@article {pmid40217076,
year = {2025},
author = {Gilbert, JA and Azad, MB and Bäckhed, F and Blaser, MJ and Byndloss, M and Chiu, CY and Chu, H and Dugas, LR and Elinav, E and Gibbons, SM and Gilbert, KE and Henn, MR and Ishaq, SL and Ley, RE and Lynch, SV and Segal, E and Spector, TD and Strandwitz, P and Suez, J and Tropini, C and Whiteson, K and Knight, R},
title = {Clinical translation of microbiome research.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40217076},
issn = {1546-170X},
abstract = {The landscape of clinical microbiome research has dramatically evolved over the past decade. By leveraging in vivo and in vitro experimentation, multiomic approaches and computational biology, we have uncovered mechanisms of action and microbial metrics of association and identified effective ways to modify the microbiome in many diseases and treatment modalities. This Review explores recent advances in the clinical application of microbiome research over the past 5 years, while acknowledging existing barriers and highlighting opportunities. We focus on the translation of microbiome research into clinical practice, spearheaded by Food and Drug Administration (FDA)-approved microbiome therapies for recurrent Clostridioides difficile infections and the emerging fields of microbiome-based diagnostics and therapeutics. We highlight key examples of studies demonstrating how microbiome mechanisms, metrics and modifiers can advance clinical practice. We also discuss forward-looking perspectives on key challenges and opportunities toward integrating microbiome data into routine clinical practice, precision medicine and personalized healthcare and nutrition.},
}

@article {pmid40217075,
year = {2025},
author = {Zitvogel, L and Derosa, L and Routy, B and Loibl, S and Heinzerling, L and de Vries, IJM and Engstrand, L and , and Segata, N and Kroemer, G},
title = {Impact of the ONCOBIOME network in cancer microbiome research.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40217075},
issn = {1546-170X},
abstract = {The European Union-sponsored ONCOBIOME network has spurred an international effort to identify and validate relevant gut microbiota-related biomarkers in oncology, generating a unique and publicly available microbiome resource. ONCOBIOME explores the effects of the microbiota on gut permeability and metabolism as well as on antimicrobial and antitumor immune responses. Methods for the diagnosis of gut dysbiosis have been developed based on oncomicrobiome signatures associated with the diagnosis, prognosis and treatment responses in patients with cancer. The mechanisms explaining how dysbiosis compromises natural or therapy-induced immunosurveillance have been explored. Through its integrative approach of leveraging multiple cohorts across populations, cancer types and stages, ONCOBIOME has laid the theoretical and practical foundations for the recognition of microbiota alterations as a hallmark of cancer. ONCOBIOME has launched microbiota-centered interventions and lobbies in favor of official guidelines for avoiding diet-induced or iatrogenic (for example, antibiotic- or proton pump inhibitor-induced) dysbiosis. Here, we review the key advances of the ONCOBIOME network and discuss the progress toward translating these into oncology clinical practice.},
}

@article {pmid40216855,
year = {2025},
author = {Novielli, P and Magarelli, M and Romano, D and Di Bitonto, P and Stellacci, AM and Monaco, A and Amoroso, N and Bellotti, R and Tangaro, S},
title = {Leveraging explainable AI to predict soil respiration sensitivity and its drivers for climate change mitigation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12527},
pmid = {40216855},
issn = {2045-2322},
mesh = {*Soil/chemistry ; *Soil Microbiology ; *Climate Change ; Carbon Dioxide/analysis/metabolism ; Machine Learning ; *Artificial Intelligence ; Global Warming ; Temperature ; },
abstract = {Global warming is one of the most pressing and critical problems facing the world today. It is mainly caused by the increase in greenhouse gases in the atmosphere, such as carbon dioxide (CO2). Understanding how soils respond to rising temperatures is critical for predicting carbon release and informing climate mitigation strategies. Q10, a measure of soil microbial respiration, quantifies the increase in CO2 release caused by a [Formula: see text] Celsius rise in temperature, serving as a key indicator of this sensitivity. However, predicting Q10 across diverse soil types remains a challenge, especially when considering the complex interactions between biochemical, microbiome, and environmental factors. In this study, we applied explainable artificial intelligence (XAI) to machine learning models to predict soil respiration sensitivity (Q10) and uncover the key factors driving this process. Using SHAP (SHapley Additive exPlanations) values, we identified glucose-induced soil respiration and the proportion of bacteria positively associated with Q10 as the most influential predictors. Our machine learning models achieved an accuracy of [Formula: see text], precision of [Formula: see text], an AUC-ROC of [Formula: see text], and an AUC-PRC of [Formula: see text], ensuring robust and reliable predictions. By leveraging t-SNE (t-distributed Stochastic Neighbor Embedding) and clustering techniques, we further segmented low Q10 soils into distinct subgroups, identifying soils with a higher probability of transitioning to high Q10 states. Our findings not only highlight the potential of XAI in making model predictions transparent and interpretable, but also provide actionable insights into managing soil carbon release in response to climate change. This research bridges the gap between AI-driven environmental modeling and practical applications in agriculture, offering new directions for targeted soil management and climate resilience strategies.},
}

