organic sheet-like nanoplatforms for targeted clearance of epithelial sEVs, which can be exploited as a nanomedicine for the treatment of allergic airway inflammation and also other allergic disorders.},
}

@article {pmid40997670,
year = {2025},
author = {Cho, HS and Lee, JW and Cha, HE and Seo, J and Lim, SK},
title = {Comparative analysis of skin microbiome across 10 sites in Koreans for forensic applications: a pilot study.},
journal = {Legal medicine (Tokyo, Japan)},
volume = {78},
number = {},
pages = {102706},
doi = {10.1016/j.legalmed.2025.102706},
pmid = {40997670},
issn = {1873-4162},
abstract = {Various microorganisms have a symbiotic relationship with human skin cells, influenced by intrinsic and extrinsic factors. The composition of the human microbiome varies based on the skin site. To investigate the microbial characteristics of different skin sites in Koreans, microbiome samples were collected from the scalp, forehead, cheek, retroauricular crease, cervical vertebrae, axilla, palm, lateral finger, femur, and plantar skin. The concentrations of human and bacterial DNA were quantified, and QIIME2 and MicrobiomeAnalyst platforms were used for microbial analysis. Forehead and cheek microbiome compositions were similar, with higher proportions of Streptococcus than that at other sites. Palm and lateral finger microbiome compositions were also similar, with higher proportions of Haemophilus than that at other sites. Lawsonella was specifically observed on the scalp, while Mycoplasma was found on cervical vertebrae. Staphylococcus, observed on all sites, was particularly predominant on axilla. The microbial composition of plantar was distinct, with no prevalent genus compared to that at other sites. Further research analyzing skin microbiomes from forensic evidence could help identify the origin of skin samples, aiding in crime scene reconstruction. Comparing our findings from Korean participants with international studies, it suggests that expanding research to include diverse populations could reveal regional and national differences in skin microbiomes, providing valuable insights for forensic science.},
}

@article {pmid40996703,
year = {2025},
author = {Sierra, MA and Ryon, K and Arikatla, MR and Elshafey, R and Bhaskar, H and Proszynski, J and Bhattacharya, C and Shaaban, H and Danko, DC and Ambrose, P and Spaulding, SA and Zambrano, MM and Consortium, TMD and Mason, CE},
title = {The Microbe Directory: a centralized database for biological interpretation of microbiome data.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
doi = {10.1093/database/baaf060},
pmid = {40996703},
issn = {1758-0463},
support = {U01DA053941/NH/NIH HHS/United States ; U54AG089334/NH/NIH HHS/United States ; R01AI151059/NH/NIH HHS/United States ; 80NSSC24K0728/NASA/NASA/United States ; 80NSSC24K1052/NASA/NASA/United States ; //WorldQuant Foundation/ ; },
mesh = {*Microbiota/genetics ; Humans ; *Databases, Genetic ; Data Curation ; Metadata ; Animals ; Metagenomics ; },
abstract = {The Microbe Directory (TMD) is a centralized database of metadata for microbes from all domains that helps with the biological interpretation of metagenomic data. The database comprises phenotypical and ecological traits of microorganisms, which have been verified by independent manual annotations. This effort has been possible by the help of a community of volunteer students worldwide who were trained in manual curation of microbiology data. To summarize this information, we have built an interactive browser that makes the database accessible to everyone, including non-bioinformaticians. We used the TMD data to analyse microbiome samples from different projects such as MetaSUB, TARA Oceans, Human Microbiome Project, and Sponge Microbiome Project, showcasing the utility of TMD. Furthermore, we compare our microbial annotations with annotations collected by artificial intelligence (AI) and demonstrate that despite the high speed of AI in reviewing and collecting microbial data, annotation requires domain knowledge and therefore manual curation. Collectively, TMD provides a unique source of information that can help to interpret microbiome data and uncover biological associations. Database URL: www.themicrobedirectory.com/.},
}

*Microbiota/genetics
Humans
*Databases, Genetic
Data Curation
Metadata
Animals
Metagenomics

@article {pmid40996271,
year = {2025},
author = {Wong, MK and Armstrong, E and Heirali, AA and Schneeberger, PHH and Chen, H and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B},
title = {Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial.},
journal = {mBio},
volume = {},
number = {},
pages = {e0190425},
doi = {10.1128/mbio.01904-25},
pmid = {40996271},
issn = {2150-7511},
abstract = {Composition and function of the gut microbiome are associated with diverse health conditions and treatment responses. Human microbiota-associated (HMA) mouse models are used to establish causal links for these associations but have important limitations. We assessed the fidelity of HMA mouse models in recapitulating ecological responses to a microbial consortium using stools collected from a human clinical trial. HMA mice were generated using different routes of consortium exposure, and their ecological features were compared to human donors by metagenomic sequencing. HMA mice resembled other mice more than their respective human donors in gut microbial composition and function, with taxa including Akkermansia muciniphila and Bacteroides spp. enriched in mouse recipients. A limited repertoire of microbes was able to engraft into HMA mice regardless of route of consortium exposure. In publicly available HMA mouse data sets from four distinct health conditions, we confirmed our observation that a taxonomically restricted set of microbes reproducibly engrafts in HMA mice and observed that stool microbiome composition of HMA mice was more like other mice than their human donor. Our data suggest that HMA mice are limited models for assessing the ecological impact of microbial consortia, with ecological effects in HMA mice being more strongly associated with host species than donor stool ecology or ecological responses to treatment in humans. Comparisons to published studies suggest this may be due to comparatively large host-species effects that overshadow ecological effects of treatments in humans that HMA models aim to recapitulate.IMPORTANCEHMA mice are models that better represent human gut ecology compared to conventional laboratory mice and are commonly used to test the effects of the gut microbiome on disease or treatment response. We evaluated the fidelity of using HMA mice as avatars of ecological response to a human microbial consortium, Microbial Ecosystem Therapeutic 4. Our results show that HMA mice in our cohort and across other published studies are more similar to each other than the human donors or inoculum they are derived from and harbor a taxonomically restricted gut microbiome. These findings highlight the limitations of HMA mice in evaluating the ecological effects of complex human microbiome-targeting interventions, such as microbial consortia.},
}

@article {pmid40990521,
year = {2025},
author = {Robinson, JM and Breed, MF},
title = {Beyond microbial exposure and colonization: multisensory shaping of the gut microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0110725},
doi = {10.1128/msystems.01107-25},
pmid = {40990521},
issn = {2379-5077},
abstract = {Microorganisms play a fundamental role in human health, contributing to digestion, immune regulation, and metabolic processes. While direct colonization by environmental microbes through ingestion, inhalation, and dermal contact has been documented, evidence suggests that multisensory interactions with nature-via visual, auditory, tactile, gustatory, and olfactory stimuli-also influence the gut microbiome through psychophysiological and immune-mediated pathways. Exposure to natural environments can regulate stress and immune responses, activate the parasympathetic nervous system, and modulate the hypothalamic-pituitary-adrenal and gut-brain axes, which in turn may alter gut microbiome composition and function. Furthermore, sensory interactions with nature may induce epigenetic changes that impact immune function and microbiome dynamics over time. Here, we review evidence for nature-based indirect shaping of the human microbiome (including multisensory and exposure-immunoregulation pathways) and suggest that after the early-life critical window of microbiome development (0-3 years), these indirect effects likely have a greater influence on gut microbiome dynamics than direct colonization by environmental microbiota (e.g., ingested directly from the air). However, this concept remains to be comprehensively tested. Therefore, understanding the relative contributions of direct microbial colonization versus indirect effects-such as multisensory stimulation and immune modulation-demands more integrated, transdisciplinary research. Integrating these insights into public health strategies, urban design, and nature-based interventions could promote microbiome eubiosis, ultimately improving human (and non-human animal) well-being in an era of increasing environmental and health challenges.},
}

@article {pmid40986279,
year = {2025},
author = {Korsurat, S and Koslovsky, MD},
title = {A Bayesian semiparametric mixture model for clustering zero-inflated microbiome data.},
journal = {Biometrics},
volume = {81},
number = {3},
pages = {},
doi = {10.1093/biomtc/ujaf125},
pmid = {40986279},
issn = {1541-0420},
support = {DMS-2245492//National Science Foundation/ ; },
mesh = {Bayes Theorem ; Humans ; Cluster Analysis ; *Models, Statistical ; Computer Simulation ; *Microbiota ; *Gastrointestinal Microbiome ; Diarrhea/microbiology ; },
abstract = {Microbiome research has immense potential for unlocking insights into human health and disease. A common goal in human microbiome research is identifying subgroups of individuals with similar microbial composition that may be linked to specific health states or environmental exposures. However, existing clustering methods are often not equipped to accommodate the complex structure of microbiome data and typically make limiting assumptions regarding the number of clusters in the data which can bias inference. Designed for zero-inflated multivariate compositional count data collected in microbiome research, we propose a novel Bayesian semiparametric mixture modeling framework that simultaneously learns the number of clusters in the data while performing cluster allocation. In simulation, we demonstrate the clustering performance of our method compared to distance- and model-based alternatives and the importance of accommodating zero-inflation when present in the data. We then apply the model to identify clusters in microbiome data collected in a study designed to investigate the relation between gut microbial composition and enteric diarrheal disease.},
}

Bayes Theorem
Humans
Cluster Analysis
*Models, Statistical
Computer Simulation
*Microbiota
*Gastrointestinal Microbiome
Diarrhea/microbiology

@article {pmid40985730,
year = {2025},
author = {Farmer, NM and Benezra, A and Maki, KA and Ishaq, SL and Kozik, AJ},
title = {Prioritizing precision: guidelines for the better use of population descriptors in human microbiome research.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0064025},
doi = {10.1128/msystems.00640-25},
pmid = {40985730},
issn = {2379-5077},
abstract = {Microbiome science is a celebration of the connections between humans, our environment, and microbial organisms. We are continually learning more about our microbial fingerprint, how each microbiome may respond to identical stimuli differently, and how the quality of the environmental conditions around us influences the microorganisms we encounter and acquire. However, in this process of self-discovery, we have utilized socially constructed ideas about ourselves as biological factors, potentially obscuring the true nature of our relationships to each other, microbes, and the planet. The concept of race, which has continuously changing definitions over hundreds of years, is frequently operationalized as a proxy for biological variation and suggested to have a real impact on the microbiome. Scientists across disciplines and through decades of research have misused race as a biological determinant, resulting in falsely scientific justifications for social and political discrimination. However, concepts of race and ethnicity are highly nuanced, inconsistent, and culturally specific. Without training, microbiome researchers risk continuing to misconstrue these concepts as fixed biological factors that have direct impacts on our microbiomes and/or health. In 2023, the National Academies of Sciences, Engineering, and Medicine released recommendations on the use of population descriptors such as race and ethnicity in genetic science. In this paper, we posit similar recommendations that can and must be translated into microbiome science to avoid re-biologizing race and that push us toward the goal of understanding the microbiome as an engine of adaptation to help us thrive in a dynamic world.},
}

@article {pmid40985585,
year = {2025},
author = {Imre, A and Crook, N},
title = {The emerging roles of non-Saccharomyces yeasts in fermented foods and human health.},
journal = {FEMS yeast research},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsyr/foaf056},
pmid = {40985585},
issn = {1567-1364},
abstract = {Yeasts play a crucial role in the maturation of fermented foods, with Saccharomyces cerevisiae standing out as the most prominent among them. However, in recent years, there has been a growing interest in the roles and applications of non-Saccharomyces yeasts in fermented products. Their contribution to shape the characteristics of fermented foods like wine, beer, sourdough bread, cheese, and kombucha is undeniable, yet our understanding of the specific effects of each species remains incomplete in certain cases. In this mini-review, we collected and summarized studies that aimed to gain deeper understanding of the microbial dynamics and roles of non-Saccharomyces yeasts during the fermentation and development of alcoholic and non-alcoholic fermentations, as well as highlight that non-Saccharomyces yeasts are recently also recognized for benefiting the human microbiome as probiotics, further expanding their potential contributions to human health and supplementation.},
}

@article {pmid40983700,
year = {2025},
author = {Xiang, G and Wang, Y and Ni, K and Luo, H and Liu, Q and Song, Y and Miao, P and He, L and Jian, Y and Yang, Z and Chen, T and Xu, K and Sun, X and Shen, Z and Ji, C and Zhao, N and He, M and Pan, Y and Luo, Y and Hu, J and Otto, M and Li, M},
title = {Nasal Staphylococcus aureus carriage promotes depressive behaviour in mice via sex hormone degradation.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40983700},
issn = {2058-5276},
support = {AI000904//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; 82472288//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82302595//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82172325//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The human microbiome has a pronounced impact on human physiology and behaviour. Despite its unique anatomical connection to the brain, the role of the nasal microbiome in neurological diseases is understudied. Here, using human data and experiments in mice, we show that nasal Staphylococcus aureus is linked to depression. Nasal microbiome analyses revealed a positive correlation between depression scores and S. aureus abundance among patients with depression and healthy controls. Metabolomics of the nasal cavity showed decreased sex hormones, estradiol and testosterone in patients with depression versus controls. Nasal microbiota transplants from patients reproduced depression-like behaviour in mice with differential abundance of S. aureus. Further homology and mutational analysis uncovered an S. aureus sex hormone-degrading enzyme, 17b-hydroxysteroid dehydrogenase (Hsd12), which degraded testosterone and estradiol in mice, leading to lower levels of dopamine and serotonin in the murine brain. These findings reveal a nasal commensal that influences depressive behaviour and provides insights into the nose-brain axis.},
}

@article {pmid40983504,
year = {2025},
author = {Zhou, T and Zhao, F},
title = {AI-empowered human microbiome research.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335946},
pmid = {40983504},
issn = {1468-3288},
abstract = {Recent advances in high-throughput microbiome profiling have generated expansive data sets that offer unprecedented opportunities to investigate the role of microbes in human health. However, the complexity and high dimensionality of these data present significant analytical challenges that often exceed the capabilities of traditional computational methods. Artificial intelligence (AI), encompassing both classical machine learning and modern deep learning approaches, has emerged as a powerful solution to these challenges. In this review, we systematically explore AI-driven methodologies in microbiome research, including clustering algorithms, dimensionality reduction techniques, convolutional and recurrent neural networks, and emerging large language models. We assess how these approaches enable the extraction of meaningful biological patterns from complex microbial data from a multiscale perspective, facilitating insights into community dynamics, host-microbe interactions and functional genomics. Additionally, we explore the transformative impact of AI on translational applications across both academic research and real-world clinical settings, including disease diagnostics, therapeutic development and precision microbiome engineering. By critically evaluating the current capabilities and limitations of AI in this context, this review aims to chart a path forward for the integration of AI into microbiome research, ultimately accelerating innovations in personalised medicine and deepening our understanding of host-microbiome relationships.},
}

@article {pmid40982389,
year = {2025},
author = {Pizzini, JD and Midani, FS and Britton, RA},
title = {Updated Protocol for the Assembly and Use of the Minibioreactor Array (MBRA).},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {223},
pages = {},
doi = {10.3791/68788},
pmid = {40982389},
issn = {1940-087X},
mesh = {*Bioreactors/microbiology ; *Microbiota/physiology ; Humans ; },
abstract = {The human microbiome comprises diverse and dynamic microbial communities that play essential roles in host health. Understanding these communities and their responses to environmental factors is critical for advancing microbiome-based therapeutics. Traditional in vitro models for cultivating human-derived microbiota often lack scalability and require extensive technical expertise, limiting their accessibility and throughput. To address these limitations, we developed the Minibioreactor Array (MBRA) system -- a modular, single-stage, continuous-flow platform for high-throughput cultivation of microbial communities. This system enables parallel cultivation of up to 48 distinct microbial communities, supporting experimental flexibility while maintaining the stable growth of complex ecosystems. This protocol provides detailed guidance on MBRA fabrication, assembly, sterilization, and operation. The system's modular design allows for easy integration into anaerobic chambers and supports customization for a wide range of experimental applications. It has been used to study microbial responses to antibiotics, dietary compounds, and pathogen invasion, and to screen for pathogen-resistant communities. With its accessibility, scalability, and reproducibility, the MBRA represents a powerful model system for investigating microbial interactions and advancing microbiome research.},
}

*Bioreactors/microbiology
*Microbiota/physiology
Humans

@article {pmid40981537,
year = {2025},
author = {Nichter, M},
title = {Public Understanding of Gut Health and the Human Microbiome in the USA: An Exploratory Study.},
journal = {Medical anthropology},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/01459740.2025.2558836},
pmid = {40981537},
issn = {1545-5882},
abstract = {At a time of rising public interest in the human microbiome and calls for increased microbe literacy in public health, few studies have explored how different segments of the US public understand gut health. To address this gap, An exploratory ethnographic study was conducted in Southern Arizona. The study identified five themes that encompass Pasteurian militaristic and post-Pasteurian ecological perceptions of gut health, gut adaptability, and probiotic/antibiotic influence on" natural immunity." Future microbe literacy programs will need to engage with local ideas about gut health, build upon points of convergence with bioscience, and identify points of divergence that challenge public health initiatives.},
}

@article {pmid40981416,
year = {2025},
author = {Mulay, SA and Vishnivetskaya, TA and Hochanadel, LH and Klingeman, DM and Lloyd, KG and Pelletier, DA and Podar, M},
title = {BONCAT-Live for isolation and cultivation of active environmental bacteria.},
journal = {mBio},
volume = {},
number = {},
pages = {e0238925},
doi = {10.1128/mbio.02389-25},
pmid = {40981416},
issn = {2150-7511},
abstract = {In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including associations with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular, and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating individual microbial cells that respond to specific changes for cultivation has been difficult. To address this, we implemented a novel bacterial isolation approach (BONCAT-Live) by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient-enriched conditions. From the Populus tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in-depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities.IMPORTANCEDynamic microbial activity transforms environments and impacts health and disease in associations with plants and animals, including humans. Identifying the contribution of individual microbes to those processes in real time has not been generally compatible with their selective cultivation. BONCAT-Live tracks which bacteria in environmental samples are translationally active and couples it with single-cell isolation and cultivation. By studying the response of individual community members to specific natural or induced physical or chemical changes in the environment and culturing those organisms, BONCAT-Live enables further insights into microbial metabolic strategies, community dynamics, and environmental adaptations.},
}

@article {pmid40972768,
year = {2025},
author = {Dhakal, B and Kishore, LS and Sayed, K},
title = {Integrating multi-compartment microbiome data with clinical parameters enhances mortality prediction using autoencoder.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107267},
doi = {10.1016/j.mimet.2025.107267},
pmid = {40972768},
issn = {1872-8359},
abstract = {The human microbiome, a complex ecosystem of microorganisms residing in different body compartments, significantly influences health outcomes and disease progression, however, leveraging this data for developing clinical prediction models remains challenging due to its high dimensionality, sparsity, and compositional nature. Traditional machine learning approaches often struggle to capture the intricate microbial interactions that contribute to mortality risk, particularly when analyzing data across multiple compartments with distinct microbial compositions. To address these limitations, we introduce a novel framework utilizing an autoencoder-based model trained on high-dimensional microbiome data collected from oral, lung, and gut compartments. Our approach encodes microbiome data into a low-dimensional latent space while preserving essential microbial community characteristics, enabling more effective feature extraction and pattern recognition than conventional dimensionality reduction techniques. Through systematic evaluation of three data configurations-microbiome taxa only, clinical data only, and an integrated model combining both-we demonstrated that the integrated approach consistently achieved superior prediction accuracy (98 % in lung microbiome) compared to using either data source independently. Clinical data alone provided reasonable but inconsistent performance (70-90 %), while microbiome taxa alone yielded the weakest results (53-65 %). Furthermore, our investigation of preprocessing techniques revealed that applying z-score normalization to the taxa data significantly enhanced performance and substantially improved recall metrics across all compartments. By analyzing compartment-specific microbial contributions, our study reveals distinct predictive roles of the oral and lung microbiomes compared to the gut microbiome, underscoring of body-site specificity in microbiome-based predictive modeling.},
}