*Soil/chemistry
*Soil Microbiology
*Climate Change
Carbon Dioxide/analysis/metabolism
Machine Learning
*Artificial Intelligence
Global Warming
Temperature

@article {pmid40216810,
year = {2025},
author = {Sarandi, E and Tsoukalas, D and Rudofsky, G and Fragoulakis, V and Liapi, C and Paramera, E and Papakonstantinou, E and Krueger Krasagakis, S and Tsatsakis, A},
title = {Identifying the metabolic profile of Hashimoto's thyroiditis from the METHAP clinical study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12410},
pmid = {40216810},
issn = {2045-2322},
mesh = {Humans ; *Hashimoto Disease/metabolism/blood/urine ; Female ; Male ; Biomarkers/blood/urine/metabolism ; Case-Control Studies ; Adult ; *Metabolome ; Middle Aged ; Metabolomics/methods ; Gas Chromatography-Mass Spectrometry ; },
abstract = {Hashimoto's thyroiditis (HT), one of the most common autoimmune diseases and the leading cause of hypothyroidism, is linked to metabolic and cellular dysfunctions that contribute to disease aetiopathogenesis. This case-control study aimed to identify potent metabolic biomarkers of HT employing machine learning techniques. 62 euthyroid patients with HT and 58 healthy individuals were included from the metabolic biomarkers in Hashimoto's thyroiditis and psoriasis (METHAP) clinical trial. Quantification of 73 metabolites was performed using gas-chromatography/mass spectrometry in plasma and urine samples of fasted participants. Changes in the tricarboxylic acid cycle, carbohydrate, neurotransmitter, microbiome and lipid metabolism were identified in the HT group. Ordinary least squares and beta regression modeling associated the presence of HT with methylmalonic acid, 4-hydroxyphenylpyruvic acid, palmitic acid, palmitoleic acid, myristoleic acid and total saturated fatty acids, adjusting for confounders. Artificial neural network analysis had good predictive accuracy with an AUC of 0.8, while debiased sparse partial correlation network analysis identified metabolite-metabolite interactions distinct for HT. These findings provide insights into novel biomarkers associated with HT, and we discuss their biological relevance and clinical significance. Hashimoto's thyroiditis is associated with mitochondrial dysfunction, micronutrient decreased bioavailability, microbiome imbalances, and carbohydrate and fatty acids dysfunctional metabolism.},
}

Humans
*Hashimoto Disease/metabolism/blood/urine
Female
Male
Biomarkers/blood/urine/metabolism
Case-Control Studies
Adult
*Metabolome
Middle Aged
Metabolomics/methods
Gas Chromatography-Mass Spectrometry

@article {pmid40216789,
year = {2025},
author = {Shekarriz, S and Szamosi, JC and Whelan, FJ and Lau, JT and Libertucci, J and Rossi, L and Fontes, ME and Wolfe, M and Lee, CH and Moayyedi, P and Surette, MG},
title = {Detecting microbial engraftment after FMT using placebo sequencing and culture enriched metagenomics to sort signals from noise.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3469},
pmid = {40216789},
issn = {2041-1723},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Metagenomics/methods ; *Colitis, Ulcerative/therapy/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Placebos ; Adult ; Middle Aged ; },
abstract = {Fecal microbiota transplantation (FMT) has shown efficacy for the treatment of ulcerative colitis but with variable response between patients and trials. The mechanisms underlying FMT's therapeutic effects remains poorly understood but is generally assumed to involve engraftment of donor microbiota into the recipient's microbiome. Reports of microbial engraftment following FMT have been inconsistent between studies. Here, we investigate microbial engraftment in a previous randomized controlled trial (NCT01545908), in which FMT was sourced from a single donor, using amplicon-based profiling, shotgun metagenomics, and culture-enriched metagenomics. Placebo samples were included to estimate engraftment noise, and a significant level of false-positive engraftment was observed which confounds the prediction of true engraftment. We show that analyzing engraftment across multiple patients from a single donor enhances the accuracy of detection. We identified a unique set of genes engrafted in responders to FMT which supports strain displacement as the primary mechanism of engraftment in our cohort.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Metagenomics/methods
*Colitis, Ulcerative/therapy/microbiology
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Male
Female
Placebos
Adult
Middle Aged

@article {pmid40216734,
year = {2025},
author = {Vallazhath, A and Thimmappa, PY and Joshi, HB and Hebbar, KR and Nayak, A and Umakanth, S and Saoji, AA and Manjunath, NK and Hadapad, BS and Joshi, MB},
title = {A comprehensive review on the implications of Yogic/Sattvic diet in reducing inflammation in type 2 diabetes.},
journal = {Nutrition & diabetes},
volume = {15},
number = {1},
pages = {14},
pmid = {40216734},
issn = {2044-4052},
support = {DST/SATYAM/2020/247 (G)//Department of Science and Technology, Ministry of Science and Technology (DST)/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 2/diet therapy/complications ; *Inflammation/diet therapy/prevention & control ; Insulin Resistance ; *Yoga ; Gastrointestinal Microbiome ; },
abstract = {Chronic inflammation in type 2 diabetes (T2D), characterized by constitutively activated immune cells and elevated pro-inflammatory mediators along with hyperglycaemia and increased free fatty acids and branched chain amino acid levels, significantly alters the immuno-metabolic axis. Over the years, dietary intervention has been explored as an effective strategy for managing T2D. Evidence from experimental and clinical studies indicates that various diets, including Mediterranean, Nordic, Palaeolithic and ketogenic diets, increase insulin sensitivity, decrease gluconeogenesis, and adiposity, and exert anti-inflammatory effects, thus preserving immuno-metabolic homeostasis in individuals with T2D. Indian dietary sources are categorized as Sattvic, Rajasic, and Tamasic, depending on their impact on health and behaviour. The Yogic diet, commonly recommended during yoga practice, is predominantly Sattvic, emphasizing plant-based whole foods while limiting processed and high-glycaemic-index items. Yogic diet is also recommended for Mitahara, emphasizing mindful eating, which is attributed to calorie restriction. Adopting a Yogic diet, featuring low-fat vegetarian principles, strongly reduces inflammatory mediator levels. This diet not only ameliorates insulin resistance and maintains a healthy body weight but also regulates immunomodulation, enhances gut microbiome diversity and provides essential phytonutrients, collectively preventing inflammation. Although, preliminary studies show aforementioned beneficial role of Yogic diet in improving diabetes associated metabolic and inflammatory changes, precise cellular and molecular mechanisms are not yet understood. Hence, further studies are warranted to decipher the mechanisms. This review summarizes the multiple roles of Yogic diet and related dietary components in mitigating inflammation and enhancing glycaemic control in T2D.},
}

Humans
*Diabetes Mellitus, Type 2/diet therapy/complications
*Inflammation/diet therapy/prevention & control
Insulin Resistance
*Yoga
Gastrointestinal Microbiome

@article {pmid40216167,
year = {2025},
author = {Sangfuang, N and Xie, Y and McCoubrey, LE and Taub, M and Favaron, A and Mai, Y and Gaisford, S and Basit, AW},
title = {Investigating the bidirectional interactions between senotherepeutic agents and human gut microbiota.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {},
number = {},
pages = {107098},
doi = {10.1016/j.ejps.2025.107098},
pmid = {40216167},
issn = {1879-0720},
abstract = {Biological ageing is a time-dependent process that has implications for health and disease. Cellular senescence is a key driver in ageing and age-related diseases. Senotherapeutic agents have been shown to slow biological ageing by eliminating senescent mammalian cells. Given the increasing awareness of the gut microbiome in regulating human health, this study aimed to investigate the effects of senotherapeutic agents as pharmacological interventions on the human gut microbiota. In this study, the bidirectional effects of four senotherapeutic agents, quercetin, fisetin, dasatinib, and sirolimus, with the gut microbiota sourced from healthy human donors were investigated. The results revealed that quercetin was completely biotransformed by the gut microbiota within six hours, while dasatinib was the most stable of the four compounds. Additionally, metagenomic analysis confirmed that all four compounds increased the abundance of bacterial species associated with healthy ageing (e.g., Bacteroides fragilis, Bifidobacterium longum, and Veillonella parvula), and decreased the abundance of pathogenic bacteria primarily associated with age-related diseases (e.g., Enterococcus faecalis and Streptococcus spp.). The findings from this study provide a comprehensive understanding of the pharmacobiomics of senotherapeutic interventions, highlighting the potential of microbiome-targeted senolytics in promoting healthy ageing.},
}