@article {pmid40970967,
year = {2025},
author = {Lee, Y and Seo, H and Lee, S and Choi, D and Kim, S and Rahim, MA and Song, HY},
title = {Therapeutic potential of Bacillus sonorensis PMC204 membrane vesicles against drug-resistant Mycobacterium tuberculosis.},
journal = {Medical microbiology and immunology},
volume = {214},
number = {1},
pages = {43},
pmid = {40970967},
issn = {1432-1831},
support = {RS-2023-00219563//Ministry of Science and ICT, South Korea/ ; },
mesh = {*Mycobacterium tuberculosis/drug effects ; Mice ; Animals ; RAW 264.7 Cells ; *Probiotics/pharmacology ; *Bacillus/physiology/metabolism ; Macrophages/microbiology ; *Tuberculosis, Multidrug-Resistant/therapy ; Proteomics ; *Extracellular Vesicles/chemistry ; Antitubercular Agents/pharmacology ; Flagellin/metabolism ; },
abstract = {Tuberculosis remains a severe global health threat, exacerbated by the rising prevalence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis. Despite the urgent need for effective interventions, the development of anti-tuberculosis drugs has been slow, and the emergence of pan-drug-resistant strains underscores the critical need for innovative therapeutic strategies. This study introduces Bacillus sonorensis PMC204, a novel probiotic strain with potent anti-tuberculosis properties identified through extensive screening. PMC204 significantly reduced M. tuberculosis H37Rv and XDR strains within Raw 264.7 macrophage cells. Moreover, membrane vesicles (MVs) derived from this strain exhibited superior inhibitory effects against both standard and XDR strains of M. tuberculosis. Proteomic analysis of the isolated MVs revealed a high abundance of flagellin proteins, which are hypothesized to play a pivotal role in the observed anti-tuberculosis effects. These findings also suggest a close link between the therapeutic efficacy of PMC204 and autophagy activation. Safety assessments further demonstrated the feasibility of PMC204 as a potential anti-tuberculosis therapeutic. The anti-tuberculosis activity of bacterial MVs represents an innovative approach in microbiome therapeutics, positioning PMC204 as a next-generation probiotic distinct from conventional strains. This study contributes to advancing the field of microbiome-based therapeutics and presents promising avenues for managing drug-resistant tuberculosis.},
}

*Mycobacterium tuberculosis/drug effects
Mice
Animals
RAW 264.7 Cells
*Probiotics/pharmacology
*Bacillus/physiology/metabolism
Macrophages/microbiology
*Tuberculosis, Multidrug-Resistant/therapy
Proteomics
*Extracellular Vesicles/chemistry
Antitubercular Agents/pharmacology
Flagellin/metabolism

@article {pmid40967861,
year = {2025},
author = {Ma, Y and Si, JH and Sun, DJY and Yu, CQ and Pang, YJ and Lyu, J and Li, LM},
title = {[Progress in population-based research of human microbiome and cardiovascular diseases].},
journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi},
volume = {46},
number = {9},
pages = {1680-1687},
doi = {10.3760/cma.j.cn112338-20241219-00816},
pmid = {40967861},
issn = {0254-6450},
support = {2023ZD0510101, 2023ZD0510100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; },
mesh = {Humans ; *Cardiovascular Diseases/microbiology ; *Microbiota ; Metagenomics ; },
abstract = {The human microbiome encompasses a diverse array of microorganisms and their functional interactions within the human body. It exhibits a vast diversity of species and complex roles across various body environments. Advanced sequencing technologies, such as 16S amplicon sequencing and metagenomic sequencing, facilitate in-depth analysis on this microbial community. Recent researches have suggested that characteristics of the human microbiome (such as diversity and composition of microbiome, involving metabolic pathways and metabolites) might be associated with the onset and progression of cardiovascular diseases. These findings provide valuable insights into the etiology of chronic diseases and might aid in the development of novel disease biomarkers and intervention strategies. This paper summarizes the designs, current status and key findings of current population-based research in this field, and introduce the future development and analyze the existing critical problems that need further investigations.},
}

Humans
*Cardiovascular Diseases/microbiology
*Microbiota
Metagenomics

@article {pmid40955307,
year = {2025},
author = {Li, W and Liu, Q and Chen, S and Zhi, M and Yang, P and Zhang, Y and Wu, Z and Zhang, J and Feng, Q},
title = {Salidroside Improves Periodontitis by Mitigating Inflammatory Reactions and Enhancing Osteogenic Differentiation of Human Periodontal Ligament Stem Cells.},
journal = {Drug design, development and therapy},
volume = {19},
number = {},
pages = {8097-8114},
pmid = {40955307},
issn = {1177-8881},
mesh = {*Periodontal Ligament/drug effects/cytology/pathology ; *Glucosides/pharmacology/administration & dosage ; Humans ; *Osteogenesis/drug effects ; *Periodontitis/drug therapy/pathology/metabolism ; *Phenols/pharmacology/administration & dosage ; *Cell Differentiation/drug effects ; Animals ; Rats ; *Stem Cells/drug effects/metabolism ; *Inflammation/drug therapy/metabolism/pathology ; Cells, Cultured ; Dose-Response Relationship, Drug ; Male ; Rats, Sprague-Dawley ; Lipopolysaccharides/antagonists & inhibitors/pharmacology ; Disease Models, Animal ; },
abstract = {PURPOSE: Salidroside (Sal), a significant bioactive compound found in Rhodiola rosea, is documented to possess various pharmacological properties. This study investigated the effects of Sal in alleviating periodontitis.

METHODS: The rat periodontitis model was utilized to assess the therapeutic impact of Sal on periodontitis. Human periodontal ligament stem cells (hPDLSCs) were used to investigate the effect of Sal on lipopolysaccharide (LPS)-inhibited osteogenic differentiation. RNA sequencing (RNA-seq), and Western blot were employed to analyze the genes and proteins impacted by Sal treatment.

RESULTS: Sal significantly alleviated the alveolar bone loss and gingival inflammation in rats periodontitis model. Sal demonstrated a dose-dependent pattern of promoting osteogenesis on hPDLSCs. A concentration of 0.5 μM Sal could effectively counteract the impact of LPS on osteogenic differentiation. Mechanically, Sal inhibited the ratios of phospho-IκBα(p-IκBα)/IκBα and phospho-p65(p-p65)/p65 in Nuclear Factor kappa-B (NF-κB) pathway and reduced the expressions of interleukin-6 (IL-6) and interleukin-8 (IL-8). Sal increased the expression of lymphoid enhancer-binding factor 1 (LEF1).

CONCLUSION: Sal promoted the osteogenic differentiation by inhibiting the activation of the NF-κB pathway and increasing the expression of LEF1.},
}

*Periodontal Ligament/drug effects/cytology/pathology
*Glucosides/pharmacology/administration & dosage
Humans
*Osteogenesis/drug effects
*Periodontitis/drug therapy/pathology/metabolism
*Phenols/pharmacology/administration & dosage
*Cell Differentiation/drug effects
Animals
Rats
*Stem Cells/drug effects/metabolism
*Inflammation/drug therapy/metabolism/pathology
Cells, Cultured
Dose-Response Relationship, Drug
Male
Rats, Sprague-Dawley
Lipopolysaccharides/antagonists & inhibitors/pharmacology
Disease Models, Animal

@article {pmid40946177,
year = {2025},
author = {Shi, JH and Tang, QL and Wang, JH and Long, YL and Zhao, SF and Zhao, Z and Xie, WT and Li, ZM and Lu, HM and Gao, TX and Fang, ZZ and Zhou, T and Li, BX and Yang, X and Gao, GQ and Qi, WW},
title = {Pigment Epithelium-Derived Factor Deficiency Impairs Hippocampal Glutamate Homeostasis and Cognitive Function by Downregulating Astrocytic GLT-1.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e00402},
doi = {10.1002/advs.202500402},
pmid = {40946177},
issn = {2198-3844},
support = {82273116//National Natural Science Foundation of China/ ; 82203661//National Natural Science Foundation of China/ ; 2024A1515010149//Guangdong Natural Science Fund/ ; 2023A1515010214//Guangdong Natural Science Fund/ ; 202102100004//Guangzhou Key Laboratory for Metabolic Diseases/ ; },
abstract = {Maintenance of glutamate homeostasis is essential for synaptic plasticity and cognition. Disrupted glutamate-glutamine cycling causes chronic excitotoxicity, a key driver of cognitive deficits in Alzheimer's disease (AD), though regulatory mechanisms remain unclear. Pigment epithelium-derived factor (PEDF), a neuroprotective protein declining with age, is demonstrated here to play a novel role in synaptic glutamate clearance. Analysis of peripheral blood samples from 19 patients with AD and 75 non-dementia control subjects revealed lower levels of PEDF in patients, and loss of PEDF correlates with cognitive decline. PEDF-deficient mice exhibit defective learning and memory, and higher susceptibility to AD. Furthermore, PEDF deficiency impaired synaptic plasticity and dendritic spine morphology. Mechanistically, PEDF inhibits ubiquitin-proteasome-dependent degradation of astrocytic glutamate transporter-1 (GLT-1) and normally guarantees elimination of synaptic glutamate by modulating the protein kinase C signaling pathway. Strikingly, restoring PEDF rescued cognitive deficits in a mouse model of AD, and upregulation of GLT-1 rescued cognitive impairment in PEDF-deficient mice. Collectively, these findings reveal PEDF is a physiologic regulator of synaptic glutamate homeostasis. Targeting PEDF deficiency-induced neural impairment may provide a novel avenue for the development of new therapeutic applications for neurodegenerative diseases associated with glutamate-induced excitotoxicity.},
}

@article {pmid40944126,
year = {2025},
author = {Napier, BA and Allegretti, JR and Feuerstadt, P and Kelly, CR and Van Hise, NW and Jäger, R and Kassam, Z and Reid, G},
title = {Multi-Species Synbiotic Supplementation Enhances Gut Microbial Diversity, Increases Urolithin A and Butyrate Production, and Reduces Inflammation in Healthy Adults: A Randomized, Placebo-Controlled Trial.},
journal = {Nutrients},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/nu17172734},
pmid = {40944126},
issn = {2072-6643},
support = {N/A//Seed Health, Inc./ ; },
abstract = {Background: In healthy adults, probiotic supplementation alone does not increase Urolithin A (UroA) and rarely increases butyrate, both microbiome-derived metabolites that influence key biological functions involved in regulating gastrointestinal symptoms. Accordingly, this clinical trial evaluated key biological functions of a multi-species synbiotic with 24 probiotic strains and a polyphenol-based prebiotic using capsule-in-capsule delivery technology. Methods: We conducted a randomized, placebo-controlled trial among healthy participants (n = 32). Participants were administered a daily synbiotic (53.6 billion AFU multi-species probiotic and 400 mg Indian pomegranate extract; DS-01) or matching placebo for 91 days. Samples were obtained at baseline Day 0, and Days 7, 14, 49, and 91. Endpoints included changes in fecal microbiome composition, urinary UroA, fecal butyrate, serum CRP, and safety. Results: The synbiotic significantly increased alpha-diversity of Bifidobacterium and Lactobacillus spp. at all timepoints, including at end-of-study (Day 91, p < 0.0001) and increased native beneficial microbes. UroA production was significantly increased in the synbiotic arm at short-term (Day 7, 12-fold, p < 0.02) and long-term (Day 91, 49-fold, p < 0.001) timepoints. A higher proportion of synbiotic participants were capable of converting polyphenols into UroA (Day 91, 100% vs. 44.4%; p < 0.01). Mechanistically, synbiotic participants showed an increased abundance of Lactobacillus species involved in UroA precursor metabolism and UroA-producing Gordonibacter species. The synbiotic also significantly increased fecal butyrate levels (p < 0.03), and butyrate-producing species, in low-baseline butyrate producers, through Day 91, and was associated with reduced systemic inflammation. Conclusions: This multi-species synbiotic significantly increases diversity and abundance of key beneficial bacteria, enhances UroA production and butyrate levels, and is associated with lowered systemic inflammation. This is the first synbiotic to increase both UroA and butyrate.},
}

@article {pmid40943494,
year = {2025},
author = {Barraza-Ortega, E and Gómez-Gil, B and García-Gasca, T and Lizárraga, D and Díaz, N and García-Gasca, A},
title = {The Impact of Lifestyle on Reproductive Health: Microbial Complexity, Hormonal Dysfunction, and Pregnancy Outcomes.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178574},
pmid = {40943494},
issn = {1422-0067},
abstract = {Endocrine dysfunctions refer to alterations in hormone production, release, or regulation that can significantly impact health. In pregnant women or those planning pregnancy, these conditions may manifest as disorders such as polycystic ovary syndrome, hypothyroidism, endometriosis, gestational diabetes mellitus, and other metabolic issues, which could potentially cause infertility or pregnancy complications. Research and clinical experience indicate that hormones play a crucial role in basic physiology and are essential for overall health and well-being. At the same time, lifestyle-defined as daily habits related to nutrition, exercise, sleep, stress management, and other factors-directly influences microbial composition and hormonal regulation. The human microbiome, a diverse community of microorganisms residing within the human body, plays essential roles in supporting overall health. The increasing prevalence of hormonal disorders, especially in urban populations, has heightened interest in how modern lifestyles-characterised by sedentary habits, chronic stress, imbalanced diets, and inadequate sleep-may contribute to the development or aggravation of these conditions, leading to higher infertility rates or pregnancy complications if untreated. This review investigates the interaction between hormonal dysfunction, the human microbiome, and lifestyle factors, with a focus on their effects on pregnant women and those seeking to conceive. Its purpose is to provide a comprehensive overview of the underlying pathophysiological mechanisms and to examine preventative and therapeutic approaches that could alter these patterns.},
}

@article {pmid40938107,
year = {2025},
author = {Stinson, LF and Pang, WW and Rea, A and Fok, D and Chua, MC and Tan, KH and Yap, F and Godfrey, KM and Shek, LP and Eriksson, JG and Chong, Y-S and Chan, S-Y and Wlodek, M and Geddes, DT},
title = {Composition of the human milk microbiome in the GUSTO cohort is shaped by intrapartum antibiotic prophylaxis and breastfeeding exclusivity.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0067725},
doi = {10.1128/msystems.00677-25},
pmid = {40938107},
issn = {2379-5077},
abstract = {Human milk contains a low biomass microbiome, which is thought to contribute to mammary and infant health. However, the determinants of the human milk microbiome across populations are poorly understood. Here, we characterized the microbiome of 266 milk samples collected from 208 mothers at 3 weeks and 3 months postpartum from the Growing Up in Singapore Toward healthy Outcomes (GUSTO) study, a multi-ethnic Asian cohort. Full-length 16S rRNA gene sequencing showed a substantial level of inter-individual variation, as well as temporal variation, highlighting the need for broad-scale longitudinal sampling in this field. Milk microbiome composition and diversity were associated with maternal, socioeconomic, and breastfeeding factors. In particular, intrapartum antibiotic prophylaxis and breastfeeding exclusivity modulated milk bacterial composition and diversity, even at 3 months postpartum. These results highlight the dynamic nature of the human milk microbiome and its relationship with clinical and breastfeeding factors, with potential implications for infant health.IMPORTANCEHuman milk exposes infants to a constant source of maternal bacteria that may influence the development of the infant immune system and gut microbiome. However, compared to other body niches, the human milk microbiome is relatively under-studied, and there is limited consensus on the factors driving variance in these bacterial communities. In this study, we performed in-depth microbiome profiling of milk samples from 208 mothers in a diverse Asian population, finding a high level of variation between individuals and over time. We found that factors such as delivery-related antibiotics, breastfeeding practices, and maternal lifestyle can influence which bacteria are present in milk. These findings suggest that the milk microbiome is not static, but dynamic and shaped by both medical and social factors. Understanding what drives variance in the milk microbiome could help inform strategies to support maternal and infant health, especially in the critical early months of life when microbial exposures can have long-term effects.},
}

@article {pmid40930165,
year = {2025},
author = {Chen, L and Zhang, Z and Yang, S and Tang, Y and Wang, X and Li, W and Yang, L and Guo, C and Fang, S and Xiao, W and Yan, M and Li, Y and Peng, T and Li, B and Zhang, XM and Huang, L},
title = {Developmental Neuroplasticity Enables Recovery from Anesthetic-Induced Synaptic Perturbations in the Immature Brain.},
journal = {Neurochemistry international},
volume = {},
number = {},
pages = {106051},
doi = {10.1016/j.neuint.2025.106051},
pmid = {40930165},
issn = {1872-9754},
abstract = {General anesthetics are essential in pediatric medicine, yet concerns persist regarding their potential neurotoxic effects on the developing brain. Whether transient synaptic disruptions caused by anesthesia lead to long-term deficits or are mitigated by endogenous plasticity remains unresolved. Here, we use longitudinal in vivo two-photon imaging in awake mice to investigate the structural and functional consequences of a single, clinically relevant exposure to sevoflurane at postnatal day 20. We find that sevoflurane induces transient behavioral hyperactivity and suppresses filopodia elimination. Remarkably, these effects are fully reversed within 24 hours. Across a 10-day follow-up, we observe no persistent alterations in synaptogenesis, neuronal activity, motor learning, or anxiety-like behavior. Electrophysiological recording and calcium imaging further confirm the restoration of normal firing and synaptic transmission in layer 5 pyramidal neurons. These findings reveal a dual-phase recovery mechanism-acute plasticity followed by chronic convergence-highlighting the developing brain's intrinsic resilience to transient anesthetic insults. Our study redefines sevoflurane not as a source of irreversible neurotoxicity but as a temporary challenge that can be effectively buffered by developmental neuroplasticity, offering important reassurance for its continued use in pediatric anesthesia.},
}

@article {pmid40928632,
year = {2025},
author = {Mafe, AN and Smart, OO and Edo, GI and Akpoghelie, PO and Gaaz, TS and Yousif, E and Isoje, EF and Igbuku, UA and Ismael, SA and Essaghah, AEA and Ahmed, DS and Ozsahin, DU and Umar, H},
title = {Genesis, Health Benefits, and Future Perspectives of Probiotics: Exploring Endogenous and Exogenous Classes, Innovations, and Research Gaps.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40928632},
issn = {1867-1314},
abstract = {Probiotics are live beneficial microorganisms that confer health benefits to the host when administered in adequate amounts, have gained considerable scientific and commercial interest for their ability to support gut health, strengthen immunity, and reduce disease risk. This review traces the genesis of probiotic science from its origins in traditional fermented foods to contemporary clinical applications, offering a conceptual understanding of its evolution. A clear distinction is drawn between endogenous probiotics, naturally resident in the human microbiome, and exogenous probiotics, introduced via dietary supplements and functional foods. The broad spectrum of documented health benefits is examined, encompassing digestive, immune, metabolic, neurological, and dermatological outcomes. Recent innovations are highlighted, including bioengineered probiotic strains with targeted therapeutic functions, the integration of probiotics with prebiotics as synbiotics, and advanced delivery systems such as microencapsulation and nanotechnology. Special attention is given to regulatory frameworks, with global comparisons and a focused case study on Argentina, alongside a structured roadmap for translating research into market-ready products. The review also addresses inclusivity in probiotic use, emphasizing safety considerations across diverse populations, and underscores the strain-specific nature of probiotic effects. Current challenges such as commercialization gaps, regulatory inconsistencies, and underexplored applications in non-digestive health domains are critically discussed. The conclusion calls for interdisciplinary collaboration among microbiologists, nutritionists, clinicians, and technologists to accelerate innovation, ensure equitable access, and maximize the potential of probiotics in promoting health and preventing disease.},
}

@article {pmid40928232,
year = {2025},
author = {Allman, HM and Bernate, EP and Franck, E and Oliaro, FJ and Hartmann, EM and Crofts, TS},
title = {Preparation of functional metagenomic libraries from low biomass samples using METa assembly and their application to capture antibiotic resistance genes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0103925},
doi = {10.1128/msystems.01039-25},
pmid = {40928232},
issn = {2379-5077},
abstract = {A significant challenge in the field of microbiology is the functional annotation of novel genes from microbiomes. The increasing pace of sequencing technology development has made solving this challenge in a high-throughput manner even more important. Functional metagenomics offers a sequence-naive and cultivation-independent solution. Unfortunately, most methods for constructing functional metagenomic libraries require large input masses of metagenomic DNA, putting many sample types out of reach. Here, we show that our functional metagenomic library preparation method, METa assembly, can be used to prepare useful libraries from much lower input DNA quantities. Standard methods of functional metagenomic library preparation generally call for 5-60 µg of input metagenomic DNA. We demonstrate that the threshold for input DNA mass can be lowered at least to 30.5 ng, a 3-log decrease from prior art. We prepared functional metagenomic libraries using between 30.5 ng and 100 ng of metagenomic DNA and found that despite their limited input mass, they were sufficient to link MFS transporters lacking substrate-specific annotations to tetracycline resistance and capture a gene encoding a novel GNAT family acetyltransferase that represents a new streptothricin acetyltransferase, satB. Our preparation of functional metagenomic libraries from aquatic samples and a human stool swab demonstrates that METa assembly can be used to prepare functional metagenomic libraries from microbiomes that were previously incompatible with this approach.IMPORTANCEBacterial genes in microbial communities, including those that give resistance to antibiotics, are often so novel that sequencing-based approaches cannot predict their functions. Functional metagenomic libraries offer a high-throughput, sequence-naive solution to this problem, but their use is often held back due to their need for large quantities of metagenomic DNA. We demonstrate that our functional metagenomic library preparation method, METa assembly, can prepare these libraries using as little as ~30 ng of DNA, approximately 1,000-fold less than other methods. We use METa assembly to prepare functional metagenomic libraries from low-biomass aquatic and fecal swab microbiomes and show that they are home to novel tetracycline efflux pumps and a new family of streptothricin resistance gene, respectively. The efficiency of the METa assembly library preparation method makes many otherwise off-limits, low-biomass microbiome samples compatible with functional metagenomics.},
}

@article {pmid40927450,
year = {2025},
author = {Montecillo, JAV and Lee, JH and Yoo, HJ and Lee, YY and Park, CM and Cho, A and Lee, H and Kim, JM and Lee, NY and Park, SH and Park, NJ and Han, HS and Chong, GO and Seo, I},
title = {Characterization of Streptococcus mitis subsp. carlssonii isolated from human vagina: prevalence, phenotypic, and genomic insights.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1625724},
pmid = {40927450},
issn = {1664-302X},
abstract = {The genus Streptococcus is a heterogenous group of commensal and pathogenic bacteria. Members of this genus are classified into two major groups, the pyogenic group and the viridans group streptococci (VGS). VGS are frequently found as normal members of the human microbiome and are regarded as commensals. In this work, we characterized a VGS strain isolated from the vaginal swab sample of a Korean patient diagnosed with endometrial cancer. Phylogenetic, phenotypic, and genome-based analyses confirmed the classification of the strain K0074 as a member of the S. mitis complex. Based on the phylogenetic analyses, the species belonged to the recently established Streptococcus mitis subsp. carlssonii. The strain was found to be rare in the vaginal microbiome, but prevalent in the oral and nasal microbiome samples. K0074 neither triggered an inflammatory response nor caused cytolytic and cytotoxic effects on human cervical cancer cell line. Genome analysis uncovered the genetic basis of the strain's metabolism, virulence factors, and potential antimicrobial resistance phenotypes. Moreover, comparative genomics of the strain and closely related species and subspecies highlighted their striking differences in gene properties and biological functions. Overall, the new strain exhibited low virulence and pathogenic potentials and thus, is regarded as a commensal member of the human microflora. The genetic divergence of K0074 from closely related strains offers a compelling foundation for future investigations into the strain's potential functional specialization and its adaptation within the vaginal microbiome.},
}

@article {pmid40925462,
year = {2025},
author = {Eggestein, A and Urban, S and Hümmer, E and Nunes, N and Zenk, J and Reiger, M and Aglas, L and Traidl-Hoffmann, C and Gilles, S},
title = {Towards real life exposure: nasal epithelial cell stimulation with pollen particle aerosols.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122762},
doi = {10.1016/j.envres.2025.122762},
pmid = {40925462},
issn = {1096-0953},
abstract = {BACKGROUND: Currently, most researchers apply pollen extracts or -suspensions to assess the effects of pollen exposure on airway epithelia. How respiratory epithelia respond to pollen aerosols is not well studied because standardised methods to aerosolize pollen were not available until recently.