@article {pmid40216091,
year = {2025},
author = {Kyriazopoulou, E and Stylianakis, E and Damoraki, G and Koufargyris, P and Kollias, I and Katrini, K and Drakou, E and Marousis, K and Spyrou, A and Symbardi, S and Alexiou, N and Alexiou, Z and Lada, M and Poulakou, G and Chrysos, G and Adamis, G and Giamarellos-Bourboulis, EJ},
title = {Procalcitonin-Guided Early Stop of Antibiotics Prevents Gut Inflammation and Preserves Gut Microbiome: Data from the PROGRESS Controlled Trial.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107507},
doi = {10.1016/j.ijantimicag.2025.107507},
pmid = {40216091},
issn = {1872-7913},
abstract = {The PROGRESS randomized trial (ClinicalTrials.gov NCT03333304) showed that early stop of antibiotics guided by procalcitonin (PCT) decreased the incidence of infections by multidrug resistant organisms and/or Clostridioides difficile and was associated with survival benefit. We investigated if benefit is associated with microbiome dysbiosis. Patients with sepsis due to lung infection, acute pyelonephritis or primary bacteremia were randomized to standard-of-care (SoC) duration of antibiotics or early stop using PCT. Faecal samples were collected before, 7 and 28 days after randomization and analyzed by 16S rRNA Nanopore sequencing. Calprotectin was measured by an enzyme immunoassay. Median (Q1-Q3) antimicrobial duration was 5 days in PCT (5-7.5) and 11 days (8-15) in SoC arm, respectively (p < 0.001). Faecal calprotectin did not differ at baseline. By day 7, it was significantly increased in SoC (p=0.002) but it was unchanged in the PCT arm. Microbiome alpha- and beta-diversity were similar at baseline in PCT (n=81) and SoC (n=76) treated patients. Shannon's index was significantly decreased in SoC by day 7 from baseline (median [Q1-Q3], 2.88 [2.37-3.39] at day 1 vs 2.24 [1.52-3.08] at day 7; pt-test=0.0013); this was not the case for the PCT arm (median [Q1-Q3], 2.73 [2.26-3.4] at day 1 vs 2.43 [1.81-3.21] at day 7; pt-test=0.037, Bonferroni corrected alpha = 0.0125). Relative abundances of Actinomycetota and Pseudomonadota were decreased in PCT arm by day 7 and relative abundance of Bacillota was increased. Early PCT-guided stop of antibiotics contributes to decreased microbiome dysbiosis by day 7.},
}

@article {pmid40216077,
year = {2025},
author = {Armengaud, J and Cardon, T and Cristobal, S and Matallana-Surget, S and Bertile, F},
title = {Novel model organisms and proteomics for a better biological understanding.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {105441},
doi = {10.1016/j.jprot.2025.105441},
pmid = {40216077},
issn = {1876-7737},
abstract = {The concept of « model organisms » is being revisited in the light of the latest advances in multi-omics technologies that can now capture the full range of molecular events that occur over time, regardless of the organism studied. Classic, well-studied models, such as Escherichia coli, Saccharomyces cerevisiae, to name a few, have long been valuable for hypothesis testing, reproducibility, and sharing common platforms among researchers. However, they are not suitable for all types of research. The complexity of unanswered questions in biology demands more elaborated systems, particularly to study plant and animal biodiversity, microbial ecosystems and their interactions with their hosts if any. More integrated systems, known as « holobionts », are emerging to describe and unify host organisms and associated microorganisms, providing an overview of all their possible interactions and trajectories. Comparative evolutionary proteomics offers interesting prospects for extrapolating knowledge from a few selected model organisms to others. This approach enables a deeper characterization of the diversity of proteins and proteoforms across the three branches of the tree of life, i.e. Bacteria, Archaea, and Eukarya. It also provides a powerful means to address remaining biological questions, such as identifying the key molecular players in organisms when they are confronted to environmental challenges, like anthropogenic toxicants, pathogens, dietary shifts or climate stressors, and proposing long-term sustainable solutions. SIGNIFICANCE: In this commentary, we reevaluated the concept of "model organisms" in light of advancements in multi-omics technologies. Traditional models have proven invaluable for hypothesis testing, reproducibility, and fostering shared research frameworks. However, we discussed that they are not universally applicable. To address complexities such as biodiversity and understand microbial ecosystems and their host interactions, integrated systems like "holobionts," which encompass host organisms and their associated microbes, are gaining prominence. Comparative evolutionary proteomics further enhances our understanding by enabling detailed exploration of protein diversity across organisms. This approach also facilitates the identification of critical molecular players in organisms facing environmental challenges, such as pollutants, pathogens, dietary changes, or climate stress, and contributes to developing sustainable long-term solutions.},
}

@article {pmid40216042,
year = {2025},
author = {Ma, H and Qiao, Q and Yu, Z and Wang, W and Li, Z and Xie, Z and Su, Y and Zhang, X and Sun, Y and Wang, P and Zhang, Z},
title = {Integrated multi-omics analysis and experimental validation reveals the mechanism of tenuifoliside A activity in Alzheimer's disease.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {119797},
doi = {10.1016/j.jep.2025.119797},
pmid = {40216042},
issn = {1872-7573},
abstract = {Alzheimer's disease (AD) is characterized by progressive cognitive dysfunction and memory loss. Tenuifoliside A (TFSA) is a constituent of RADIX POLYGALAE, a medicinal herb traditionally used in the clinical treatment of AD in China. However, the therapeutic mechanism of this compound is unknown.

AIM OF THE STUDY: To investigate the effects and pharmacological mechanisms of TFSA in ameliorating AD symptoms in APP/PS1 mice.

MATERIALS AND METHODS: The neuroprotective effects of TFSA were assessed using behavioral tests, transmission electron microscopy, and immunofluorescence staining. The differential metabolites in the feces of model mice were obtained from non-targeted metabolomics analysis. Differential abundances of microbiota in the gut were investigated by 16S rRNA sequencing, and correlations among differential metabolites and microbiota were investigated using an integrated approach.

RESULTS: Cognitive impairment and Aβ burden were mitigated in APP/PS1 mice treated with TFSA. TFSA intervention led to an increase in the diversity of gut microbiota and a reduction in the relative abundance of Firmicutes, Bacteroidetes, and Proteobacteria. There were 71 differential metabolites in mice given high dose of TFSA. In comparison to the AD group, the mice treated with TFSA exhibited a notable enrichment in various pathways including glucose and lipid metabolism, tryptophan metabolism. Based on integrated metabolomics and 16S rRNA sequencing, 23 metabolite-microbiota pairs were different between the TFSA and AD groups, and there was an especially strong correlation between Alistipes and 2,3-dinor-8-epi-prostaglandin F2α. Validation experiment demonstrated TFSA ameliorates AD by regulating metabolism pathways and inhibiting neuroinflammation.

CONCLUSIONS: This study offers a theoretical basis for elucidating the molecular mechanism of TFSA's amelioration of AD. Although the potential pharmacological mechanisms of TFSA are still unknown, we have demonstrated that TFSA inhibits neuroinflammation and improves AD symptoms in APP/PS1 mice by remodeling the microbiota and its metabolites.},
}

@article {pmid40215444,
year = {2025},
author = {Kerwin, AH and Ohdera, A and Bier, J and Goodman, D and Mammone, M and Sharp, V and Echeandía, A and Medina, M},
title = {Cassiopea xamachana microbiome across anatomy, development, and geography.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0319944},
doi = {10.1371/journal.pone.0319944},
pmid = {40215444},
issn = {1932-6203},
mesh = {Animals ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Larva/microbiology ; *Hydrozoa/microbiology/growth & development/anatomy & histology ; Female ; Phylogeny ; Symbiosis ; Male ; Geography ; },
abstract = {The upside-down jellyfish holobiont, Cassiopea xamachana, is a useful model system for tri-partite interactions between the cnidarian host, the photosymbiont, and the bacterial microbiome. While the interaction between the host and photosymbiont has been well studied, less is understood of the associated bacterial community. To date, the bacterial microbiome of wild C. xamachana has remained largely uncharacterized. Thus, wild medusae (n=6) and larvae (n=3) were collected from two sites in the Florida Keys. Bacterial community composition was characterized via amplicon sequencing of the 16S rRNA gene V4 region. The medusa bacterial community was dominated by members of the Alphaproteobacteria and Gammaproteobacteria, while Planctomycetota, Actinomycetota, Bacteroidota, and Bacillota were also present, among others. Community composition was consistent between locations and across medusa structures (oral arm, bell, and gonad). The larval bacterial community clustered apart from the medusa community in beta diversity analysis and was characterized by the presence of several Pseudomonadota taxa that were not present in the medusa, including the Alteromonas, Pseudoalteromonas, and Thalassobius genera. A bacterial isolate library encompassing much of the amplicon sequencing diversity was also developed and tested via metabolic assays in a separate culture-dependent analysis of isolates from medusa bells, oral arms, and laplets. Most characteristics were not correlated with host sex or medusa structure, but gelatinase production was more common in laplet isolates, while lactose fermentation was more common in female oral arm isolates. The Endozoicomonas genus was dominant in both amplicon sequencing and in our isolate library, and was equally prevalent across all medusa structures and in both sexes. Understanding the bacterial component of the C. xamachana holobiont will allow us to further develop this important model cnidarian holobiont.},
}

Animals
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Larva/microbiology
*Hydrozoa/microbiology/growth & development/anatomy & histology
Female
Phylogeny
Symbiosis
Male
Geography

@article {pmid40214948,
year = {2025},
author = {Côco, LZ and de Souza Belisário, E and Vasquez, EC and Pereira, TMC and Aires, R and Campagnaro, BP},
title = {Probiotics: a promising future in the treatment of ulcerative colitis?.},
journal = {Pharmacological reports : PR},
volume = {},
number = {},
pages = {},
pmid = {40214948},
issn = {2299-5684},
support = {305740/2019-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 309431/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 308220/2021-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; Edital 15/2022 - PROFIX: 708/2022//Fundação de Amparo à Pesquisa e Inovação do Espírito Santo/ ; Edital 15/2022 - PROFIX: 630/2022//Fundação de Amparo à Pesquisa e Inovação do Espírito Santo/ ; },
abstract = {Ulcerative colitis is an idiopathic and chronic inflammatory bowel disease, characterized by inflammation of the mucosa of the colon and rectum. Clinical manifestations commonly include abdominal pain, diarrhea (with or without hematochezia), and weight loss. The pathogenesis of ulcerative colitis is multifactorial, involving a combination of genetic predispositions and lifestyle factors. High consumption of processed food, sedentary habits, alcohol intake, and stress are among the lifestyle factors implicated in disease onset and progression. Current treatment strategies focus on managing symptoms and inducing remission, however, the chronic nature of the disease, along with the adverse effects of conventional therapies, often compromises patient's quality of life. Therefore, exploring alternative therapies that can prolong remission and reduce symptom burden is important. Experimental evidence suggests that probiotics may extend remission duration in ulcerative colitis. Moreover, probiotics exhibit efficacy in amelioration clinical symptoms by reducing inflammation markers, preserving, and restoring intestinal epithelial. This review explores the advantages of the administration of probiotics in the treatment of ulcerative colitis, elucidating their mechanism of action.},
}