AIM OF STUDY: To develop and test a near-natural exposure model for pollen grains based on differentiated human nasal epithelial cells and a novel particle aerosoliser.

METHODS: Primary human nasal epithelial cells were differentiated at the air-liquid interface and exposed to birch, timothy grass and ragweed pollen, either as aqueous extract, suspension, or particle aerosol generated with the VitroCell PowderX device. Morphology, physical barrier function, and cytokine responses were compared.

RESULTS: The cells responded to pollen aerosol exposure with strong mucus production and coordinated ciliary beating in attempt to clear the pollen grains. Pollen aerosols did not affect the transepithelial electrical resistance (TEER), whereas grass pollen extracts led to a significant TEER decrease. Extract exposure resulted in apical and basolateral cytokine release; aerosol exposure led to a directed, predominantly basolateral dose-dependent cytokine response. Cytokine responses to birch, grass and ragweed pollen differed, with birch pollen inducing lower levels of inflammatory cytokines, while timothy and ragweed pollen induced high levels of inflammatory cytokines and alarmins.

CONCLUSION: We were able to establish and characterize a biologically relevant pollen aerosol exposure system characterized by a directed cytokine response. The differences in response patterns to different pollen types likely reflect differential sensitization mechanisms, warranting further research.},
}

@article {pmid40920071,
year = {2025},
author = {Dallon, E and Moran, HM and Chidambaran, SR and Kian, A and Huang, BYH and Fried, SD and DiRuggiero, J},
title = {Investigation of the global translational response to oxidative stress in the model archaeon Haloferax volcanii reveals untranslated small RNAs with ribosome occupancy.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0034325},
doi = {10.1128/msphere.00343-25},
pmid = {40920071},
issn = {2379-5042},
abstract = {Oxidative stress induces a wide range of cellular damage, often causing disease and cell death. While many organisms are susceptible to the effects of oxidative stress, haloarchaea have adapted to be highly resistant. Several aspects of the haloarchaeal oxidative stress response have been characterized; however, little is known about the impacts of oxidative stress at the translation level. Using the model archaeon Haloferax volcanii, we performed RNA-seq and ribosome profiling (Ribo-seq) to characterize the global translation landscape during oxidative stress. We identified 281 genes with differential translation efficiency (TE). Downregulated genes were enriched in ribosomal and translation proteins, in addition to peroxidases and genes involved in the TCA cycle. We also identified 42 small noncoding RNAs (sRNAs) with ribosome occupancy. Size distributions of ribosome footprints revealed distinct patterns for coding and noncoding genes, with 12 sRNAs matching the pattern of coding genes, and mass spectrometry confirming the presence of seven small proteins encoded by these sRNAs. However, the majority of sRNAs with ribosome occupancy had no evidence of coding potential. Of these ribosome-associated sRNAs, 12 had differential ribosome occupancy or TE during oxidative stress, suggesting that they may play a regulatory role during the oxidative stress response. Our findings on ribosomal regulation during oxidative stress, coupled with potential roles for ribosome-associated noncoding sRNAs and sRNA-derived small proteins in H. volcanii, revealed additional regulatory layers and underscored the multifaceted architecture of stress-responsive regulatory networks.IMPORTANCEArchaea are found in diverse environments, including as members of the human microbiome, and are known to play essential ecological roles in major geochemical cycles. The study of archaeal biology has expanded our understanding of the evolution of eukaryotes, uncovered novel biological systems, and revealed new opportunities for applications in biotechnology and bioremediation. Many archaeal systems, however, remain poorly characterized. Using Haloferax volcanii as a model, we investigated the global translation landscape during oxidative stress. Our findings expand current knowledge of translational regulation in archaea and further illustrate the complexity of stress-responsive gene regulation.},
}

@article {pmid40915424,
year = {2025},
author = {Mancera Azamar, KM and Sudi, SD and Mohammadalizadeh, Z and Coffin, C and Parker, IK and Porras, AM},
title = {Innovative engineering approaches to model host-microbiome interactions in vitro.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {115677},
doi = {10.1016/j.addr.2025.115677},
pmid = {40915424},
issn = {1872-8294},
abstract = {The human microbiome plays a critical role in health and disease. Disruptions in microbiota composition or function have been implicated not only as markers but also as drivers of diverse pathologies, creating opportunities for targeted microbiome interventions. Advancing these therapies requires experimental models that can unravel the complex, bidirectional interactions between human tissue and microbial communities. This scoping review examines emerging engineering approaches to design in vitro platforms that successfully integrate host and microbial components to model these interactions. Compared to traditional in vitro and in vivo approaches, these advanced microphysiological systems offer greater experimental control, human-specific biology, and reduced cost and ethical concerns. Here, we identify key challenges in the creation of these in vitro models and innovative solutions to address them by leveraging microfluidics, biomaterials, and organoid technologies, among others. These strategies have enabled the development of co-culture systems that replicate critical features of host-microbiome interfaces, including mucosal barriers, oxygen and pH gradients, mechanical stimuli, and host cell diversity. We also describe how these physiologically relevant models are uncovering new insights into epithelial-microbiota crosstalk, immune modulation by commensal microbes, and systemic effects of microbiota and their metabolites across multiple body sites. We conclude by discussing opportunities to expand these systems in scale, complexity, and clinical relevance. As these models continue to evolve, they hold the potential to transform our ability to mechanistically probe microbiome interactions, personalize therapeutic strategies, and accelerate the translation of microbiome science into clinical practice.},
}

@article {pmid40915391,
year = {2025},
author = {Suvi T, J and Anh, NN and Xiaobo, H and Kirsten, N and Leo, H and Lari, P and Pirkka T, P and Pia, D and Tinja, L and Nelli, H and Santtu, H and Sini M, L and Anu, K and Olli, V and Tomas, S and Jussi, H and Maria F, P and Eliisa, K},
title = {B cell dysregulation during acute COVID-19 is transient.},
journal = {Immunology letters},
volume = {},
number = {},
pages = {107086},
doi = {10.1016/j.imlet.2025.107086},
pmid = {40915391},
issn = {1879-0542},
abstract = {BACKGROUND: COVID-19 is still a significant health concern worldwide. B cell responses to COVID-19 have been extensively studied in acute severe disease, but less so during extended follow-up or mild disease. Persisting immunological changes together with herpesvirus reactivations during acute COVID-19 have been suggested as contributing factors for post-acute sequelae of COVID-19 (PASC). Here, we evaluated the natural kinetics of B cell subpopulations together with serological markers of increased B cell activity during acute COVID-19 and long-term follow-up. We also measured human herpesvirus reactivations during acute COVID-19.

METHODS: We collected plasma and peripheral blood mononuclear cell samples from 120 SARS-CoV-2 positive patients (outpatients = 56, inpatients = 64) at up to five timepoints during acute disease and recovery (up to 460 days since symptom onset, dsso). We determined circulating B cell and Th cell subpopulations using flow cytometry, and measured free light chains, in addition to Epstein-Barr virus (EBV) serology, and herpesvirus qPCR from the plasma samples. The presence of anosmia as a proxy for PASC was self-reported at 3-12 months post-COVID.

RESULTS: All changes in B cell subpopulation proportions normalized within 200 dsso. Likewise, the acute alterations observed in circulating T follicular helper and T follicular regulatory cell proportions stabilized soon after. Free light chains were high in acute COVID-19, especially in inpatients, but normalized during follow-up. EBV and human herpesvirus 6B (HHV-6B) reactivations were significantly more common in inpatients than outpatients, with reactivation in 47 and 19% of inpatients and 4.3 and 0% of outpatients respectively. Anosmia was not significantly associated with any herpesvirus reactivation.

CONCLUSIONS: The circulating B cell and Th cell subpopulations experience transitional changes during SARS-CoV-2 infection, but these changes recover in follow-up. EBV and HHV-6B reactivations are common in inpatients, but they are not associated with persisting anosmia.},
}

@article {pmid40913709,
year = {2025},
author = {Jamal, A and Kamal, MA and Alqurashi, YE and Al-Malki, ES and Naiyer, MM and Hussain, SA and Hattiwale, HM},
title = {The microbiome-cancer axis as a hidden contributor to early-onset tumorigenesis.},
journal = {Medical oncology (Northwood, London, England)},
volume = {42},
number = {10},
pages = {464},
pmid = {40913709},
issn = {1559-131X},
mesh = {Humans ; *Neoplasms/microbiology ; *Carcinogenesis/pathology ; *Gastrointestinal Microbiome ; *Microbiota ; Dysbiosis/microbiology ; Age of Onset ; },
abstract = {The global incidence of early-onset cancer has surged by nearly 80% over the past three decades, yet the underlying causes remain poorly understood. While genetics and lifestyle are among the traditional risk factors, emerging evidence implicates the human microbiome as a potent and overlooked contributor to early tumorigenesis. Increases in the studies that are exploring the tissue-specific microbiome signatures such as the enrichment of Actinomyces and Bacteroidia in early-onset colorectal cancer, or Enterobacter and Neisseria in pancreatic tumors offer compelling evidence for age-stratified microbial contributions. Additionally, the recent works on the establishment of gut-testis, oral-gut, and gut-liver microbial axes are being explored to understand the modulation of systemic immune and endocrine landscapes in younger individuals that might unravel their unique predisposition to malignancy. Further, the microbiome-cancer axis has been regarded as a hidden driver in the initiation and progression of early-onset malignancies across diverse tissue types. Understanding this link will provide the missing mechanistic insights showcasing how microbial dysbiosis, biofilm formation, and microbially derived metabolites promote oncogenic inflammation, DNA damage, and immune evasion contributing to early-onset cancers. Considering the potential of these studies, microbial biomarkers with diagnostic promises that include probiotics, fecal microbiota transplantation, and diet have also been explored as emerging tools for prevention and therapy. Through this study, we aim to understand early-onset cancer through a patient microbiota and underscore an urgent need to integrate microbial dynamics into cancer surveillance and intervention strategies, especially for young and largely asymptomatic populations.},
}

Humans
*Neoplasms/microbiology
*Carcinogenesis/pathology
*Gastrointestinal Microbiome
*Microbiota
Dysbiosis/microbiology
Age of Onset

@article {pmid40904056,
year = {2025},
author = {Dassanayake, P and Diksha, D and Varela-Mattatall, G and Sun, Q and Donnelly, SC and Suchy, M and Bartolome, D and Furlong, S and Deans, L and Biernaski, H and Huston, Y and Thompson, RT and Burton, JP and Moran, G and Gelman, N and Prato, FS and Kovacs, MS and Thiessen, JD and Goldhawk, DE and Schellenberg, J and Fox, MS},
title = {Biodistribution and dosimetry of [89]Zirconium-labeled microbiota transplants in the pig gut.},
journal = {Medical physics},
volume = {52},
number = {9},
pages = {e18087},
doi = {10.1002/mp.18087},
pmid = {40904056},
issn = {2473-4209},
mesh = {Animals ; *Zirconium/chemistry ; *Radioisotopes/chemistry ; Swine ; Tissue Distribution ; Radiometry ; Female ; Escherichia coli ; *Gastrointestinal Microbiome ; Positron-Emission Tomography ; Magnetic Resonance Imaging ; Isotope Labeling ; },
abstract = {BACKGROUND: The gastrointestinal (GI) microbiota, composed of diverse microbial communities, is essential for physiological processes, including immune modulation. Strains such as Escherichia coli Nissle 1917 support gut health by reducing inflammation and resisting pathogens. Microbial therapies using such strains may restore GI balance and offer alternatives to antibiotics, whose overuse contributes to antibiotic resistance. However, effective treatment will require optimizing delivery and understanding microbial dissemination and engraftment.

PURPOSE: We developed a method to monitor microbial migration and GI permeability post-ingestion using hybrid PET/MRI. To simulate probiotic therapy, bacteria were radiolabeled with [89]Zr, encapsulated, and administered to pigs. Organ level and whole-body dosimetry was determined from the time activity curves recorded over 7 days post ingestion.

METHODS: We administered [89]Zr-labeled Lactobacillus crispatus ATCC33820 (Gram-positive) to six female Duroc pigs (weight = 33.3 ± 4.6 kg) and E. coli Nissle 1917 (Gram-negative). Scans were performed between 6 h and 7 days post-ingestion using a hybrid PET/MRI system. The mean administered dose was 74.7 ± 12.9 MBq. Whole-body PET scans were acquired simultaneously with MRI using a T2-weighted HASTE sequence. Images were processed using 3D-Slicer co-registering PET with MRI and semi-automated organ segmentation was performed. Gender-averaged human equivalent organ-level effective doses (ED) and whole body ED were calculated using OLINDA.

RESULTS: PET imaging showed [89]Zr-labeled L. crispatus and E. coli post-ingestion localized primarily within the GI tract before excretion within feces. The highest mean ED for [89]Zr-labeled L. crispatus and E. coli were in the distal colon (26.8 ± 4.9 µSv/MBq and 28.4 ± 7.9 µSv/MBq, respectively) and proximal colon (17.9 ± 3.7 µSv/MBq and 18.4 ± 5.1 µSv/MBq, respectively). EDs in other organs were low. Whole body ED were 60.5 ± 9.5 µSv/MBq (L. crispatus) and 66.7 ± 14.9 µSv/MBq (E. coli).

CONCLUSIONS: The whole-body ED for L. crispatus and E. coli is lower than reported values for ingested tracers, such as that from [89]Zr labelled antibodies and [111]In labelled "meals" used to determine gut transit times. Hence ingestion of [89]Zr labelled bacteria shows promise for becoming a human nuclear-medicine procedure to determine the effectiveness of probiotic therapies.},
}

Animals
*Zirconium/chemistry
*Radioisotopes/chemistry
Swine
Tissue Distribution
Radiometry
Female
Escherichia coli
*Gastrointestinal Microbiome
Positron-Emission Tomography
Magnetic Resonance Imaging
Isotope Labeling

@article {pmid40903859,
year = {2025},
author = {Sugawara, K and Hozumi, K and Mizuma, H and Sasaki, D and Shinohara, M and Kondo, A and Watanabe, Y and Ogawa, W},
title = {Similarities and differences in the intestinal actions of metformin and imeglimin.},
journal = {Diabetes, obesity & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.70075},
pmid = {40903859},
issn = {1463-1326},
support = {//Boehringer Ingelheim Japan/ ; //Suzuken Memorial Foundation/ ; //Cell Science Research Foundation/ ; 22K18393//Japan Society for the Promotion of Science/ ; 23K08007//Japan Society for the Promotion of Science/ ; //Japan Diabetes Foundation/ ; 24ek0210192h0002//Japan Agency for Medical Research and Development/ ; },
abstract = {AIMS: Imeglimin is a novel antidiabetic drug that shares structural similarity with metformin. While the intestinal effects of metformin have attracted widespread attention, those of imeglimin remain underexplored.

MATERIALS AND METHODS: C57BL/6J mice were treated with metformin or imeglimin for RNA sequencing of intestinal tissue. Gut microbiota composition was evaluated in KK-A[y] mice by 16S rRNA sequencing of faecal samples. To assess direct effects on the human microbiome, a gut simulator was used with faecal samples from healthy and diabetic individuals. Intestinal glucose dynamics were assessed in C57BL/6J mice following administration of [[18]F]fluorodeoxyglucose, with subsequent analysis of tissue distribution.

RESULTS: Bulk RNA-sequencing of colonic tissue revealed that both drugs induced similar patterns of gene expression changes, including a prominent upregulation of Gdf15. However, single-cell RNA-sequencing uncovered distinct effects of the two drugs, with metformin having a pronounced impact on the functional properties of enterocytes and imeglimin increasing the proportion of IgA-producing plasma cells. Metformin reduced gut microbial diversity and induced substantial changes in microbial composition, whereas imeglimin exerted less pronounced effects. Gut simulator analysis with human faecal samples showed that both drugs directly altered gut microbial populations but in different ways. Finally, metformin promoted glucose excretion into the intestinal lumen, whereas imeglimin had a minimal effect on this process.

CONCLUSIONS: In conclusion, although metformin and imeglimin exerted similar effects on gene expression in the colon at the whole-tissue level, they showed distinct cell type-specific actions, and they differed in their influence on gut microbiota and intestinal glucose dynamics.},
}

@article {pmid40902606,
year = {2025},
author = {Zhang, D and Zou, Y and Shi, Y and Zhang, J and Liu, J and Wu, G and Zhang, J and Gao, Y and Chen, M and Li, YX},
title = {Systematically investigating and identifying bacteriocins in the human gut microbiome.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100983},
doi = {10.1016/j.xgen.2025.100983},
pmid = {40902606},
issn = {2666-979X},
abstract = {Human gut microbiota produces unmodified bacteriocins, natural antimicrobial peptides that protect against pathogens and regulate host physiology. However, current bioinformatic tools limit the comprehensive investigation of bacteriocins' biosynthesis, obstructing research into their biological functions. Here, we introduce IIBacFinder, a superior analysis pipeline for identifying unmodified class II bacteriocins. Through large-scale bioinformatic analysis and experimental validation, we demonstrate their widespread distribution across the bacterial kingdom, with most being habitat specific. Analyzing over 280,000 bacterial genomes, we reveal the diverse potential of human gut bacteria to produce these bacteriocins. Guided by meta-omics analysis, we synthesized 26 hypothetical bacteriocins from gut commensal species, with 16 showing antibacterial activities. Further ex vivo tests show minimal impact of narrow-spectrum bacteriocins on human fecal microbiota. Our study highlights the huge biosynthetic potential of unmodified bacteriocins in the human gut, paving the way for understanding their biological functions and health implications.},
}

@article {pmid40897518,
year = {2025},
author = {Salihoglu, R},
title = {The Microbiome Shaping Cancer Development, Progression, and Therapeutic Response.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00091.2025},
pmid = {40897518},
issn = {1531-2267},
abstract = {The human microbiome is emerging as a key regulator of cancer biology, modulating tumor development, immune dynamics, and therapeutic responses across diverse malignancies. In this review, recent insights are synthesized regarding how microbial communities (bacterial, fungal, and viral) shape oncogenic signaling, immune checkpoint blockade (ICB) efficacy, and metabolic reprogramming in lung, pancreatic, colorectal, breast, cervical, melanoma, and gastric cancers. Mechanistic links between microbial metabolites, intratumoral colonization, and host immune phenotypes are highlighted proposing that the microbiome constitutes a programmable axis within the tumor immune-metabolic ecosystem. Drawing on multi-omics integration and translational studies, a shift from associative profiling toward causal, spatially resolved, and intervention-ready frameworks is proposed. This perspective positions the microbiome not as a passive bystander, but as a co-evolving participant in tumor progression and treatment response, with the potential to reshape diagnostics, prognostics, and therapeutic strategies in precision oncology.},
}

@article {pmid40897178,
year = {2025},
author = {Xu, T and Jiao, X and Liu, G and Chen, X and Luo, Q and Zhang, G and Li, B and Zhang, Y and Li, X and Cheung, Y and Chai, X and Huang, Y and Wu, H and Deng, F and Chen, F and Liang, G},
title = {Oral virome metagenomic catalog links Porphyromonas gingivalis phages to obesity and type 2 diabetes.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102325},
doi = {10.1016/j.xcrm.2025.102325},
pmid = {40897178},
issn = {2666-3791},
abstract = {The human microbiota has a critical role in maintaining human microbiome homeostasis and health, yet the viral component of the oral microbiome remains largely unidentified. We establish the Human Oral Virome Database (HOVD) catalog, a freely accessible online resource cataloging 24,440 bacteriophage viral operational taxonomic units and 83 eukaryotic viral genomes. Utilizing HOVD, we investigate oral virome variation and its correlation with oral bacteria and gut virome in 220 obese individuals with or without type 2 diabetes mellitus (T2D). Obese individuals with T2D exhibit reduced oral viral diversity, lower correlations with clinical features, disrupted viral-bacterial correlations, and enhanced oral-gut virome transmission. Furthermore, we computationally identify bacteriophages that infect Porphyromonas gingivalis and screen six putative endolysins. Experimental validation reveals that a mixture of three endolysins significantly inhibits Porphyromonas gingivalis growth. These findings highlight the potential of phage-derived endolysins for periodontitis with T2D, offering a path toward oral and systemic disease intervention.},
}

@article {pmid40892293,
year = {2025},
author = {Chen, C and Krzyżewska-Dudek, E and Patpatia, S and Dulipati, V and Mapelli, SN and Meral, A and Kotimaa, J and Kiljunen, S and Meri, S},
title = {Antibiotic-resistant Acinetobacter baumannii can be killed by a combination of bacteriophages and complement.},
journal = {Medical microbiology and immunology},
volume = {214},
number = {1},
pages = {40},
pmid = {40892293},
issn = {1432-1831},
mesh = {*Acinetobacter baumannii/virology/drug effects/immunology/genetics ; *Bacteriophages/physiology/growth & development/immunology ; *Complement System Proteins/immunology ; *Drug Resistance, Multiple, Bacterial ; Acinetobacter Infections/therapy/microbiology ; Bacterial Capsules/metabolism ; Humans ; Anti-Bacterial Agents/pharmacology ; Lipopolysaccharides ; DNA Transposable Elements ; Microbial Viability ; },
abstract = {Infections caused by multidrug-resistant Acinetobacter baumannii are an emerging global health threat. Although phages have shown promising results in treating bacterial infections, the mechanisms of the combined effect of phages and innate immunity on clearing A. baumannii remain unclear. Here, we report a synergistic effect of the complement system and phages on clearing multidrug-resistant A. baumannii. We show that A. baumannii rapidly adapts and becomes resistant to phage or serum complement by modifying the expression of capsule and lipooligosaccharides, which can be regulated through reversible transposon mutagenesis in the K locus. Compared to the encapsulated phenotype, the non-encapsulated, phage-resistant A. baumannii showed a higher level of membrane attack complex deposition and were susceptible to killing by complement. In contrast, the encapsulated phenotype escaped the complement system by shedding the membrane attack complex to the environment. Thus, while the complement system targets the non-encapsulated phenotype, the phage infects and eliminates the encapsulated subpopulation. These results suggest means of combatting antibiotic-resistant A. baumannii by a simultaneous treatment with phages and complement, a combination which can be supplemented further with antibacterial antibodies.},
}

*Acinetobacter baumannii/virology/drug effects/immunology/genetics
*Bacteriophages/physiology/growth & development/immunology
*Complement System Proteins/immunology
*Drug Resistance, Multiple, Bacterial
Acinetobacter Infections/therapy/microbiology
Bacterial Capsules/metabolism
Humans
Anti-Bacterial Agents/pharmacology
Lipopolysaccharides
DNA Transposable Elements
Microbial Viability

@article {pmid40891819,
year = {2025},
author = {De Boeck, I and Spacova, I and Cauwenberghs, E and Eilers, T and Gehrmann, T and Van den Bossche, K and Martens, K and Condori-Catachura, S and Michiels, K and De Winter, F and Kumar-Singh, S and Bruffaerts, N and Packeu, A and Hellings, PW and Vroegop, A and Van Gool, K and Vanderveken, OM and Lebeer, S},
title = {Lacticaseibacillus rhamnosus GG in a chewable colonizes the nose and facilitates local immune benefits in allergic rhinoconjunctivitis patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0077325},
doi = {10.1128/spectrum.00773-25},
pmid = {40891819},
issn = {2165-0497},
abstract = {Current treatments fall short in managing allergic rhinitis (AR), emphasizing the need for additional strategies. Beneficial bacteria application shows promise in AR; however, most studies focus on oral probiotic administration without monitoring the applied strains in the upper respiratory tract (URT) and their local effects. In this randomized, double-blind, placebo-controlled trial, the probiotic Lacticaseibacillus rhamnosus GG was administered via chewable tablets in seasonal AR patients, randomized to probiotic (n = 33) or placebo (n = 31) groups. Per-protocol analysis of the URT microbiome, immune markers, and AR symptoms was performed. L. rhamnosus GG trafficked from chewables to the oropharynx (77%, P = 0.02) and nasopharynx (41%, P < 0.0001). Control of self-reported AR symptoms via validated questionnaires under grass pollen exposure was observed after 2 weeks of probiotic administration and not upon placebo. A local decrease in salivary interleukin-4 (P < 0.05) and nasal IL-13 (P < 0.0001) was observed in the probiotic group. These data indicate that L. rhamnosus GG chewables can target the URT and exert local effects on key allergy cytokines after temporal probiotic engraftment.IMPORTANCEAllergic rhinitis (AR) or hay fever is a highly prevalent condition, impacting nearly half the population in some countries. Supplementation of beneficial bacteria or probiotics has gained increasing attention in AR, and a key innovative way to do this is direct administration to the upper airways. Our study shows for the first time that the model probiotic strain Lacticaseibacillus rhamnosus GG can traffic to the nose in AR patients when administered via a slow-releasing chewable tablet. This trafficking is associated with local benefits in the airways, including on grass pollen-induced nasal symptoms and allergy-related cytokines.},
}

@article {pmid40884907,
year = {2025},
author = {Sanati, S and Bakhti, A and Mohammadipanah, F},
title = {Long-term toxic effects of nanoparticles on human microbiota.},
journal = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)},
volume = {91},
number = {},
pages = {127723},
doi = {10.1016/j.jtemb.2025.127723},
pmid = {40884907},
issn = {1878-3252},
abstract = {Synthetic nanomaterials can penetrate various organs, such as the skin, lungs, and gastrointestinal tract, enter systemic circulation, and ultimately reach tissues and human cells. Nanomaterials used in medicine, food, cosmetics, and agricultural processes can accumulate in our intestines and cause dysbiosis. The direct and indirect detrimental impacts of nanomaterials on humans by altering our cells and microbiota are discussed in this paper. These adverse effects of nanomaterials can be slightly reduced by changing their physicochemical characteristics. Some of the gut microbiota can reduce or mitigate the toxicity of nanomaterials through various strategies providing approaches for pro- or postbiotics with detoxifying function. Moreover, nanomaterials influence the rate of horizontal gene transfer. The use of nanomaterials in food, water, and medicines needs to be legitimized based on the duration, dose, type, and level of toxicity. The negative implications of nanomaterials in human cells and their microbiota are surveyed in this paper.},
}

@article {pmid40884571,
year = {2025},
author = {Brindangnanam, P and Coumar, MS},
title = {Integrated Microbiome Data Analysis Reveals Potential Pneumonia Microbial Biomarkers in ICU Patients: A Machine Learning Approach.},
journal = {Current microbiology},
volume = {82},
number = {10},
pages = {483},
pmid = {40884571},
issn = {1432-0991},
mesh = {Humans ; *Machine Learning ; Intensive Care Units ; Biomarkers/analysis ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Pneumonia/microbiology/diagnosis ; Bacteria/genetics/classification/isolation & purification ; Lung/microbiology ; Data Analysis ; },
abstract = {The human microbiome is pivotal in maintaining health and managing diseases. By examining the core microbiome in intensive care units (ICU) patients with pneumonia, we can gain valuable insights into the microbial communities associated with disease conditions. Pneumonia is the second most common infection in ICU settings, and recent research has highlighted the significance of endotracheal aspirate (ETA) microbiota in influencing pneumonia. Analysis of 16S rRNA sequencing data from lung microbiota of ICU patients revealed Pseudomonas as a key microbial biomarker, with machine learning model (xgbTree) achieving high predictive accuracy (prAUC: 0.98 and 0.7 log loss). Functional profile analysis revealed that the ATP-binding cassette (ABC) transporters and tetracycline-resistant ribosomal protection (Tet RPPs) proteins were possible molecular biomarkers that can be targeted to address the abundant pathogenic microbiome in pneumonia patients. These findings provide critical insights into pneumonia-specific microbiome signatures, highlighting Pseudomonas as a diagnostic marker and resistance-associated functional pathways as potential intervention targets. This study contributes to the development of precision medicine strategies for pneumonia management in ICU settings.},
}

Humans
*Machine Learning
Intensive Care Units
Biomarkers/analysis
*Microbiota
RNA, Ribosomal, 16S/genetics
*Pneumonia/microbiology/diagnosis
Bacteria/genetics/classification/isolation & purification
Lung/microbiology
Data Analysis

@article {pmid40879391,
year = {2025},
author = {Devotta, H and Lavelle, A and Korpela, K and Hurley, S and Shannon, E and Lunjani, N and Ambikan, A and Neogi, U and Venter, C and Walter, J and Hourihane, J and O'Mahony, L},
title = {Microbial Sharing Between Siblings Supports Metabolic Functions Protective Against Allergy.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70033},
pmid = {40879391},
issn = {1398-9995},
support = {/SFI_/Science Foundation Ireland/Ireland ; //Royal College of Surgeons in Ireland/ ; //Temple Street Hospital Foundation/ ; //Clemens Von Pirquet Foundation/ ; 12/RC/2273_P2//Research Ireland/ ; 21/FFP-A/10000//Research Ireland Frontiers for the Future Awards/ ; 23/FFP-A/12076//Research Ireland Frontiers for the Future Awards/ ; },
}

@article {pmid40871739,
year = {2025},
author = {Lupu, A and Adam-Raileanu, A and Bozomitu, LI and Gimiga, N and Forna, L and Anton, CR and Sasaran, MO and Nedelcu, AH and Ghica, DC and Anton, E and Morariu, ID and Fotea, S and Beser, OF and Lupu, VV},
title = {Helicobacter pylori and Compositional Patterns of Digestive Tract Microbiome in Children: A Literature Review.},
journal = {Nutrients},
volume = {17},
number = {16},
pages = {},
doi = {10.3390/nu17162711},
pmid = {40871739},
issn = {2072-6643},
mesh = {Humans ; *Helicobacter pylori ; *Gastrointestinal Microbiome ; Child ; *Helicobacter Infections/microbiology/drug therapy ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Helicobacter pylori (H. pylori) represents a major healthcare problem, colonizing more than half of the population worldwide. Usually acquired during childhood, it has a significant impact on human health. After forty years of extensive research, there are aspects of the complex H. pylori-human organism interplay that require further investigation. A comprehensive review was conducted after an extensive literature search in the PubMed/Medline, Web of Science, and EMBASE databases concerning H. pylori and human microbiota reports. Although the exact nature of H. pylori's relation with the human microbiome remains elusive, its presence as well as its eradication treatment are associated with the alteration of bacterial communities' composition not only in the gastric microenvironment but also in all digestive tract levels, with particular changes in both children and adults. Understanding microbiota composition is a step towards personalized medicine. Although the current literature on pediatric patients related to this topic is scarce, the available positive results reported in adult studies encourage pediatric research on microbiota manipulation, promising beneficial outcomes.},
}

Humans
*Helicobacter pylori
*Gastrointestinal Microbiome
Child
*Helicobacter Infections/microbiology/drug therapy
Anti-Bacterial Agents/therapeutic use

@article {pmid40868571,
year = {2025},
author = {Aldawood, E and Alzamil, L and Faqih, L and Almuhayya, S},
title = {Knowledge of Vaginal Microbiota and Its Association with Perceptions of Vulvovaginal Aesthetic Procedures Among Saudi Women.},
journal = {Healthcare (Basel, Switzerland)},
volume = {13},
number = {16},
pages = {},
doi = {10.3390/healthcare13161955},
pmid = {40868571},
issn = {2227-9032},
support = {ORF-2025-1475//Ongoing Research Funding program, King Saud University, Riyadh, Saudi Arabia./ ; },
abstract = {BACKGROUND: The human microbiome includes trillions of microorganisms, with the vaginal microbiota playing a vital role in women's reproductive health. Concurrently, interest in vulvovaginal esthetic procedures (VVEP) is increasing. This study aimed to compare single and married or previously married women in terms of their knowledge of the human microbiome, particularly the vaginal microbiota, and their perceptions of VVEP. It also examined associations between microbiota awareness, attitudes toward VVEP, and sociodemographic factors.

METHODS: A cross-sectional, online survey was distributed to women aged 18 years and older in Saudi Arabia. A total of 1019 responses were collected. Chi-square tests compared knowledge responses between marital groups, while linear regression was used to explore associations between microbiota knowledge and participant characteristics.

RESULTS: Single women showed greater awareness of general microbiome concepts, with 42% correctly identifying the term "microbiome" compared to 29.89% of married or previously married women. In contrast, married or previously married women demonstrated better knowledge of vaginal microbiota and the effects of antibiotic misuse. Of the participants, 6.6% had undergone one or more VVEP. Furthermore, 19.7% of single women and 18.3% of married or previously married women expressed future interest in undergoing such procedures. Marital status influenced perceptions of specific procedures, with married or previously married women more likely to justify interventions such as augmentation of the labia minora/"G-spot" augmentation and vaginal rejuvenation. Justification for augmentation of the labia minora/"G-spot" augmentation in this group was associated with lower vaginal microbiota knowledge. Healthcare professionals exhibited significantly higher microbiota awareness.

CONCLUSION: Enhancing women's knowledge of vaginal microbiota can enhance informed decision-making and reduce unnecessary esthetic interventions among Saudi women, thereby supporting better reproductive health outcomes.},
}

@article {pmid40868183,
year = {2025},
author = {Kim, JH and Seo, H and Kim, S and Rahim, MA and Jo, S and Barman, I and Tajdozian, H and Sarafraz, F and Shuvo, MSH and Song, HY and Song, YS},
title = {Association of Intratumoral Microbiota Modulation with Prostate Cancer Progression: A Microbiome Analysis of Prostatic Tissue.},
journal = {Biomedicines},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/biomedicines13081929},
pmid = {40868183},
issn = {2227-9059},
support = {RS-2024-00333544, RS-2023-00219563//Ministry of Science and ICT/ ; NA//National Research Foundation of Korea (NRF)/ ; NA//Soonchunhyang University Research Fund/ ; },
abstract = {Background: The involvement of the intratumoral microbiome in prostate cancer progression is becoming increasingly acknowledged. This study analyzed the microbiome of prostate cancer tissues from patients with localized prostate cancer (LPC, stages 1-2) and advanced prostate cancer (APC, stages 3-4) to determine its association with cancer progression. Methods: Paraffin-embedded tissue samples obtained during radical prostatectomy underwent 16S rRNA amplicon-based profiling. Results: The profile of the bacterial communities in LPC and APC differed remarkably. While species diversity remained stable, species richness (as determined by the ACE analysis) was significantly lower in APC, correlating with a decrease in Enhydrobacter (which is more abundant in LPC) and an increase in Lautropia (enriched in APC). The role of Lautropia in the progression of cancer was confirmed by in vitro studies employing cell lines from prostate cancer. Conclusions: These findings demonstrate the potential of microbiome-targeted interventions in the management of prostate cancer.},
}

@article {pmid40867601,
year = {2025},
author = {Jin, S and Ku, C and Kim, HJ and Kim, JG and Kim, SH and Han, H and Kang, HC and Hwang, JS and Kim, MJ},
title = {The Role of miRNA167 in Skin Improvement: Insight from Extracellular Vesicles Derived from Rock Samphire (Crithmum maritimum).},
journal = {Biomolecules},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/biom15081157},
pmid = {40867601},
issn = {2218-273X},
mesh = {*Extracellular Vesicles/metabolism/genetics ; *MicroRNAs/genetics/metabolism ; Humans ; *Skin/metabolism ; Wound Healing ; Fibroblasts/metabolism ; Vascular Endothelial Growth Factor A/genetics/metabolism ; Collagen Type I/genetics/metabolism ; Matrix Metalloproteinase 1/genetics/metabolism ; Collagen Type I, alpha 1 Chain ; Regeneration ; },
abstract = {Samphire (Crithmum matrimum), a halophyte, thrives in saline environments due to its salt tolerance, which is partly attributed to miR167. However, the functional role of miR167 in human cells is unclear. This study explores the role of extracellular vesicles (EVs) derived from C. matrimum callus in skin regeneration, highlighting the potential of miRNA tae-miR167c-5p (miR167). Calluses were successfully induced and scaled for EV isolation. Characterization confirmed the presence of plant EV biomarkers and EVs with an average size of 136.6 nm. Cm-callus EVs enhanced wound healing and skin regeneration in human fibroblasts (HFF cells and CCD-986Sk cells) by modulating key genes, in particular, by downregulating MMP1 and upregulating COL1A1 and VEGFA. Small RNA sequencing revealed an enrichment of miR167 in Cm-callus EVs. Transfection with an miR167 mimic replicated these regenerative effects. Computational predictions identified PPP3R2, which is linked to the MAPK and NFAT pathways, as a potential target of miR167. This study demonstrates the efficacy of Cm-callus EVs and miR167 in promoting skin regeneration without cytotoxicity, providing insights into their therapeutic potential and calling for further experimental validation of target interactions.},
}

*Extracellular Vesicles/metabolism/genetics
*MicroRNAs/genetics/metabolism
Humans
*Skin/metabolism
Wound Healing
Fibroblasts/metabolism
Vascular Endothelial Growth Factor A/genetics/metabolism
Collagen Type I/genetics/metabolism
Matrix Metalloproteinase 1/genetics/metabolism
Collagen Type I, alpha 1 Chain
Regeneration

@article {pmid40867553,
year = {2025},
author = {Jin, S and Kim, JG and Kim, HJ and Kim, JY and Kim, SH and Kang, HC and Kim, MJ},
title = {miRNA408 from Camellia japonica L. Mediates Cross-Kingdom Regulation in Human Skin Recovery.},
journal = {Biomolecules},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/biom15081108},
pmid = {40867553},
issn = {2218-273X},
mesh = {Humans ; *Camellia/genetics/chemistry/metabolism ; *MicroRNAs/genetics/metabolism ; *Wound Healing/drug effects/genetics ; *Skin/metabolism ; Fibroblasts/metabolism/drug effects ; Extracellular Vesicles/metabolism ; Keratinocytes/metabolism/drug effects ; },
abstract = {Wound healing is a complex and dynamic process involving several stages of tissue repair. This study has shown that extracellular vesicles (EVs) derived from the callus of Camellia japonica L. and their associated microRNAs (miRNAs) possess significant wound healing activities. In human fibroblasts, EVs from C. japonica L. stimulated wound healing and upregulated collagen gene expression. The EVs also decreased inflammation levels in human keratinocytes, supporting wound healing. Among the miRNAs identified, miR408, one of the abundant miRNAs in the EVs, also showed similar wound healing efficacy. These findings suggest that both EVs and miR408 from the callus of C. japonica L. play a pivotal role in promoting wound healing. Additionally, this study shows that the regulation of miRNAs between different kingdoms can be achieved and suggests a new direction for the utilization of plant-derived components.},
}

Humans
*Camellia/genetics/chemistry/metabolism
*MicroRNAs/genetics/metabolism
*Wound Healing/drug effects/genetics
*Skin/metabolism
Fibroblasts/metabolism/drug effects
Extracellular Vesicles/metabolism
Keratinocytes/metabolism/drug effects

@article {pmid40866318,
year = {2025},
author = {Inoue, N and Shibata, T and Sawada, R and Yamanishi, Y},
title = {Human Microbiome-Based Prediction of Health Effects of Foods via Machine Learning.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c06318},
pmid = {40866318},
issn = {1520-5118},
abstract = {Food absorption is dependent on the activities of internal microorganisms. When exploring food functionality, considering the food compounds and their metabolites produced by microbial metabolism is crucial. In this study, we developed a machine learning method to predict food functionalities using microorganism and metabolic data. The prediction was performed on the chemical properties of 70,478 constituent compounds and 24,255 metabolites and their interactions with target proteins in disease-related pathways. This identified potential functional associations between 941 foods and 83 diseases, providing insights into the mechanisms involved, particularly those related to microorganisms. The effects of microorganism-mediated foods on diseases can be categorized based on food type. For example, the microorganisms associated with diseases within each food category indicated the potential involvement of the Bacteroidetes phylum in dyslipidemia and the Firmicutes phylum in Parkinson's disease. This method could aid in identifying disease-associated microorganisms, identifying prebiotic foods, and highlighting the potential of food interventions in the preventive medicine field. Furthermore, this approach is expected to be useful for elucidating novel mechanisms of food-disease interactions mediated by microbial metabolites.},
}