@article {pmid40214782,
year = {2025},
author = {Koponen, K and McDonald, D and Jousilahti, P and Meric, G and Inouye, M and Lahti, L and Niiranen, T and Männistö, S and Havulinna, A and Knight, R and Salomaa, V},
title = {Associations of alcohol with the human gut microbiome and prospective health outcomes in the FINRISK 2002 cohort.},
journal = {European journal of nutrition},
volume = {64},
number = {4},
pages = {153},
pmid = {40214782},
issn = {1436-6215},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Female ; Male ; Middle Aged ; Adult ; Prospective Studies ; *Alcohol Drinking/adverse effects ; Aged ; Feces/microbiology ; Finland/epidemiology ; Cohort Studies ; *Ethanol ; Bacteria/classification ; },
abstract = {BACKGROUND AND AIMS: Alcohol remains a global risk factor for non-communicable diseases with the gut microbiome emerging as a novel elucidator. We investigated how gut microbiome associates with alcohol on population level, if there is mediation reflected in health outcomes, and how functional potential is related.

METHODS: Our sample consisted of 4575 shallow-shotgun sequenced fecal samples from the FINRISK 2002 cohort (25-74yrs., 52.5% women). Alcohol (g 100% alcohol/week) use was self-reported. Diversity and differential species abundances were analyzed using multiple linear regression. Compositional differences were analyzed using PERMANOVA, and prospective associations with Cox-regression. Connections between alcohol, microbiome, inflammatory markers, and outcomes were assessed using serial mediation. Functional associations were assessed using KEGG-orthologies and multiple linear regression.

RESULTS: High-risk alcohol consumers had significantly lower bacterial diversity when compared to low-risk consumers (mean±SD:4.04±0.41 vs. 4.11±0.43, p = 9.56 × 10[- 4]). Alcohol also associated with significant shifts in overall composition (PERMANOVA; p ≤ 1.00 × 10[- 4]) and differential abundances of 344 species (ANCOM-BC2; q ≤ 0.05). These shifts were characterized by an increase in relative abundances of Gram-negative bacteria, the top genera of which were Bacteroides and Prevotella, and a decrease in putatively beneficial species in genera such as Lactobacillus, Bifidobacterium, and Akkermansia. Prospective associations with all-cause mortality (HR:1.12 [1.02-1.23]), and liver disease (HR:1.53 [1.22-1.92]) were observed. The association between alcohol and liver disease had a mediating link via a proinflammatory beta-diversity principal coordinate (OR:1.04 [1.001-1.10]). Functional associations were observed with 1643 KO-groups (q < 0.05, npositive=431, nnegative=1212). Antioxidative and gut integrity maintaining functions were diminished and lipopolysaccharide synthesis enriched.

CONCLUSIONS: Alcohol use is associated with community-level shifts in composition towards enriched Gram-negative bacteria, and diminished levels of putatively beneficial bacteria. Alcohol use associates with a proinflammatory gut microbiome profile that mediates alcohol's effect on incident liver disease risk, possibly via increased proliferation of endotoxins through the gut epithelial lining.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Female
Male
Middle Aged
Adult
Prospective Studies
*Alcohol Drinking/adverse effects
Aged
Feces/microbiology
Finland/epidemiology
Cohort Studies
*Ethanol
Bacteria/classification

@article {pmid40214675,
year = {2025},
author = {Liu, S and Liu, J and Mei, Y and Zhang, W},
title = {Gut microbiota affects PD-L1 therapy and its mechanism in melanoma.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {74},
number = {5},
pages = {169},
pmid = {40214675},
issn = {1432-0851},
support = {BLSA [2024] No. 2, 2024300CC0020//The grants of Science and Technology Projects of Beijing Life Science Academy/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Melanoma/immunology/drug therapy/microbiology/pathology/metabolism ; *B7-H1 Antigen/antagonists & inhibitors/metabolism/immunology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Tumor Microenvironment/immunology ; Animals ; Immunotherapy/methods ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/metabolism ; },
abstract = {Immune checkpoint inhibitors (ICIs), particularly PD-1/PD-L1 blockade, have shown great success in treating melanoma. PD-L1 (B7-H1, CD274), a ligand of PD-1, binds to PD-1 on T cells, inhibiting their activation and proliferation through multiple pathways, thus dampening tumor-reactive T cell activity. Studies have linked PD-L1 expression in melanoma with tumor growth, invasion, and metastasis, making the PD-1/PD-L1 pathway a critical target in melanoma therapy. However, immune-related adverse events are common, reducing the effectiveness of anti-PD-L1 treatments. Recent evidence suggests that the gut microbiome significantly influences anti-tumor immunity, with the microbiome potentially reprogramming the tumor microenvironment and overcoming resistance to anti-PD-1 therapies in melanoma patients. This review explores the mechanisms of PD-1/PD-L1 in melanoma and examines how gut microbiota and its metabolites may help address resistance to anti-PD-1 therapy, offering new insights for improving melanoma treatment strategies.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Melanoma/immunology/drug therapy/microbiology/pathology/metabolism
*B7-H1 Antigen/antagonists & inhibitors/metabolism/immunology
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Tumor Microenvironment/immunology
Animals
Immunotherapy/methods
Programmed Cell Death 1 Receptor/antagonists & inhibitors/metabolism

@article {pmid40214509,
year = {2025},
author = {Khazaei, M and Parsasefat, M and Bahar, A and Tahmasebi, H and Oksenych, V},
title = {Behavioral Cooperation or Conflict of Human Intestinal Roundworms and Microbiomes: A Bio-Activity Perspective.},
journal = {Cells},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/cells14070556},
pmid = {40214509},
issn = {2073-4409},
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome ; *Nematoda/physiology ; *Intestines/parasitology/microbiology ; },
abstract = {Human infections are greatly impacted by intestinal nematodes. These nematodes, which encompass the large roundworms, have a direct impact on human health and well-being due to their close cohabitation with the host's microorganisms. When nematodes infect a host, the microbiome composition changes, and this can impact the host's ability to control the parasites. We aimed to find out if the small intestinal roundworms produce substances that have antimicrobial properties and respond to their microbial environment, and if the immune and regulatory reactions to nematodes are altered in humans lacking gut microbes. There is no doubt that different nematodes living in the intestines can alter the balance of intestinal bacteria. Nonetheless, our knowledge about the parasite's influence on the gut microbiome remains restricted. The last two decades of study have revealed that the type of iron utilized can influence the activation of unique virulence factors. However, some roundworm proteins like P43, which makes up a large portion of the worm's excretory-secretory product, have an unknown role. This review explores how the bacterial iron regulatory network contributes to the adaptability of this opportunistic pathogen, allowing it to successfully infect nematodes in different host environments.},
}

Humans
Animals
*Gastrointestinal Microbiome
*Nematoda/physiology
*Intestines/parasitology/microbiology

@article {pmid40214493,
year = {2025},
author = {Rahim, MA and Seo, H and Barman, I and Hossain, MS and Shuvo, MSH and Song, HY},
title = {Insights into Autophagy in Microbiome Therapeutic Approaches for Drug-Resistant Tuberculosis.},
journal = {Cells},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/cells14070540},
pmid = {40214493},
issn = {2073-4409},
support = {RS-2023-00219563//National Research Foundation of Korea/ ; P248400003//Korea Institute for Advancement of Technology (KIAT)/ ; Soonchunhyang University Research Fund//Soonchunhyang University/ ; },
mesh = {Humans ; *Autophagy ; *Tuberculosis, Multidrug-Resistant/therapy/microbiology ; *Microbiota ; Mycobacterium tuberculosis/drug effects ; Animals ; Antitubercular Agents/therapeutic use/pharmacology ; },
abstract = {Tuberculosis, primarily caused by Mycobacterium tuberculosis, is an airborne lung disease and continues to pose a significant global health threat, resulting in millions of deaths annually. The current treatment for tuberculosis involves a prolonged regimen of antibiotics, which leads to complications such as recurrence, drug resistance, reinfection, and a range of side effects. This scenario underscores the urgent need for novel therapeutic strategies to combat this lethal pathogen. Over the last two decades, microbiome therapeutics have emerged as promising next-generation drug candidates, offering advantages over traditional medications. In 2022, the Food and Drug Administration approved the first microbiome therapeutic for recurrent Clostridium infections, and extensive research is underway on microbiome treatments for various challenging diseases, including metabolic disorders and cancer. Research on microbiomes concerning tuberculosis commenced roughly a decade ago, and the scope of this research has broadened considerably over the last five years, with microbiome therapeutics now viewed as viable options for managing drug-resistant tuberculosis. Nevertheless, the understanding of their mechanisms is still in its infancy. Although autophagy has been extensively studied in other diseases, research into its role in tuberculosis is just beginning, with preliminary developments in progress. Against this backdrop, this comprehensive review begins by succinctly outlining tuberculosis' characteristics and assessing existing treatments' strengths and weaknesses, followed by a detailed examination of microbiome-based therapeutic approaches for drug-resistant tuberculosis. Additionally, this review focuses on establishing a basic understanding of microbiome treatments for tuberculosis, mainly through the lens of autophagy as a mechanism of action. Ultimately, this review aims to contribute to the foundational comprehension of microbiome-based therapies for tuberculosis, thereby setting the stage for the further advancement of microbiome therapeutics for drug-resistant tuberculosis.},
}

Humans
*Autophagy
*Tuberculosis, Multidrug-Resistant/therapy/microbiology
*Microbiota
Mycobacterium tuberculosis/drug effects
Animals
Antitubercular Agents/therapeutic use/pharmacology