@article {pmid40856313,
year = {2025},
author = {Klier, K and Mehrjerd, A and Fässler, D and Franck, M and Weihs, A and Budde, K and Bahls, M and Frost, F and Henning, AK and Heinken, A and Völzke, H and Dörr, M and Nauck, M and Grabe, HJ and Friedrich, N and Hertel, J},
title = {Integrating population-based metabolomics with computational microbiome modelling identifies methanol as a urinary biomarker for protective diet-microbiome-host interactions.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo00761e},
pmid = {40856313},
issn = {2042-650X},
abstract = {Background: Diet-microbiome interactions are core to human health, in particular through bacterial fibre degradation pathways. However, biomarkers reflective of these interactions are not well described. Methods: Using the population-based SHIP-START-0 cohort (n = 4017), we combined metabolome-wide screenings with elastic net machine learning models on 33 food items captured using a food frequency questionnaire (FFQ) and 43 targeted urine nuclear magnetic resonance (NMR) metabolites, identifying methanol as a marker of plant-derived food items. We utilised the independent SHIP-START-0 cohort for the replication of food-metabolite associations. Moreover, constraint-based microbiome community modelling using the Human Microbiome data (n = 149) was performed to predict and analyse the contribution of the microbiome to the human methanol pools through bacterial fibre degradation. Finally, we employed prospective survival analysis in the SHIP-START-0 cohort, testing urinary methanol on its predictive value for mortality. Results: Among 21 metabolites associated with 17 dietary FFQ variables after correction for multiple testing, urinary methanol emerged as the top hit for a range of plant-derived food items. In line with this, constraint-based community modelling demonstrated that gut microbiomes can produce methanol via pectin degradation with the genera Bacteroides (68.9%) and Faecalibacterium (20.6%) being primarily responsible. Moreover, microbial methanol production capacity was a marker of high microbiome diversity. Finally, prospective survival analysis in SHIP-START-0 revealed that higher urinary methanol is associated with lower all-cause mortality in fully adjusted Cox regressions. Conclusion: Integrating population-based metabolomics and computational microbiome modelling identified urinary methanol as a promising biomarker for protective diet-microbiome interactions linked to microbial pectin degradation.},
}

@article {pmid40852123,
year = {2025},
author = {Linehan, K and Healy, K and Hurley, E and O'Shea, CA and Ryan, CA and Ross, RP and Stanton, C and Dempsey, EM},
title = {Perinatal factors influencing the earliest establishment of the infant microbiome.},
journal = {Microbiome research reports},
volume = {4},
number = {2},
pages = {24},
pmid = {40852123},
issn = {2771-5965},
abstract = {Background: While extensive research exists on the human microbiome, a number of outstanding questions remain regarding the infant microbiome in the initial stages of life. This study aimed to determine the timing of very early microbial colonization in humans, assess the contribution of maternal microbial sources to their offspring and examine the effects of perinatal factors such as delivery mode, gestational age, and feeding practices on the maternal and infant microbiota in early life. Methods: Using a cohort of 18 healthy mother-infant dyads, maternal saliva (within 24 h postpartum), vaginal (1 h prepartum), and placental (1 h postpartum) samples were collected. From their corresponding infants, saliva (within 24 h postpartum) and meconium (within 96 h postpartum) samples were collected. 16S rRNA amplicon sequencing was utilized to assess the taxonomic and inferred functional compositions of the bacterial communities from both mothers and infants. Results: Our results consolidate and corroborate recent findings addressing the existence of a meconium microbiome and the absence of a placental microbiome. We show that significant sharing of microbiota, primarily Streptococcus and Veillonella species, between the maternal oral cavity and the infant oral cavity occurs in early life. Perinatal factors such as vaginal delivery and exclusive breastfeeding were strongly associated with enhanced microbial richness and diversity in infants. Conclusions: This study provides information on the relationship between health and delivery factors and the first establishment of the infant microbiota. These findings could offer valuable guidance to clinicians and mothers in optimizing the infant microbiota toward health during infancy and later life.},
}

@article {pmid40850975,
year = {2025},
author = {Yeo, LF and Lee, AWY and Tee, PYE and Chin, JSF and Lee, BKB and Lim, J and Teo, SH and Pan, JW},
title = {Characterization of intra-tumoral microbiota from transcriptomic sequencing of Asian breast cancer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {31147},
pmid = {40850975},
issn = {2045-2322},
mesh = {Humans ; *Breast Neoplasms/microbiology/genetics/pathology/immunology ; Female ; *Microbiota/genetics ; *Transcriptome ; Middle Aged ; Tumor Microenvironment/genetics/immunology ; Malaysia ; Asian People/genetics ; Gene Expression Profiling ; Adult ; Aged ; },
abstract = {The human microbiome has garnered significant interest in recent years as an important driver of human health and disease. Likewise, it has been suggested that the intra-tumoral microbiome may be associated with specific features of cancer such as tumour progression and metastasis. However, additional research is needed to validate these findings in diverse populations. In this study, we characterized the intra-tumoral microbiota of 883 Malaysian breast cancer patients using transcriptomic data from bulk tumours and investigated their association with clinical variables and immune scores. We found that the tumour microbiome was not associated with breast cancer molecular subtype, cancer stage, tumour grade, or patient age, but was weakly associated with immune scores. We also found that the tumour microbiome was associated with immune scores in our cohort using random forest models, suggesting the possibility of an interaction between the tumour microbiome and the tumour immune microenvironment in Asian breast cancer.},
}

Humans
*Breast Neoplasms/microbiology/genetics/pathology/immunology
Female
*Microbiota/genetics
*Transcriptome
Middle Aged
Tumor Microenvironment/genetics/immunology
Malaysia
Asian People/genetics
Gene Expression Profiling
Adult
Aged

@article {pmid40846688,
year = {2025},
author = {Ding, SQ and Lei, Y and Zhao, ZM and Li, XY and Lang, JX and Zhang, JK and Li, YS and Zhang, CD and Dai, DQ},
title = {Crosstalk Between Microbiome and Ferroptosis in Diseases: From Mechanism to Therapy.},
journal = {Comprehensive Physiology},
volume = {15},
number = {4},
pages = {e70042},
doi = {10.1002/cph4.70042},
pmid = {40846688},
issn = {2040-4603},
support = {81972322//National Natural Science Foundation of China/ ; JYTMS20230108//Scientific Study Project for Institutes of Higher Learning, Ministry of Education, Liaoning Province/ ; RXXM202302//Young Backbone Talents of China Medical University/ ; 2023-MS-163//Liaoning Provincial Natural Science Foundation/ ; },
mesh = {*Ferroptosis/physiology ; Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; Iron/metabolism ; Dysbiosis/metabolism ; Reactive Oxygen Species/metabolism ; *Microbiota/physiology ; Lipid Peroxidation ; },
abstract = {The human microbiome is a unique organ and maintains host immunomodulation and nutrient metabolism. Structural and functional microbiome alterations are commonly known as dysbiosis, which is strongly associated with disease progression. Ferroptosis is a novel iron-dependent cell death mode characterized by intracellular iron accumulation, increased reactive oxygen species (ROS), and lipid peroxidation (LPO). Importantly, the complex crosstalk between the microbiome and ferroptosis in disease has attracted considerable research attention. The microbiome influences ferroptosis by regulating host iron homeostasis, mitochondrial metabolism, and LPO, among many other pathways. Thus, the in-depth analysis of microbiome-ferroptosis crosstalk and associated mechanisms could provide new strategies to treat human diseases. Therefore, understanding this crosstalk is critical. Here, we systematically explore the associations between gut microbiome and ferroptosis across multiple diseases. We show that the oral microbiome also influences disease progression by regulating ferroptosis. Furthermore, we provide a potential for certain disease therapies by targeting the crosstalk between the microbiome and ferroptosis.},
}

*Ferroptosis/physiology
Humans
*Gastrointestinal Microbiome/physiology
Animals
Iron/metabolism
Dysbiosis/metabolism
Reactive Oxygen Species/metabolism
*Microbiota/physiology
Lipid Peroxidation

@article {pmid40842971,
year = {2025},
author = {Fukuyo, M and Takahashi, N and Hanada, K and Ishikawa, K and Venclovas, Č and Yahara, K and Yonezawa, H and Terabayashi, T and Katsura, Y and Osada, N and Kaneda, A and Camargo, MC and Rabkin, CS and Uchiyama, I and Osaki, T and Kobayashi, I},
title = {Helicobacter pylori base-excision restriction enzyme in stomach carcinogenesis.},
journal = {PNAS nexus},
volume = {4},
number = {8},
pages = {pgaf244},
pmid = {40842971},
issn = {2752-6542},
abstract = {Many recent lines of evidence from the human microbiome and other fields indicate bacterial involvement in various types of cancer. Helicobacter pylori has been recognized as the major cause of stomach cancer (gastric cancer), but the mechanism by which it destabilizes the human genome to cause cancer remains unclear. Our recent studies have identified a unique family of toxic restriction enzymes that excise a base (A: adenine) from their recognition sequence (5'-GTAC). At the resulting abasic sites (5'-GT_C), its inherent endonuclease activity or that of a separate endonuclease may yield atypical strand breaks that resist repair by ligation. Here, we present evidence demonstrating involvement of its H. pylori member, HpPabI, in stomach carcinogenesis: (i) Association of intact HpPabI gene with gastric cancer in the global H. pylori Genome Project and the open genomes; (ii) Frequent mutations at A in 5'-GTAC in the gastric cancer genomes as well as in H. pylori genomes; (iii) Its induction of chromosomal double-strand breaks in infected human cells and of mutagenesis in bacterial test systems. In addition, its unique regions that interact with DNA exhibit signs of diversifying selection. Our further analysis revealed similar oncogenic bacterium-restriction-enzyme pairs for other types of cancer. These results set another stage for cancer research and medicine around oncogenic restriction enzymes.},
}

@article {pmid40839108,
year = {2025},
author = {Mukherjea, N and Khandelwal, A and Saluja, R and Kalra, N},
title = {The Role of the human microbiome in neurodegenerative diseases: A Perspective.},
journal = {Current genetics},
volume = {71},
number = {1},
pages = {17},
pmid = {40839108},
issn = {1432-0983},
mesh = {Humans ; *Neurodegenerative Diseases/microbiology ; *Microbiota ; Parkinson Disease/microbiology ; *Gastrointestinal Microbiome ; Alzheimer Disease/microbiology ; Inflammasomes ; Inflammation/microbiology ; },
abstract = {Advances in diagnostics, therapeutics, and large-scale clinical studies have significantly expanded our understanding how human health is shaped by the microorganisms that colonize the body since birth. This article explores the rapidly evolving field of human microbiome research, focusing upon how microbial communities influence neurological health and contribute to the development of neurodegenerative diseases (NDs). Multiple factors, including age, lifestyle, and immunological memory, are recognized as major determinants of an individual's microbiome composition, which in turn can influence the onset and the progression of disorders such as Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. These conditions have been linked to mechanisms including the aggregation of pathogenic proteins (e.g., amyloid-β and α-synuclein), inflammation driven by activation of the Toll-like receptor (TLR) signaling pathway, the NLRP3 inflammasome, as well as the modulatory effect of microbial metabolites such as short-chain fatty acids (SCFAs) and lipopolysaccharides (LPS). The article also highlights ongoing research and emerging strategies aimed at leveraging the human microbiome for better diagnosis, and management of NDs.},
}

Humans
*Neurodegenerative Diseases/microbiology
*Microbiota
Parkinson Disease/microbiology
*Gastrointestinal Microbiome
Alzheimer Disease/microbiology
Inflammasomes
Inflammation/microbiology

@article {pmid40836109,
year = {2025},
author = {Hyvönen, S and Saarikivi, A and Mälkönen, J and Solasaari, T and Korpela, K and de Vos, WM and Salonen, A and Ruuska-Loewald, T and Kolho, KL},
title = {The association of maternal and infant early gut microbiota with respiratory infections in infants.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {40836109},
issn = {1530-0447},
support = {200141/WT_/Wellcome Trust/United Kingdom ; 210168//the Foundation for Pediatric research/ ; grant not numbered//the Foundation for Pediatric research/ ; 5044//Signe ja Ane Gyllenbergin Säätiö/ ; 329/31/2015//Tekes/ ; grant not numbered//Juho Vainion Säätiö/ ; 5851//the Finnish Medical Foundation/ ; },
abstract = {BACKGROUND: There are limited data on the proposed association of early gut microbiota composition and the risk of respiratory tract infections (RTI) in infants from prospective studies.

METHODS: We investigated the maternal and infant gut microbiota in infants prospectively followed up for their RTIs in the HELMi cohort from Helsinki, Finland. The 16S rRNA gene amplicon data was assessed at weeks 3 and 6 from 461 infants, of whom 178 developed RTIs within 3 and 6 months of life. Fecal samples collected near the due date were available from 261 mothers.

RESULTS: There was no difference in the maternal or early infant gut microbiota in the overall microbiota composition in alpha or beta diversity between infants with or without RTIs within the first 3 and 6 months of life. The relative abundances of adult-type butyrate producers and some Enterobacteriaceae were significantly more higher at 3 and to some extent also at 6 weeks of age in the infection group compared to controls, while their mothers' microbiota was significantly enriched with Enterococcus, Citrobacter, and Enterobacter spp., and Clostridium being less abundant.

CONCLUSION: The maternal and early-life infant gut microbiota may play a role in predisposition to RTIs in infants.

IMPACT: The maternal and early-life infant gut microbiota profile was associated with infants' respiratory tract infections within the first 6 months of life. In infants, the higher abundance of adult-type butyrate producers and some Enterobacteriaceae were associated with respiratory tract infections, while mothers' microbiota was significantly enriched with Enterococcus, Citrobacter, and Enterobacter spp. in the group of infants with infections. The results indicate that maternal and infant gut microbiota may play a role in predisposing an infant to infections during early life. Further studies are warranted on how this link is mediated.},
}

@article {pmid40835787,
year = {2025},
author = {Nguyen, TT and Kim, YK and Nguyen, TVT and Kwon, J and Bang, YJ},
title = {Metabolic profiling and genetic tool development in the mucosal bacterium Selenomonas sputigena.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {40835787},
issn = {2092-9293},
support = {Creative-Pioneering Researchers Program//Seoul National University/ ; RS-2023-00217157//Ministry of Education, Science and Technology/ ; 800-20240293//College of Medicine, Seoul National University/ ; },
abstract = {BACKGROUND: Selenomonas sputigena is an anaerobic mucosa-associated bacterium with dual roles in human health-acting as a pathobiont in periodontal disease and exhibiting protective effects in allergic airway inflammation. Despite its clinical significance, its metabolic functions and underlying mechanisms remain poorly defined.

OBJECTIVE: This study aimed to systematically characterize S. sputigena's metabolic capacity and develop genetic tools for functional studies.

METHODS: We reconstructed central carbon metabolic networks through in silico analysis. Growth kinetics, substrate utilization, and fermentation profiles were evaluated experimentally across five carbon sources: glucose, gluconate, glycerol, glutamate, and succinate. Expression of key metabolic genes was quantified by qRT-PCR. Native promoter constructs were developed and tested for GFP reporter expression.

RESULTS: Selenomonas sputigena displayed glucose-preferential growth with rapid consumption (0.70 ± 0.05 mM h⁻[1]) and substantial acetate production (17.76 ± 2.05 mM). Gluconate and glycerol supported moderate growth, while glutamate and succinate were poorly utilized. Gene expression analysis revealed strong substrate-dependent regulation of glycolytic genes, with gap expression correlating with growth performance, while TCA cycle genes maintained constitutive basal expression. Four native promoters successfully drove reporter expression, with Pgap demonstrating superior performance as a growth-responsive reporter.

CONCLUSIONS: This study establishes the first comprehensive metabolic and genetic framework for S. sputigena, revealing glucose-dependent fermentation with high acetate production that may contribute to host interactions. The validated promoter system enables future investigations of host-microbe interactions and therapeutic applications in mucosal environments.},
}

@article {pmid40830911,
year = {2025},
author = {Qi, Q and Gao, C and Meng, X and Liu, W and Xue, Y and Yan, Y},
title = {Oral Microbiota Dynamics Across the Lifespan: Age, Sex, Race and Socioeconomic Influences in the US Population.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70016},
pmid = {40830911},
issn = {1600-051X},
support = {82473650//National Natural Science Foundation of China/ ; 82073572//National Natural Science Foundation of China/ ; 20230484467//Beijing Nova Program/ ; },
abstract = {AIM: The oral microbiota, a complex and dynamic ecosystem, plays a crucial role in human health, yet systematic studies across the lifespan remain limited. This study aimed to investigate variations in the oral microbiota and the effects of key influencing factors on the oral microbiota at different age groups.

MATERIALS AND METHODS: In this study, we analysed the oral microbiota of 9662 individuals aged 14-69 years from the US National Health and Nutrition Examination Survey (NHANES) to explore the impact of demographic, lifestyle and environmental factors on microbial diversity and composition. Microbiological characterisation was done using the participants' oral rinses by 16S ribosomal RNA gene sequencing.

RESULTS: Our findings revealed a clear age-related trend in microbial diversity, with Shannon diversity peaking in middle-aged and declining in older adults. The composition of the oral microbiota also varied significantly with age, as different genera exhibited distinct abundance patterns across the lifespan. Gender and race emerged as key influencing factors, with males showing greater Shannon diversity and greater relative abundances of Atopobium, Megasphaera and Porphyromonas spp., and Whites were enriched in Rothia and Veillonella. Socioeconomic factors and lifestyle, particularly smoking, were strongly associated with shifts in microbial communities.

CONCLUSIONS: These findings provide a comprehensive overview of the dynamic changes in the oral microbiota throughout life and underscore the intricate interplay between host and environmental factors in shaping microbial composition, offering a foundation for future research on microbiota-related health interventions.},
}

@article {pmid40828642,
year = {2025},
author = {Davies, RG and Wood, LA and Hengist, A and O'Donovan, C and Barton, W and Crispie, F and Walhin, JP and Valdivia-Garcia, MA and Garcia-Perez, I and Frost, G and O'Sullivan, O and Cotter, PD and Gonzalez, JT and Betts, JA and Koumanov, F and Thompson, D},
title = {Effects of a combined energy restriction and vigorous-intensity exercise intervention on the human gut microbiome: A randomised controlled trial.},
journal = {The Journal of physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/JP287424},
pmid = {40828642},
issn = {1469-7793},
support = {MR/P002927/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {Metabolic health improvements in response to exercise and energy restriction may be mediated by the gut microbiome, yet causal evidence in humans remains limited. We used a 3-week exercise and energy restriction intervention to examine changes to the gut microbiome in otherwise healthy sedentary men and postmenopausal women with overweight/obesity. Intervention participants (n = 18) reduced habitual energy intake by 5000 kcal/week and expended 2000 kcal/week in addition to habitual physical activity through treadmill walking at 70% V̇O2Peak. Control participants (n = 12) maintained their usual lifestyle. Participants underwent dual-energy X-ray absorptiometry (DEXA), and samples of faeces, fasted venous blood, subcutaneous adipose tissue and skeletal muscle were collected. Faecal DNA was sequenced and profiled using shotgun metagenomics, Kraken2/Bracken and Human Microbiome Project Unified Metabolic Analysis Network 2 (HUMAnN2). The intervention significantly reduced body mass (mean Δ ± SD: -2.6 ± 1.5 kg), fat mass (-1.5 ± 1.3 kg), fasted insulin (-23.5 ± 38.1 pmol/l), leptin (-10.6 ± 7.3 ng/ml) and total cholesterol (-0.70 ± 0.42 mmol/l) concentrations, and also improved insulin sensitivity (HOMA2%S (homeostatic model of assessment)). Despite these significant metabolic changes the gut microbiome was unchanged in terms of α and β diversity and relative abundance. Thus, despite clinically meaningful improvements in body composition and metabolic health, we found no evidence for changes to the gut microbiome. In conclusion early metabolic changes with weight loss in humans are unlikely to be mediated by changes to the gut microbiome. KEY POINTS: Changes to the gut microbiome could contribute to metabolic improvements associated with weight loss in humans, but there have been limited attempts to address this question using robust randomised controlled trials (RCTs). We used a parallel-group RCT to examine whether a 3-week combined energy intake restriction and vigorous-intensity exercise intervention in people with overweight and obesity was temporally associated with changes to gut microbiome taxonomic composition and functional potential, short-chain fatty acid concentrations and expression of genes related to host-microbiome interactions in skeletal muscle and subcutaneous adipose tissue. We found that the human gut microbiome remains unchanged in the face of an intensive energy intake restriction and vigorous exercise intervention that significantly improved body composition and metabolic health in people with overweight/obesity. These findings indicate that early metabolic changes with weight loss in humans are unlikely to be mediated by changes to the gut microbiome.},
}

@article {pmid40827925,
year = {2025},
author = {Caffrey, EB and Olm, MR and Kothe, CI and Wastyk, HC and Evans, JD and Sonnenburg, JL},
title = {MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0014125},
doi = {10.1128/msystems.00141-25},
pmid = {40827925},
issn = {2379-5077},
abstract = {Fermented foods, which contain a diversity of microbes and microbial metabolites, have been used for millennia to increase food security, flavor, and nutritional content; more recently, they have been recognized as potential mediators of human health. Metagenomics is a powerful approach to characterize microbes in fermented foods, providing high taxonomic resolution and functional insights. Here, we introduce the Microbial Food DataBase, a metagenomics-based approach designed for the identification of fermentation-associated microbes. Using this primary database of metagenome-assembled genomes and relevant deposited genomes of prokaryotes, eukaryotes, and common food-relevant substrates, we investigated 89 fermented food samples. We present a streamlined high-confidence characterization of microbial diversity in fermented food, identifying previously undiscovered genomes and facilitating strain-level tracking across food environments. The easy and robust functionality of the workflow has significant implications for advancing food safety, promoting desired microbial communities, and increasing sustainability in food production.IMPORTANCEFermented foods have microbial communities that influence food safety, flavor, and human health. Microbial Food DataBase (MiFoDB), an alignment-based sequencing workflow and database, addresses the limitations of existing tools by enabling strain-level resolution, identifying novel genomes, and providing functional insights into microbial communities. Applying MiFoDB to fermented food samples, we demonstrate its ability to uncover novel species, track microbial strains across substrates, and integrate functional annotations. Additionally, the outlined workflow is highly customizable and can be used to generate alignment-based databases for other microbial ecosystems. This work highlights the importance of fermentation-specific workflows for studying microbial food ecosystems, advancing food safety, sustainability, and innovation in fermented food research.},
}

@article {pmid40827869,
year = {2025},
author = {Allen, JM},
title = {Rediscovering the wild: MiFoDB brings fermented food microbiomes into focus.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0059925},
doi = {10.1128/msystems.00599-25},
pmid = {40827869},
issn = {2379-5077},
abstract = {Fermented foods have sustained human societies for thousands of years, with their microbial communities subtly shaping flavor, nutrient preservation, and health. Yet despite this long-standing relationship, much of the microbial complexity within fermented foods remains unresolved. In recent work, Caffrey et al. (E. B. Caffrey, M. R. Olm, C. I. Kothe, H. C. Wastyk, et al., mSystems 10:e00141-25, 2025, https://doi.org/10.1128/msystems.00141-25) put forth a new tool, MiFoDB, a metagenomic workflow that offers a promising alternative for advancing food microbiome science. By enabling strain-level resolution, functional gene annotation, and microbial tracking across substrates and time, MiFoDB provides a clearer view into the ecological and functional landscape of the fermented food microbiota. This work also bridges gaps between food and human microbiome research and brings us closer to a mechanistic understanding of how fermented foods influence health, helping transform ancient dietary practices into actionable and targeted nutritional strategies for improving human health and well-being.},
}

@article {pmid40823863,
year = {2025},
author = {Glowacki, RW and Engelhart, MJ and Till, JM and Kadam, A and Nemet, I and Sangwan, N and Ahern, PP},
title = {Identification of strain-specific cues that regulate biofilm formation in Bacteroides thetaiotaomicron.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0341924},
doi = {10.1128/spectrum.03419-24},
pmid = {40823863},
issn = {2165-0497},
abstract = {Members of the gut microbiome encounter a barrage of host- and microbe-derived microbiocidal factors that must be overcome to maintain fitness in the intestine. The long-term stability of many gut microbiome strains within the microbiome suggests the existence of strain-specific strategies that have evolved to foster resilience to such insults. Despite this, little is known about the mechanisms that mediate this resistance. Biofilm formation represents one commonly employed defense strategy against stressors like those found in the intestine. Here, we demonstrate strain-level variation in the capacity of the gut symbiont Bacteroides thetaiotaomicron to form biofilms. Despite the potent induction of biofilm formation by bile in most strains, we show that the specific bile acid species driving biofilm formation differs among strains and uncover that a secondary bile acid, lithocholic acid, and its conjugated forms potently induce biofilm formation in a strain-specific manner. Additionally, we found that the short-chain fatty acid, acetic acid, could suppress biofilm formation. Thus, our data define molecular components of bile that can promote biofilm formation in B. thetaiotaomicron and reveal that distinct molecular cues trigger the induction or inhibition of this process. Moreover, we uncover strain-level variation in these responses, thus identifying that both shared and strain-specific determinants govern biofilm formation in this species.IMPORTANCEIn order to thrive within the intestine, it is imperative that gut microbes resist the multitude of insults derived from the host immune system and other microbiome members. As such, they have evolved strategies that ensure their survival within the intestine. We investigated one such strategy, biofilm formation, in Bacteroides thetaiotaomicron, a common member of the human microbiome. We uncovered significant variation in natural biofilm formation in the absence of an overt stimulus among different B. thetaiotaomicron strains and revealed that different strains adopted a biofilm lifestyle in response to distinct molecular stimuli. Thus, our studies provide novel insights into factors mediating gut symbiont resiliency, revealing strain-specific and shared strategies in these responses. Collectively, our findings underscore the prevalence of strain-level differences that should be factored into our understanding of gut microbiome functions.},
}

@article {pmid40818485,
year = {2025},
author = {Shah, ND and Staudacher, HM},
title = {Cultural competence in the delivery of nutrition and symptom care in irritable bowel syndrome.},
journal = {The lancet. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2468-1253(25)00236-5},
pmid = {40818485},
issn = {2468-1253},
}

@article {pmid40813370,
year = {2025},
author = {Rakoff-Nahoum, S and Debelius, J and Valles-Colomer, M and Noordzij, HT and Esteban-Torres, M and Zhernakova, A and Brusselaers, N and Pettersen, VK},
title = {A reconceptualized framework for human microbiome transmission in early life.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7546},
pmid = {40813370},
issn = {2041-1723},
abstract = {Human development and physiology are fundamentally linked with the microbiome. This is particularly true during early life, a critical period for microbiome assembly and its impact on the host. Understanding microbial acquisition in early life is thus central to both our basic understanding of the human microbiome and strategies for disease prevention and treatment. Here, we review the historical approaches to categorize microbial transmission originating from the fields of infectious disease epidemiology and evolutionary biology and discuss how this lexicon has influenced our approach to studying the early-life microbiome, often leading to confusion and misinterpretation. We then present a conceptual framework to capture the multifaceted nature of human microbiome acquisition based on four key components: what, where, who, and when. We present ways these parameters may be assigned, with a particular focus on the 'transmitted strain' through metagenomics to capture these elements. We end with a discussion of approaches for implementing this framework toward defining each component of microbiome acquisition.},
}

@article {pmid40791541,
year = {2025},
author = {Horvath, M and Kang, HG and Wu, TC and Aiken, E and Cadena Castaneda, D and Akkurt, S and Marches, F and Anczuków, O and Palucka, K and Oh, J},
title = {Host-specific bacterial modulation of airway gene expression and alternative splicing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.18.665426},
pmid = {40791541},
issn = {2692-8205},
abstract = {The human microbiome varies extensively between individuals. While there are numerous studies investigating the effects of inter-individual differences on microbiome composition, there are few studies investigating inter-individual effects on microbial modulation of the host, or host-specific effects. To address this knowledge gap, we colonized human bronchial epithelial air-liquid interface tissue cultures generated from six different adults with one of three phylogenetically diverse bacteria and compared how each microbe differentially modulated host gene expression in each of the six donors. Microbial treatment had the strongest effect on transcription, followed by donor-specific effects. Gene pathways differed markedly in their donor- and microbe-specificity; interferon expression was highly donor-dependent while transcription of epithelial barrier and antibacterial innate immunity genes were predominantly microbially driven. Moreover, we evaluated whether microbial regulation of alternative splicing was modulated by donor. Strikingly, we found significant non-redundant, donor-specific regulation of alternative splicing exclusively in the Gram-positive commensal microbes. These findings highlight that microbial effects on the human airway epithelium are not only species-specific but also deeply individualized, scoring the importance of host context in shaping microbe-induced transcriptional and splicing responses.},
}

@article {pmid40653354,
year = {2025},
author = {Gupta, R and Gaur, S},
title = {Effect of diet and lifestyle on microbiome composition.},
journal = {International review of cell and molecular biology},
volume = {395},
number = {},
pages = {157-174},
doi = {10.1016/bs.ircmb.2024.12.008},
pmid = {40653354},
issn = {1937-6448},
mesh = {Humans ; *Life Style ; *Diet ; *Microbiota ; Animals ; },
abstract = {Microbes are major drivers of many important physiological pathways in the human body. A well-adapted and established microbial community at key body sites performs a wide range of functions, including digestive and immunological roles. However, the structure of these microbial communities depends on numerous factors, both genetic and external. Diet and lifestyle are the most common external factors influencing microbiome composition. A healthy diet and lifestyle promote the growth of beneficial microbes, while disturbances in these factors can alter the entire microbial dynamics, potentially leading to pathogenesis. These perturbations can occur at any stage of life, from birth to old age, and may result in serious clinical conditions such as obesity, diabetes, cancers, metabolic syndromes, and many others. Therefore, it is essential to identify the dietary and lifestyle factors that support a healthy microbiome and prevent dysbiosis. This chapter aims to discuss the role of various component of diet and life style that can ultimately shape the human microbiome.},
}

Humans
*Life Style
*Diet
*Microbiota
Animals

@article {pmid40623763,
year = {2025},
author = {Agrawal, P and Mendhey, P and Kumar, R and Patel, S and Kaushik, PK and Dadsena, A and Kumar, S},
title = {Introduction to microbiomes in health and diseases.},
journal = {International review of cell and molecular biology},
volume = {394},
number = {},
pages = {1-42},
doi = {10.1016/bs.ircmb.2024.12.010},
pmid = {40623763},
issn = {1937-6448},
mesh = {Humans ; *Microbiota ; *Health ; *Disease ; Animals ; },
abstract = {The human microbiome is a complex ecological system of commensal, symbiotic, and pathogenic microorganisms that plays a crucial role in human health and disease. The microbiome includes both the living microorganisms also called microbiota and their synthesized metabolites and structural components. It is distributed to the gastrointestinal tract, skin, respiratory system, and oral cavity, each with a distinct microbial composition. Dysbiosis, or imbalance in the microbiome is linked to numerous diseases such as eczema, gastric ulcers, cardiovascular diseases, and cancer. The axes of microbial activity and their connections to disease, including the gut-skin, gut-lung, gut-brain, and gut-kidney play a crucial role in health and disease conditions. Also, the role of the microbiome in cancer development and response to therapy is examined. This book chapter underscores the importance of maintaining a balanced microbiome for overall health and the potential for microbiome-based interventions in disease prevention and treatment.},
}

Humans
*Microbiota
*Health
*Disease
Animals

@article {pmid40586419,
year = {2025},
author = {Dason, MS and Corà, D and Re, A},
title = {Sequence modeling tools to decode the biosynthetic diversity of the human microbiome.},
journal = {mSystems},
volume = {10},
number = {7},
pages = {e0033325},
pmid = {40586419},
issn = {2379-5077},
support = {P2022AFS8P//Next Generation EU - MUR/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Biosynthetic Pathways/genetics ; Multigene Family ; *Computational Biology/methods ; Bacteria/genetics/metabolism ; },
abstract = {Understanding the biosynthetic potential of the human microbiome remains a significant challenge with far-reaching scientific and translational implications. Analyses of human-associated (meta)genomic sequencing data undeniably show that the biosynthetic diversity encoded in these genomes is largely underexplored. A crucial step in studying specialized metabolites involves the sequence-based identification of genes encoding biosynthetic pathways, typically organized into biosynthetic gene clusters (BGCs). In this review, we provide a concise and updated overview of the widening range of computational approaches that have effectively addressed the sequence-based identification of BGCs across both isolated genomes and complex microbial communities. These advancements are set to deepen our understanding of the biosynthetic potential and diversity of microorganisms residing in different human body sites.},
}

Humans
*Microbiota/genetics
*Biosynthetic Pathways/genetics
Multigene Family
*Computational Biology/methods
Bacteria/genetics/metabolism

@article {pmid40448869,
year = {2025},
author = {Dash, HR and Al-Snan, NR},
title = {DNA forensics at forty: the way forward.},
journal = {International journal of legal medicine},
volume = {139},
number = {5},
pages = {2023-2046},
pmid = {40448869},
issn = {1437-1596},
abstract = {Forensic DNA analysis has transformed criminal investigations since its inception in 1985. Over four decades, this field has evolved through various phases-from the early stages of exploration to today's highly sophisticated methodologies. Key advancements such as the development of rapid DNA analysis techniques, microchip-based systems, and next-generation sequencing have improved the speed, reliability, and utility of DNA forensics. However, despite these technological advances, the field still faces considerable challenges, particularly with increasing case backlogs, limited population-specific databases, and the difficulties associated with analyzing degraded or challenging samples like bones and touch DNA. Emerging technologies such as single-cell genomic analysis, lineage markers, proteomics, and human microbiome analysis offer promising solutions to these challenges. Furthermore, the integration of artificial intelligence (AI) and machine learning (ML) in forensic workflows is enhancing the ability to analyze complex DNA samples efficiently, paving the way for faster and more accurate results. As forensic DNA analysis enters its next phase, the focus will be on expanding databases, refining quality control and assurance protocols, and standardizing training for forensic professionals worldwide. The journey of forensic DNA analysis over the past 40 years demonstrates a field in continuous development. Although significant progress has been made, there remain opportunities for further innovation, particularly in overcoming the current limitations and addressing ethical and legal concerns. By doing so, forensic DNA analysis will continue to play a pivotal role in the future of criminal justice.},
}

@article {pmid40411594,
year = {2025},
author = {Dash, HR and Patel, A},
title = {Genealogically bewildered individuals and forensic identification: a review of current and emerging solutions.},
journal = {International journal of legal medicine},
volume = {139},
number = {5},
pages = {2001-2021},
pmid = {40411594},
issn = {1437-1596},
abstract = {The increasing use of assisted reproductive technologies (ART) with donor gametes is driven by rising infertility rates, delayed parenthood, and the need to prevent hereditary diseases. Greater social acceptance of diverse family structures, advancements in reproductive medicine, and improving success rates also contribute. Accessibility, affordability, and cross-border reproductive care further expand ART's reach, making donor gametes a preferred option for many individuals and couples worldwide. The widespread application of ART has led to an increasing number of donor-conceived individuals, many of whom are now reaching reproductive maturity. This demographic shift introduces significant challenges for traditional forensic genetic identification methods, which rely on biological reference samples from genetically related individuals. The absence of such samples complicates the identification process, particularly for individuals conceived via gamete donation or adoption, where biological and legal parentage are incongruent. Conventional forensic genetic analyses, including short tandem repeat (STR) and single nucleotide polymorphism (SNP) profiling of autosomal, Y-chromosome, X-chromosome, and mitochondrial DNA, exhibit limited efficacy in these scenarios. While these methods can sometimes identify individuals conceived using a single donor gamete, they are insufficient for cases involving dual donor gametes or mitochondrial replacement therapy. Emerging methodologies such as forensic genetic genealogy, DNA methylation profiling, and human microbiome analysis offer innovative approaches but necessitate further clinical validation and standardization.},
}

@article {pmid40363959,
year = {2025},
author = {Gullo, G and Satullo, M and Billone, V and De Paola, L and Petousis, S and Kotlik, Y and Margioula-Siarkou, C and Perino, A and Cucinella, G},
title = {The Role of the Genital Tract Microbiome in Human Fertility: A Literature Review.},
journal = {Journal of clinical medicine},
volume = {14},
number = {9},
pages = {},
pmid = {40363959},
issn = {2077-0383},
abstract = {Background/Objectives: Infertility is a multifactorial condition influenced by various factors, including dysbiosis and alterations in the genital tract microbiome. Recent studies emphasize the microbiome's significant role in influencing a woman's fertility potential, thereby affecting the chances of spontaneous conception and the outcomes of assisted reproductive treatments. Understanding the microbial characteristics and unique features of a healthy genital microbiome, as well as how changes in its composition can impact fertility, would allow for a more comprehensive and personalized approach to managing assisted reproductive treatments. The microbiome also influences pregnancy outcomes, and restoring its balance has been shown to improve fertility in infertile couples. The human microbiome plays a key role in maintaining the body's overall health. Disruptions in microbiome balance among women of reproductive age can contribute to a range of pregnancy-related complications, with notable consequences for both maternal and fetal well-being. Emerging research has highlighted a connection between the reproductive tract microbiome and outcomes of assisted reproductive technologies (ART), suggesting that re-establishing a healthy microbial environment may enhance fertility in couples facing infertility. Methods: We conducted a search on PubMed using the keywords "microbiome", "infertility", and "ART" over the past 10 years. This article aims to provide an updated overview of the role of the microbiome in female reproductive health, with a focus on its implications for fertility treatment. Results: The microbiome has a significant role in influencing women's fertility. Conclusions: Understanding the microbiome's impact on fertility and pregnancy outcomes may lead to more effective and personalized approaches in fertility treatments, improving the chances of successful conception and pregnancy.},
}

@article {pmid40297591,
year = {2025},
author = {Pei, X and Liu, L and Han, Y},
title = {Advances in human microbiome and prostate cancer research.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1576679},
pmid = {40297591},
issn = {1664-3224},
mesh = {Humans ; *Prostatic Neoplasms/microbiology/therapy/immunology/metabolism/etiology ; Male ; *Microbiota ; *Gastrointestinal Microbiome ; Tumor Microenvironment/immunology ; Animals ; },
abstract = {Prostate cancer (PCa) is the second most common malignant tumor in men worldwide, and its metastatic and heterogeneous nature makes it significantly more difficult to treat. Recent studies have revealed the critical role of microbiota in PCa occurrence, progression, and treatment. Accumulating evidence from 16S rRNA and metagenomic sequencing suggests the presence of specific microbiota in prostate tissues and macrogenomics techniques: cancerous tissues are enriched with pro-inflammatory genera (e.g., Fusobacterium, Propionibacterium acnes), whereas commensal bacteria (e.g., Pseudomonas) are more common in paracancerous tissues. The microbiota drive tumor progression through activation of the NF-κB/STAT3 pathway to induce chronic inflammation, modulation of the immune microenvironment (e.g., Treg/Th17 imbalance and M2-type macrophage polarization), and metabolite (e.g., LPS, short-chain fatty acids)-mediated hormonal and epigenetic regulation. In terms of clinical translation, urinary microbiota characterization combined with metabolomics analysis may enhance diagnostic specificity, while gut flora modulation (e.g., probiotic interventions or fecal transplants) may improve resistance to androgen deprivation therapy. Current challenges include sequencing accuracy of low-biomass samples, limitations of causal mechanism validation models, and large cohort heterogeneity. In the future, it will be necessary to integrate multi-omics technologies to explore the bidirectional regulation of the "gut-prostate axis" and develop personalized therapeutic strategies targeting microorganisms. In this paper, we systematically review the interactions between microbiota and PCa and their clinical potentials to provide a theoretical basis for precision diagnosis and treatment.},
}

Humans
*Prostatic Neoplasms/microbiology/therapy/immunology/metabolism/etiology
Male
*Microbiota
*Gastrointestinal Microbiome
Tumor Microenvironment/immunology
Animals

@article {pmid40166302,
year = {2025},
author = {Walker, AR and Pham, DN and Noeparvar, P and Peterson, AM and Lipp, MK and Lemos, JA and Zeng, L},
title = {FRUCTOSE ACTIVATES A STRESS RESPONSE SHARED BY METHYLGLYOXAL AND HYDROGEN PEROXIDE IN STREPTOCOCCUS MUTANS.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.26.620100},
pmid = {40166302},
issn = {2692-8205},
abstract = {Fructose catabolism by Streptococcus mutans is initiated by three PTS transporters yielding either fructose-1-phoshate (F-1-P) or fructose-6-phosphate (F-6-P). Deletion of one such F-1-P-generating PTS, fruI, has been shown to reduce the cariogenicity of S. mutans in rats fed a high-sucrose diet. Moreover, a recent study linked fructose metabolism in S. mutans to a reactive electrophile species (RES) methylglyoxal. Here, we conducted a comparative transcriptomic analysis of exponentially grown S. mutans shocked with 50 mM fructose, 50 mM glucose, 5 mM methylglyoxal, or 0.5 mM hydrogen peroxide (H2O2). The results revealed a striking overlap between the fructose and methylglyoxal transcriptomes, totaling 176 genes, 61 of which were also shared with the H2O2 transcriptome. This core of 61 genes encompassed many of the same pathways affected by exposure to low pH or zinc intoxication. Consistent with these findings, fructose negatively impacted metal homeostasis of a mutant deficient in zinc expulsion and the growth of a mutant of the major oxidative stress regulator SpxA1. We further demonstrated the induction of the superoxide dismutase (sodA) and the fruRKI operon by different levels of fructose. Finally, fructose metabolism lowered culture pH at a faster pace, allowed better survival under acidic and nutrient-depleted conditions, and enhanced the competitiveness of S. mutans against Streptococcus sanguinis, although a moderated level of F-1-P might further boost some of these benefits. In conclusion, fructose metabolism is integrated into the stress core of S. mutans and regulates critical functions required for survival in both the oral cavity and during systemic infections. Importance. Fructose is a common monosaccharide in the biosphere, yet its overconsumption has been linked to various health problems in humans including insulin resistance, obesity, diabetes, and non-alcoholic liver diseases. These effects are in large part attributed to the unique biochemical characteristics and metabolic responses associated with the degradation of fructose. Yet, an understanding of the effects of fructose on the physiology of bacteria and its implications to the human microbiome is severely lacking. Here we performed a series of analyses on the gene regulation of a dental pathogen Streptococcus mutans by exposing it to fructose and other important stress agents. Further supported by growth, persistence, and competition assays, our findings revealed the ability of fructose to activate a set of cellular functions that may prove critical to the ability of the bacterium to persist and cause diseases both within and without of the oral cavity.},
}

@article {pmid40119155,
year = {2025},
author = {Heidrich, V and Valles-Colomer, M and Segata, N},
title = {Human microbiome acquisition and transmission.},
journal = {Nature reviews. Microbiology},
volume = {23},
number = {9},
pages = {568-584},
pmid = {40119155},
issn = {1740-1534},
abstract = {As humans, we host personal microbiomes intricately connected to our biology and health. Far from being isolated entities, our microbiomes are dynamically shaped by microbial exchange with the surroundings, in lifelong microbiome acquisition and transmission processes. In this Review, we explore recent studies on how our microbiomes are transmitted, beginning at birth and during interactions with other humans and the environment. We also describe the key methodological aspects of transmission inference, based on the uniqueness of the building blocks of the microbiome - single microbial strains. A better understanding of human microbiome transmission will have implications for studies of microbial host regulation, of microbiome-associated diseases, and for effective microbiome-targeting strategies. Besides exchanging strains with other humans, there is also preliminary evidence we acquire microorganisms from animals and food, and thus a complete understanding of microbiome acquisition and transmission can only be attained by adopting a One Health perspective.},
}

@article {pmid40111698,
year = {2025},
author = {Vernon, JJ},
title = {Modulation of the Human Microbiome: Probiotics, Prebiotics, and Microbial Transplants.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {277-294},
pmid = {40111698},
issn = {0065-2598},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; *Prebiotics/administration & dosage ; *Microbiota/physiology ; *Mouth/microbiology ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; },
abstract = {The balance between health and disease is intrinsically linked to the interactions between microbial communities and the host. This complex environment of antagonism and synergy involves both prokaryotic and eukaryotic cells, whose collaborative metabolic pathways and immunomodulatory elements influence system homeostasis. As with the gut and other niches, the oral microbiome has the capacity to affect distal host sites. The ability to manipulate this environment holds the potential to impact local and systemic disease.With the increasing threat of antimicrobial resistance, novel approaches to reduce the burden of disease are essential. The use of probiotics and prebiotics is one such strategy. Probiotics introduce non-pathogenic bacteria into the environment to compete with pathogens for nutrients and attachment sites, or to produce metabolites that counteract disease aetiologies. Prebiotic compounds enhance the growth of health-associated organisms, offering additional benefits, whilst a conjunctive approach with probiotics potentially holds even greater promise. Though widely studied in the gastrointestinal context, their potential for treating oral diseases, such as dental caries and periodontitis, is less understood. Additionally, the use of microbial transplantations has demonstrated efficacy in other areas, reducing systemic inflammation and recolonising with commensal bacteria. Here we evaluate their use in the oral context and their modulatory impact on overall health.In this chapter, we discuss how pro- and prebiotic strategies seek to modulate both the oral and gut environments to promote oral health and prevent disease. We assess novel approaches for utilising health-associated microorganisms to combat oral disorders, either administered locally in the mouth or imparting influence through immune modulation via the oral-gut axis. By examining available clinical trial data, we aim to further understand the intricacies involved in this discipline. Furthermore, we consider the challenges facing the research community, including optimal candidate organism/compound selection and colonisation retention, as well as considerations for future research.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
*Prebiotics/administration & dosage
*Microbiota/physiology
*Mouth/microbiology
*Gastrointestinal Microbiome
Fecal Microbiota Transplantation

@article {pmid40072555,
year = {2025},
author = {Shah, H and Patel, P and Nath, A and Shah, U and Sarkar, R},
title = {Role of human microbiota in facilitating the metastatic journey of cancer cells.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {398},
number = {8},
pages = {9767-9796},
pmid = {40072555},
issn = {1432-1912},
abstract = {Cancer continues to be the leading cause of mortality worldwide, with metastasis being the primary contributor to cancer-related deaths. Despite significant advancements in cancer therapies, metastasis remains a major challenge in effective cancer management. Metastasis, the process by which cancer cells spread from the primary tumor to distant organs, is a complex phenomenon influenced by multiple factors, including the human microbiota. The human body encompasses various microorganisms, comprising bacteria, viruses, fungi, and protozoa, collectively known as microbiota. In fact, the microbiota is more abundant than human cells, and its disruption, leading to an imbalance in host-microbiota interactions (dysbiosis), has been linked to various diseases, including cancer. Among all microbiota, bacteria are one of the key contributors to cancer progression. Bacteria and bacteria-derived components such as secondary metabolites, QSPs, and toxins play a pivotal role in the metastatic progression of cancers. This review explores the intricate relationship between the human microbiota and cancer progression, focusing on different bacterial species which have been implicated in tumorigenesis, immune evasion, and metastasis. The present review explores the role of the human microbiome, specifically of bacteria in promoting metastasis in different types of cancers, demonstrating its ability to impact both the spread of tumors and their underlying mechanisms. This review also highlights the therapeutic potential and challenges of microbiome-based interventions in combating metastatic cancers. By addressing these challenges and by integrating microbiome-targeted strategies into clinical cancer treatment could represent a transformative approach in the fight against metastasis.},
}

@article {pmid39298326,
year = {2024},
author = {Gordon, JI and Barratt, MJ and Hibberd, MC and Rahman, M and Ahmed, T},
title = {Establishing human microbial observatory programs in low- and middle-income countries.},
journal = {Annals of the New York Academy of Sciences},
volume = {1540},
number = {1},
pages = {13-20},
doi = {10.1111/nyas.15224},
pmid = {39298326},
issn = {1749-6632},
support = {//Fondazione Internazionale Premio Balzan/ ; //Bill and Melinda Gates Foundation/ ; /NH/NIH HHS/United States ; /NH/NIH HHS/United States ; },
mesh = {Humans ; *Developing Countries ; Global Health ; *Microbiota ; },
abstract = {Studies of the human microbiome are progressing rapidly but have largely focused on populations living in high-income countries. With increasing evidence that the microbiome contributes to the pathogenesis of diseases that affect infants, children, and adults in low- and middle-income countries (LMICs), and with profound and rapid ongoing changes occurring in our lifestyles and biosphere, understanding the origins of and developing microbiome-directed therapeutics for treating a number of global health challenges requires the development of programs for studying human microbial ecology in LMICs. Here, we discuss how the establishment of long-term human microbial observatory programs in selected LMICs could provide one timely approach.},
}

Humans
*Developing Countries
Global Health
*Microbiota

@article {pmid39217206,
year = {2024},
author = {Duller, S and Vrbancic, S and Szydłowski, Ł and Mahnert, A and Blohs, M and Predl, M and Kumpitsch, C and Zrim, V and Högenauer, C and Kosciolek, T and Schmitz, RA and Eberhard, A and Dragovan, M and Schmidberger, L and Zurabischvili, T and Weinberger, V and Moser, AM and Kolb, D and Pernitsch, D and Mohammadzadeh, R and Kühnast, T and Rattei, T and Moissl-Eichinger, C},
title = {Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7593},
pmid = {39217206},
issn = {2041-1723},
support = {P 30796//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; SFB F-83//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; COE 7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; },
mesh = {*Methanobrevibacter/genetics/isolation & purification/metabolism ; Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Genome, Archaeal ; Methane/metabolism ; Phylogeny ; Adult ; Male ; Female ; Gastrointestinal Tract/microbiology ; },
abstract = {Archaea are vital components of the human microbiome, yet their study within the gastrointestinal tract (GIT) is limited by the scarcity of cultured representatives. Our study presents a method for the targeted enrichment and isolation of methanogenic archaea from human fecal samples. The procedure combines methane breath testing, in silico metabolic modeling, media optimization, FACS, dilution series, and genomic sequencing through Nanopore technology. Additional analyzes include the co-cultured bacteriome, comparative genomics of archaeal genomes, functional comparisons, and structure-based protein function prediction of unknown differential traits. Successful establishment of stable archaeal cultures from 14 out of 16 fecal samples yielded nine previously uncultivated strains, eight of which are absent from a recent archaeome genome catalog. Comparative genomic and functional assessments of Methanobrevibacter smithii and Candidatus Methanobrevibacter intestini strains from individual donors revealed features potentially associated with gastrointestinal diseases. Our work broadens available archaeal representatives for GIT studies, and offers insights into Candidatus Methanobrevibacter intestini genomes' adaptability in critical microbiome contexts.},
}

*Methanobrevibacter/genetics/isolation & purification/metabolism
Humans
*Feces/microbiology
*Gastrointestinal Microbiome/genetics
*Genome, Archaeal
Methane/metabolism
Phylogeny
Adult
Male
Female
Gastrointestinal Tract/microbiology

@article {pmid39167930,
year = {2024},
author = {Mohamed, KA and Kruf, S and Büll, C},
title = {Putting a cap on the glycome: Dissecting human sialyltransferase functions.},
journal = {Carbohydrate research},
volume = {544},
number = {},
pages = {109242},
doi = {10.1016/j.carres.2024.109242},
pmid = {39167930},
issn = {1873-426X},
mesh = {Humans ; *Sialyltransferases/metabolism ; Polysaccharides/metabolism/chemistry ; },
abstract = {Human glycans are capped with sialic acids and these nine-carbon sugars mediate many of the biological functions and interactions of glycans. Structurally diverse sialic acid caps mark human cells as self and they form the ligands for the Siglec immune receptors and other glycan-binding proteins. Sialic acids enable host interactions with the human microbiome and many human pathogens utilize sialic acids to infect host cells. Alterations in sialic acid-carrying glycans, sialoglycans, can be found in every major human disease including inflammatory conditions and cancer. Twenty sialyltransferase family members in the Golgi apparatus of human cells transfer sialic acids to distinct glycans and glycoconjugates. Sialyltransferases catalyze specific reactions to form unique sialoglycans or they have shared functions where multiple family members generate the same sialoglycan product. Moreover, some sialyltransferases compete for the same glycan substrate, but create different sialic acid caps. The redundant and competing functions make it difficult to understand the individual roles of the human sialyltransferases in biology and to reveal the specific contributions to pathobiological processes. Recent insights hint towards the existence of biosynthetic rules formed by the individual functions of sialyltransferases, their interactions, and cues from the local Golgi environment that coordinate sialoglycan biosynthesis. In this review, we discuss the current structural and functional understanding of the human sialyltransferase family and we review recent technological advances that enable the dissection of individual sialyltransferase activities.},
}

Humans
*Sialyltransferases/metabolism
Polysaccharides/metabolism/chemistry

@article {pmid39166876,
year = {2024},
author = {de Palma, TH and Powers, C and McPartland, MJ and Mark Welch, J and Ramsey, M},
title = {Essential genes for Haemophilus parainfluenzae survival and biofilm growth.},
journal = {mSystems},
volume = {9},
number = {9},
pages = {e0067424},
pmid = {39166876},
issn = {2379-5077},
support = {R01 DE027958/DE/NIDCR NIH HHS/United States ; 1017848//U.S. Department of Agriculture (USDA)/ ; R01DE027958//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
mesh = {*Biofilms/growth & development ; *Haemophilus parainfluenzae/genetics ; *Genes, Essential/genetics ; Humans ; Genome, Bacterial/genetics ; DNA Transposable Elements/genetics ; Microbial Viability/genetics ; },
abstract = {Haemophilus parainfluenzae (Hp) is a Gram-negative, highly prevalent, and abundant commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the supragingival plaque biofilm. Little is known about how Hp interacts with its neighbors in healthy biofilms nor its mechanisms of pathogenesis as an opportunistic pathogen. To address this, we identified the essential genome and conditionally essential genes in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain (Hp 392) and oral isolate EL1 (Hp EL1), we show that the essential genomes of Hp 392 and Hp EL1 are composed of 395 (20%) and 384 (19%) genes, respectively. The core essential genome, consisting of 341 (17%) essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains. RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo habitat. This library presents a valuable tool for investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.IMPORTANCEHaemophilus parainfluenzae is a highly abundant human commensal microbe, present in most healthy individuals where it colonizes the mouth. H. parainfluenzae correlates with good oral health and may play a role in preservation of healthy host status. Also, H. parainfluenzae can cause opportunistic infections outside of the oral cavity. To date, little is known about how H. parainfluenzae colonizes the human host, despite being such a frequent and abundant part of our human microbiome. Here, we demonstrate the creation and use of a powerful tool, a TnSeq library, used to identify genes necessary for both the outright growth of this organism and also genes conditionally essential for growth in varying oxygen status which it can encounter in the human host. This tool and these data serve as a foundation for further study of this relatively unknown organism that may play a role in preserving human health.},
}

*Biofilms/growth & development
*Haemophilus parainfluenzae/genetics
*Genes, Essential/genetics
Humans
Genome, Bacterial/genetics
DNA Transposable Elements/genetics
Microbial Viability/genetics

@article {pmid39136453,
year = {2024},
author = {Etlin, S and Rose, J and Bielski, L and Walter, C and Kleinman, AS and Mason, CE},
title = {The human microbiome in space: parallels between Earth-based dysbiosis, implications for long-duration spaceflight, and possible mitigation strategies.},
journal = {Clinical microbiology reviews},
volume = {37},
number = {3},
pages = {e0016322},
pmid = {39136453},
issn = {1098-6618},
mesh = {Humans ; *Space Flight ; *Dysbiosis/microbiology ; *Astronauts ; Microbiota/physiology ; Gastrointestinal Microbiome/physiology ; },
abstract = {SUMMARYThe human microbiota encompasses the diverse communities of microorganisms that reside in, on, and around various parts of the human body, such as the skin, nasal passages, and gastrointestinal tract. Although research is ongoing, it is well established that the microbiota exert a substantial influence on the body through the production and modification of metabolites and small molecules. Disruptions in the composition of the microbiota-dysbiosis-have also been linked to various negative health outcomes. As humans embark upon longer-duration space missions, it is important to understand how the conditions of space travel impact the microbiota and, consequently, astronaut health. This article will first characterize the main taxa of the human gut microbiota and their associated metabolites, before discussing potential dysbiosis and negative health consequences. It will also detail the microbial changes observed in astronauts during spaceflight, focusing on gut microbiota composition and pathogenic virulence and survival. Analysis will then turn to how astronaut health may be protected from adverse microbial changes via diet, exercise, and antibiotics before concluding with a discussion of the microbiota of spacecraft and microbial culturing methods in space. The implications of this review are critical, particularly with NASA's ongoing implementation of the Moon to Mars Architecture, which will include weeks or months of living in space and new habitats.},
}

Humans
*Space Flight
*Dysbiosis/microbiology
*Astronauts
Microbiota/physiology
Gastrointestinal Microbiome/physiology

@article {pmid39101047,
year = {2024},
author = {Liu, J and Zhang, X and Lin, T and Chen, R and Zhong, Y and Chen, T and Wu, T and Liu, C and Huang, A and Nguyen, TT and Lee, EE and Jeste, DV and Tu, XM},
title = {A New Paradigm for High-dimensional Data: Distance-Based Semiparametric Feature Aggregation Framework via Between-Subject Attributes.},
journal = {Scandinavian journal of statistics, theory and applications},
volume = {51},
number = {2},
pages = {672-696},
pmid = {39101047},
issn = {0303-6898},
support = {K23 MH118435/MH/NIMH NIH HHS/United States ; K23 MH119375/MH/NIMH NIH HHS/United States ; R01 MH094151/MH/NIMH NIH HHS/United States ; R01 MH135147/MH/NIMH NIH HHS/United States ; },
abstract = {This article proposes a distance-based framework incentivized by the paradigm shift towards feature aggregation for high-dimensional data, which does not rely on the sparse-feature assumption or the permutation-based inference. Focusing on distance-based outcomes that preserve information without truncating any features, a class of semiparametric regression has been developed, which encapsulates multiple sources of high-dimensional variables using pairwise outcomes of between-subject attributes. Further, we propose a strategy to address the interlocking correlations among pairs via the U-statistics-based estimating equations (UGEE), which correspond to their unique efficient influence function (EIF). Hence, the resulting semiparametric estimators are robust to distributional misspecification while enjoying root-n consistency and asymptotic optimality to facilitate inference. In essence, the proposed approach not only circumvents information loss due to feature selection but also improves the model's interpretability and computational feasibility. Simulation studies and applications to the human microbiome and wearables data are provided, where the feature dimensions are tens of thousands.},
}

@article {pmid38974672,
year = {2024},
author = {Castaño-Henao, L and Mendez, DFG and Egan, S and Sanabria, J},
title = {Changes in groundwater and surface water bacterial communities under disinfection processes: Chlorination, ozonization, photo-fenton and ultraviolet radiation.},
journal = {Current research in microbial sciences},
volume = {7},
number = {},
pages = {100244},
pmid = {38974672},
issn = {2666-5174},
abstract = {Pathogenic bacteria, introduced in water sources through faecal contamination, have traditionally been investigated as individual species, leading to the establishment of microbial, sanitary, and environmental quality indicators. Recent advancements in our understanding of the microbiome and its intricate interactions within the human-microbiome-environment network advocate for a broader evaluation of the impact of disinfection on the entire microbial community. In this study, we conducted a comprehensive screening experiment involving four disinfection processes; ozone, ultraviolet radiation with wavelengths between 200 - 280 nm (UV-C), photo-Fenton, and chlorination, applied to two distinct water sources; surface (SW) and groundwater (GW). The cells that remained viable after treatment were recovered using Brain Heart Infusion (BHI) broth, and 16S rRNA gene sequencing was used for their identification. Our findings confirmed the presence of faecal contamination in the water sources and revealed distinct effects of each treatment on the recovered bacterial populations. The chlorination of groundwater samples likely had a greater impact on bacteria in a vegetative state than on spores. Consequently, this led to a higher abundance in the BHI cultures of sporulating bacteria such as Bacillus (increasing from 0.36 to 93.62 %), while ozonation led to an elevated recovery of Pseudomonas (increasing from 45.2 to 69.9 %). Conversely, in surface water, calcium hypochlorite and ozone treatments favored the selection of Staphylococcus and Bacillus, whose relative abundance in the cultures increased from 0 to 39.22 % and from 0.35 to 96.6 %, respectively. In groundwater, Pseudomonas was resistant to UV-C radiation and their relative abundance increased from 45.2 % to 93.56 %, while photo-Fenton was effective against this bacterial group decreasing its relative abundance to 0.46 %. However, other genera such as Bacteroides, Aeromonas, and Citrobacter seemed to be less injured by this disinfection process. BHI broth was successful in recovering various bacterial groups that exhibited resistance to sublethal water disinfection.},
}

@article {pmid38850297,
year = {2024},
author = {Hoisington, AJ and Stamper, CE and Ellis, JC and Lowry, CA and Brenner, LA},
title = {Quantifying variation across 16S rRNA gene sequencing runs in human microbiome studies.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {367},
pmid = {38850297},
issn = {1432-0614},
support = {U.S. Department of Veterans Affairs//U.S. Department of Veterans Affairs/ ; 140755//Mindsource Brain Injury Network/ ; },
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Microbiota/genetics ; *Sequence Analysis, DNA/methods ; *DNA, Bacterial/genetics ; Bacteria/genetics/classification/isolation & purification ; Reproducibility of Results ; Mouth/microbiology ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Recent microbiome research has incorporated a higher number of samples through more participants in a study, longitudinal studies, and metanalysis between studies. Physical limitations in a sequencing machine can result in samples spread across sequencing runs. Here we present the results of sequencing nearly 1000 16S rRNA gene sequences in fecal (stabilized and swab) and oral (swab) samples from multiple human microbiome studies and positive controls that were conducted with identical standard operating procedures. Sequencing was performed in the same center across 18 different runs. The simplified mock community showed limitations in accuracy, while precision (e.g., technical variation) was robust for the mock community and actual human positive control samples. Technical variation was the lowest for stabilized fecal samples, followed by fecal swab samples, and then oral swab samples. The order of technical variation stability was inverse of DNA concentrations (e.g., highest in stabilized fecal samples), highlighting the importance of DNA concentration in reproducibility and urging caution when analyzing low biomass samples. Coefficients of variation at the genus level also followed the same trend for lower variation with higher DNA concentrations. Technical variation across both sample types and the two human sampling locations was significantly less than the observed biological variation. Overall, this research providing comparisons between technical and biological variation, highlights the importance of using positive controls, and provides semi-quantified data to better understand variation introduced by sequencing runs. KEY POINTS: • Mock community and positive control accuracy were lower than precision. • Samples with lower DNA concentration had increased technical variation across sequencing runs. • Biological variation was significantly higher than technical variation due to sequencing runs.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*Feces/microbiology
*Microbiota/genetics
*Sequence Analysis, DNA/methods
*DNA, Bacterial/genetics
Bacteria/genetics/classification/isolation & purification
Reproducibility of Results
Mouth/microbiology
High-Throughput Nucleotide Sequencing/methods

@article {pmid38830853,
year = {2024},
author = {Kitsios, GD and Sayed, K and Fitch, A and Yang, H and Britton, N and Shah, F and Bain, W and Evankovich, JW and Qin, S and Wang, X and Li, K and Patel, A and Zhang, Y and Radder, J and Dela Cruz, C and Okin, DA and Huang, CY and Van Tyne, D and Benos, PV and Methé, B and Lai, P and Morris, A and McVerry, BJ},
title = {Longitudinal multicompartment characterization of host-microbiota interactions in patients with acute respiratory failure.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4708},
pmid = {38830853},
issn = {2041-1723},
support = {R03 HL162655/HL/NHLBI NIH HHS/United States ; COVID-19 Respiratory Virus Research//American Lung Association (Lung Association)/ ; IK2 BX004886/BX/BLRD VA/United States ; IK2BX004886//U.S. Department of Veterans Affairs (Department of Veterans Affairs)/ ; P01 HL114453/HL/NHLBI NIH HHS/United States ; T32 HL116275/HL/NHLBI NIH HHS/United States ; T32 HL007563/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; Female ; Male ; *Dysbiosis/microbiology ; Middle Aged ; *Lung/microbiology ; *COVID-19/microbiology/virology ; Aged ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Host Microbial Interactions/genetics ; Longitudinal Studies ; RNA, Ribosomal, 16S/genetics ; Respiratory Insufficiency/microbiology ; SARS-CoV-2/genetics/isolation & purification ; Adult ; Respiration, Artificial ; Bacteria/genetics/classification/isolation & purification ; Critical Illness ; Metagenomics/methods ; },
abstract = {Critical illness can significantly alter the composition and function of the human microbiome, but few studies have examined these changes over time. Here, we conduct a comprehensive analysis of the oral, lung, and gut microbiota in 479 mechanically ventilated patients (223 females, 256 males) with acute respiratory failure. We use advanced DNA sequencing technologies, including Illumina amplicon sequencing (utilizing 16S and ITS rRNA genes for bacteria and fungi, respectively, in all sample types) and Nanopore metagenomics for lung microbiota. Our results reveal a progressive dysbiosis in all three body compartments, characterized by a reduction in microbial diversity, a decrease in beneficial anaerobes, and an increase in pathogens. We find that clinical factors, such as chronic obstructive pulmonary disease, immunosuppression, and antibiotic exposure, are associated with specific patterns of dysbiosis. Interestingly, unsupervised clustering of lung microbiota diversity and composition by 16S independently predicted survival and performed better than traditional clinical and host-response predictors. These observations are validated in two separate cohorts of COVID-19 patients, highlighting the potential of lung microbiota as valuable prognostic biomarkers in critical care. Understanding these microbiome changes during critical illness points to new opportunities for microbiota-targeted precision medicine interventions.},
}

Humans
Female
Male
*Dysbiosis/microbiology
Middle Aged
*Lung/microbiology
*COVID-19/microbiology/virology
Aged
*Microbiota/genetics
*Gastrointestinal Microbiome/genetics
Host Microbial Interactions/genetics
Longitudinal Studies
RNA, Ribosomal, 16S/genetics
Respiratory Insufficiency/microbiology
SARS-CoV-2/genetics/isolation & purification
Adult
Respiration, Artificial
Bacteria/genetics/classification/isolation & purification
Critical Illness
Metagenomics/methods

@article {pmid38076985,
year = {2023},
author = {Jain, R and Hadjigeorgiou, A and Harkos, C and Mishra, A and Morad, G and Johnson, S and Ajami, N and Wargo, J and Munn, L and Stylianopoulos, T},
title = {Dissecting the Impact of the Gut Microbiome on Cancer Immunotherapy.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {38076985},
issn = {2693-5015},
support = {F32 CA260769/CA/NCI NIH HHS/United States ; R01 NS118929/NS/NINDS NIH HHS/United States ; U01 CA224348/CA/NCI NIH HHS/United States ; R01 CA259253/CA/NCI NIH HHS/United States ; R21 EB031982/EB/NIBIB NIH HHS/United States ; R35 CA197743/CA/NCI NIH HHS/United States ; R01 CA208205/CA/NCI NIH HHS/United States ; R01 CA247441/CA/NCI NIH HHS/United States ; R01 CA219896/CA/NCI NIH HHS/United States ; U01 CA261842/CA/NCI NIH HHS/United States ; },
abstract = {The gut microbiome has emerged as a key regulator of response to cancer immunotherapy. However, there is a gap in our understanding of the underlying mechanisms by which the microbiome influences immunotherapy. To this end, we developed a mathematical model based on i) gut microbiome data derived from preclinical studies on melanomas after fecal microbiota transplant, ii) mechanistic modeling of antitumor immune response, and iii) robust association analysis of murine and human microbiome profiles with model-predicted immune profiles. Using our model, we could distill the complexity of these murine and human studies on microbiome modulation in terms of just two model parameters: the activation and killing rate constants of immune cells. We further investigated associations between specific bacterial taxonomies and antitumor immunity and immunotherapy efficacy. This model can guide the design of studies to refine and validate mechanistic links between the microbiome and immune system.},
}

@article {pmid37637212,
year = {2023},
author = {Li, W and Mirone, J and Prasad, A and Miolane, N and Legrand, C and Dao Duc, K},
title = {Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets.},
journal = {Frontiers in bioinformatics},
volume = {3},
number = {},
pages = {1211819},
pmid = {37637212},
issn = {2673-7647},
abstract = {Conventional dimensionality reduction methods like Multidimensional Scaling (MDS) are sensitive to the presence of orthogonal outliers, leading to significant defects in the embedding. We introduce a robust MDS method, called DeCOr-MDS (Detection and Correction of Orthogonal outliers using MDS), based on the geometry and statistics of simplices formed by data points, that allows to detect orthogonal outliers and subsequently reduce dimensionality. We validate our methods using synthetic datasets, and further show how it can be applied to a variety of large real biological datasets, including cancer image cell data, human microbiome project data and single cell RNA sequencing data, to address the task of data cleaning and visualization.},
}

@article {pmid37457284,
year = {2023},
author = {Lugones-Sánchez, C and Santos-Mínguez, S and Salvado, R and González-Sánchez, S and Tamayo-Morales, O and Hoya-González, A and Ramírez-Manent, JI and Magallón-Botaya, R and Quesada-Rico, JA and Garcia-Cubillas, MD and Rodríguez-Sánchez, E and Gómez-Marcos, MA and Benito-Sanchez, R and Mira, A and Hernandez-Rivas, JM and Garcia-Ortiz, L and , },
title = {Lifestyles, arterial aging, and its relationship with the intestinal and oral microbiota (MIVAS III study): a research protocol for a cross-sectional multicenter study.},
journal = {Frontiers in public health},
volume = {11},
number = {},
pages = {1164453},
pmid = {37457284},
issn = {2296-2565},
mesh = {Humans ; Middle Aged ; Aged ; Cross-Sectional Studies ; *Cardiovascular Diseases/epidemiology ; Blood Pressure/physiology ; Pulse Wave Analysis/methods ; RNA, Ribosomal, 16S ; Aging ; Life Style ; *Diet, Mediterranean ; *Microbiota ; Multicenter Studies as Topic ; },
abstract = {BACKGROUND: The microbiota is increasingly recognized as a significant factor in the pathophysiology of many diseases, including cardiometabolic diseases, with lifestyles probably exerting the greatest influence on the composition of the human microbiome. The main objectives of the study are to analyze the association of lifestyles (diet, physical activity, tobacco, and alcohol) with the gut and oral microbiota, arterial aging, and cognitive function in subjects without cardiovascular disease in the Iberian Peninsula. In addition, the study will examine the mediating role of the microbiome in mediating the association between lifestyles and arterial aging as well as cognitive function.

METHODS AND ANALYSIS: MIVAS III is a multicenter cross-sectional study that will take place in the Iberian Peninsula. One thousand subjects aged between 45 and 74 years without cardiovascular disease will be selected. The main variables are demographic information, anthropometric measurements, and habits (tobacco and alcohol). Dietary patterns will be assessed using a frequency consumption questionnaire (FFQ) and the Mediterranean diet adherence questionnaire. Physical activity levels will be evaluated using the International Physical Activity Questionnaire (IPAQ), Marshall Questionnaire, and an Accelerometer (Actigraph). Body composition will be measured using the Inbody 230 impedance meter. Arterial aging will be assessed through various means, including measuring medium intimate carotid thickness using the Sonosite Micromax, conducting analysis with pulse wave velocity (PWA), and measuring pulse wave velocity (cf-PWV) using the Sphygmocor System. Additional cardiovascular indicators such as Cardio Ankle Vascular Index (CAVI), ba-PWV, and ankle-brachial index (Vasera VS-2000[®]) will also be examined. The study will analyze the intestinal microbiota using the OMNIgene GUT kit (OMR-200) and profile the microbiome through massive sequencing of the 16S rRNA gene. Linear discriminant analysis (LDA), effect size (LEfSe), and compositional analysis, such as ANCOM-BC, will be used to identify differentially abundant taxa between groups. After rarefying the samples, further analyses will be conducted using MicrobiomeAnalyst and R v.4.2.1 software. These analyses will include various aspects, such as assessing α and β diversity, conducting abundance profiling, and performing clustering analysis.

DISCUSSION: Lifestyle acts as a modifier of microbiota composition. However, there are no conclusive results demonstrating the mediating effect of the microbiota in the relationship between lifestyles and cardiovascular diseases. Understanding this relationship may facilitate the implementation of strategies for improving population health by modifying the gut and oral microbiota.

TRIAL REGISTRATION: clinicaltrials.gov/ct2/show/NCT04924907, ClinicalTrials.gov, identifier: NCT04924907. Registered on 21 April 2021.},
}

Humans
Middle Aged
Aged
Cross-Sectional Studies
*Cardiovascular Diseases/epidemiology
Blood Pressure/physiology
Pulse Wave Analysis/methods
RNA, Ribosomal, 16S
Aging
Life Style
*Diet, Mediterranean
*Microbiota
Multicenter Studies as Topic

@article {pmid36464584,
year = {2023},
author = {Villemin, C and Six, A and Neville, BA and Lawley, TD and Robinson, MJ and Bakdash, G},
title = {The heightened importance of the microbiome in cancer immunotherapy.},
journal = {Trends in immunology},
volume = {44},
number = {1},
pages = {44-59},
doi = {10.1016/j.it.2022.11.002},
pmid = {36464584},
issn = {1471-4981},
mesh = {Humans ; *Microbiota ; *Neoplasms/therapy/microbiology ; Immunotherapy ; Bacteria ; },
abstract = {The human microbiome is recognized as a key factor in health and disease. This has been further corroborated by identifying changes in microbiome composition and function as a novel hallmark in cancer. These effects are exerted through microbiome interactions with host cells, impacting a wide variety of developmental and physiological processes. In this review, we discuss some of the latest findings on how the bacterial component of the microbiome can influence outcomes for different cancer immunotherapy modalities, highlighting identified mechanisms of action. We also address the clinical efforts to utilize this knowledge to achieve better responses to immunotherapy. A refined understanding of microbiome variations in patients and microbiome-host interactions with cancer therapies is essential to realize optimal clinical responses.},
}

Humans
*Microbiota
*Neoplasms/therapy/microbiology
Immunotherapy
Bacteria

@article {pmid36270683,
year = {2022},
author = {Mahapatra, S and Mohanty, S and Mishra, R and Prasad, P},
title = {An overview of cancer and the human microbiome.},
journal = {Progress in molecular biology and translational science},
volume = {191},
number = {1},
pages = {83-139},
doi = {10.1016/bs.pmbts.2022.07.007},
pmid = {36270683},
issn = {1878-0814},
mesh = {Humans ; *Microbiota ; Symbiosis ; *Neoplasms ; },
abstract = {Mutual beneficial associations with the microbial consortia are an essential requisite of human life. Microbial communities have both a symbiotic and a pathogenic standpoint, which portrays a context-dependent scenario of the human microbiome. The symbiotic assemblage works to develop indispensable functions of the human body such as immune system, digestive system, defense against colonization by pathobionts and their toxins, etc. Furthermore, any deviation in the resource utilization by the symbionts due to host factors comprising lifestyle changes, diet, drugs, immunocompromised states, and co-morbidities could perturb beneficial microbes communities and promote the invasion by opportunistic pathogens thus, disrupting the homeostatic state. Microbial infestations have proved to be carcinogenic but this does not spontaneously establish a cancer hallmark, rather they initiate a cascade of events that disturbs the normal cellular activities finally these defective machineries invade distant sites of the body, submitting to a devastative transformed internal milieu. Significant technological and system biology advances have been made in elucidating a lucid but complex basis of such microbe-associated malignancies. This chapter discusses the recent advances, without compromising the concepts of the inception studies, including a brief version of the microbial status in cancer generation, mechanistic approaches adapted, therapeutic interventions, system biology approaches with special mention on the study design gaps, challenges in addressing the drawbacks and finally with a perspective of the future targeted studies, has been a focus of this piece of work.},
}

Humans
*Microbiota
Symbiosis
*Neoplasms

@article {pmid36109831,
year = {2022},
author = {Roussel, C and Anunciação Braga Guebara, S and Plante, PL and Desjardins, Y and Di Marzo, V and Silvestri, C},
title = {Short-term supplementation with ω-3 polyunsaturated fatty acids modulates primarily mucolytic species from the gut luminal mucin niche in a human fermentation system.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2120344},
pmid = {36109831},
issn = {1949-0984},
mesh = {Akkermansia ; Docosahexaenoic Acids/pharmacology ; Eicosapentaenoic Acid/pharmacology ; Expectorants/pharmacology ; *Fatty Acids, Omega-3/pharmacology ; Fatty Acids, Volatile ; Fermentation ; Firmicutes ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Mucins ; Prebiotics ; Propionates/pharmacology ; Verrucomicrobia ; },
abstract = {Consumption of omega-3 polyunsaturated fatty acids (ω-3 PUFAs) eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) provides multifaceted health benefits. Recent studies suggest that ω-3 PUFAs modulate the gut microbiota by enhancing health-promoting bacteria, such as the mucin specialist Akkermansia muciniphila. However, these prebiotic properties have been poorly investigated and direct effects on the gut microbiome have never been explored dynamically across gut regions and niches (lumen vs. mucus-associated microbiota). Thus, we studied the effects of 1 week EPA- and DHA-enriched ω-3 fish-oil supplementation on the composition and functionality of the human microbiome in a Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME®). Gut microbial communities derived from one individual harvested in two different seasons were tested in duplicate. Luminal and outer mucus-associated microbiota of the ileum, ascending, transverse and descending colons were cultivated over 28 d from fecal inoculates and supplemented with ω-3 PUFAs for the last 7 d. We show that ω-3 PUFA supplementation modulates the microbiota in a gut region- and niche-dependent fashion. The outer mucus-associated microbiota displayed a higher resilience than the luminal mucin habitat to ω-3 PUFAs, with a remarkable blooming of Akkermansia muciniphila in opposition to a decrease of Firmicutes-mucolytic bacteria. The ω-3 PUFAs also induced a gradual and significant depletion of non-mucolytic Clostridia members in luminal habitats. Finally, increased concentrations of the short chain fatty acids (SCFA) propionate in colon regions at the end of the supplementation was associated positively with the bloom of Akkermansia muciniphila and members of the Desulfovibrionia class.},
}

Akkermansia
Docosahexaenoic Acids/pharmacology
Eicosapentaenoic Acid/pharmacology
Expectorants/pharmacology
*Fatty Acids, Omega-3/pharmacology
Fatty Acids, Volatile
Fermentation
Firmicutes
*Gastrointestinal Microbiome
Humans
*Microbiota
Mucins
Prebiotics
Propionates/pharmacology
Verrucomicrobia

@article {pmid36068270,
year = {2022},
author = {Ke, S and Weiss, ST and Liu, YY},
title = {Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {5235},
pmid = {36068270},
issn = {2041-1723},
support = {U19 AI095219/AI/NIAID NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; RF1 AG067744/AG/NIA NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; UH3 OD023268/OD/NIH HHS/United States ; },
mesh = {*COVID-19 ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome/genetics ; *Microbiota ; SARS-CoV-2/genetics ; },
abstract = {Coronavirus disease 2019 (COVID-19), primarily a respiratory disease caused by infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is often accompanied by gastrointestinal symptoms. However, little is known about the relation between the human microbiome and COVID-19, largely due to the fact that most previous studies fail to provide high taxonomic resolution to identify microbes that likely interact with SARS-CoV-2 infection. Here we used whole-metagenome shotgun sequencing data together with assembly and binning strategies to reconstruct metagenome-assembled genomes (MAGs) from 514 COVID-19 related nasopharyngeal and fecal samples in six independent cohorts. We reconstructed a total of 11,584 medium-and high-quality microbial MAGs and obtained 5403 non-redundant MAGs (nrMAGs) with strain-level resolution. We found that there is a significant reduction of strain richness for many species in the gut microbiome of COVID-19 patients. The gut microbiome signatures can accurately distinguish COVID-19 cases from healthy controls and predict the progression of COVID-19. Moreover, we identified a set of nrMAGs with a putative causal role in the clinical manifestations of COVID-19 and revealed their functional pathways that potentially interact with SARS-CoV-2 infection. Finally, we demonstrated that the main findings of our study can be largely validated in three independent cohorts. The presented results highlight the importance of incorporating the human gut microbiome in our understanding of SARS-CoV-2 infection and disease progression.},
}

*COVID-19
*Gastrointestinal Microbiome/genetics
Humans
Metagenome/genetics
*Microbiota
SARS-CoV-2/genetics

@article {pmid36014818,
year = {2022},
author = {Lane, MM and Lotfaliany, M and Forbes, M and Loughman, A and Rocks, T and O'Neil, A and Machado, P and Jacka, FN and Hodge, A and Marx, W},
title = {Higher Ultra-Processed Food Consumption Is Associated with Greater High-Sensitivity C-Reactive Protein Concentration in Adults: Cross-Sectional Results from the Melbourne Collaborative Cohort Study.},
journal = {Nutrients},
volume = {14},
number = {16},
pages = {},
pmid = {36014818},
issn = {2072-6643},
mesh = {Adult ; *C-Reactive Protein/analysis ; Cohort Studies ; Cross-Sectional Studies ; Diet ; *Energy Intake ; Fast Foods/adverse effects/analysis ; Food Handling ; Humans ; },
abstract = {Background: Few studies have examined associations between ultra-processed food intake and biomarkers of inflammation, and inconsistent results have been reported in the small number of studies that do exist. As such, further investigation is required. Methods: Cross-sectional baseline data from the Melbourne Collaborative Cohort Study (MCCS) were analysed (n = 2018). We applied the NOVA food classification system to data from a food frequency questionnaire (FFQ) to determine ultra-processed food intake (g/day). The outcome was high-sensitivity C-reactive protein concentration (hsCRP; mg/L). We fitted unadjusted and adjusted linear regression analyses, with sociodemographic characteristics and lifestyle- and health-related behaviours as covariates. Supplementary analyses further adjusted for body mass index (kg/m2). Sex was assessed as a possible effect modifier. Ultra-processed food intake was modelled as 100 g increments and the magnitude of associations expressed as estimated relative change in hsCRP concentration with accompanying 95% confidence intervals (95%CIs). Results: After adjustment, every 100 g increase in ultra-processed food intake was associated with a 4.0% increase in hsCRP concentration (95%CIs: 2.1−5.9%, p < 0.001). Supplementary analyses showed that part of this association was independent of body mass index (estimated relative change in hsCRP: 2.5%; 95%CIs: 0.8−4.3%, p = 0.004). No interaction was observed between sex and ultra-processed food intake. Conclusion: Higher ultra-processed food intake was cross-sectionally associated with elevated hsCRP, which appeared to occur independent of body mass index. Future prospective and intervention studies are necessary to confirm directionality and whether the observed association is causal.},
}

Adult
*C-Reactive Protein/analysis
Cohort Studies
Cross-Sectional Studies
Diet
*Energy Intake
Fast Foods/adverse effects/analysis
Food Handling
Humans