@article {pmid40214226,
year = {2025},
author = {Costello, MK and McClure, JC and Brown, JA and Amorín de Hegedüs, R and Mantovani, HC and Ricke, SC},
title = {The gastrointestinal tract microbiome of Holstein × Angus cross cattle is negatively impacted by the pre-harvest process.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0259924},
doi = {10.1128/aem.02599-24},
pmid = {40214226},
issn = {1098-5336},
abstract = {Stress during the beef pre-harvest period can induce an inflammatory response and acidotic conditions in the gastrointestinal tract (GIT), which affects the gastrointestinal tract microbiome. The objective of this study was to characterize the status of the GIT microbiome at harvest in beef cattle entering a small USDA processing facility. Nine beef cattle were shipped from a producer in Columbia County, WI, to the USDA processing facility at the University of Wisconsin-Madison and were harvested across four dates. Digesta samples were collected from eight GIT locations: rumen solids, rumen liquids, abomasum, duodenum, jejunum, ileum, cecum, and large intestines. After DNA extraction, the V4 region of the 16S rRNA gene was amplified and sequenced on the Illumina MiSeq platform. Sequences were analyzed for alpha and beta diversity metrics, core microbiome, differential abundance, and co-occurrence network analyses. Harvest date, finishing weight, and GIT location had a significant impact on microbial diversity and community composition (P < 0.05), and there was an interaction between GIT location and harvest date (P < 0.05). Taxonomic composition shifted throughout the GIT, though Prevotella and Treponema were core members in several different GIT locations. The co-occurrence analysis revealed microorganisms potentially associated with clinical infections, with Moryella in the rumen and Acinetobacter in the hindgut emerging as the highest scoring hubs. These results suggest that the pre-harvest period may negatively impact the beef cattle GIT microbiome. Modulating the GIT microbiome during the pre-harvest period may offer an opportunity to improve food safety.IMPORTANCEWith the global rise in antimicrobial resistance and the threat of foodborne illness, determining intervention strategies prior to harvest is a promising solution. The period between transportation from the feedlot to harvest may increase the risk of foodborne illness. During this period, cattle are withheld feed to reduce gastrointestinal tract (GIT) contents during carcass dressing. Feed withdrawal has many unintended consequences, such as acidosis and an increase in GIT pathogenic bacteria, that may result in foodborne pathogens on the final product. These consequences have yet to be thoroughly investigated in dairy-beef cross cattle, which have been rising in prominence in the United States. The GIT microbiome of dairy-beef cross cattle has been scarcely characterized despite its influence on preventing the proliferation of common pathogens in the GIT. Therefore, it is necessary to determine the impacts of feed withdrawal on the GIT microbiome and its relation to foodborne illness.},
}

@article {pmid40214217,
year = {2025},
author = {Geniselli da Silva, V and Mullaney, JA and Roy, NC and Smith, NW and Wall, C and Tatton, CJ and McNabb, WC},
title = {Complementary foods in infants: an in vitro study of the faecal microbial composition and organic acid production.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo00414d},
pmid = {40214217},
issn = {2042-650X},
abstract = {The transition from breastmilk to complementary foods is critical for maturing the colonic microbiota of infants. Dietary choices at weaning can lead to long-lasting microbial changes, potentially influencing health later in life. However, the weaning phase remains underexplored in colonic microbiome research, and the current understanding of how complementary foods impact the infant's colonic microbiota is limited. To address this knowledge gap, this study assessed the influence of 13 food ingredients on the in vitro microbial composition and production of organic acids by the faecal microbiota in New Zealand infants aged 5 to 11 months. To better represent real feeding practices, ingredients were combined with infant formula, other complementary foods, or both infant formula and other foods. Among the individual food ingredients, fermentation with peeled kūmara (sweet potato) increased the production of lactate and the relative abundance of the genus Enterococcus. Fermentation with blackcurrants, strawberries, or raspberries enhanced acetate and propionate production. Additionally, fermentation with blackcurrants increased the relative abundance of the genus Parabacteroides, while raspberry fermentation increased the relative abundance of the genera Parabacteroides and Eubacterium. When combined with infant formula or with blackcurrants, fermenting black beans increased butyrate production and stimulated the relative abundance of Clostridium sensu stricto 1. These foods are promising candidates for future clinical trials.},
}

@article {pmid40214103,
year = {2025},
author = {Hoedt, EC and Carroll, G and Stephensen, B and Morrison, M and Vishnoi, V and Cuskelly, A and Draganic, B and McManus, B and Clarke, L and Shah, K and Smith, SR and Talley, NJ and Keely, S and Pockney, P},
title = {Preoperative Antibiotics and Mechanical Bowel Preparation Impact the Colonic Mucosa Associated Microbiota But Not Anastomotic Leak Rate After Colorectal Resection.},
journal = {Diseases of the colon and rectum},
volume = {},
number = {},
pages = {},
doi = {10.1097/DCR.0000000000003775},
pmid = {40214103},
issn = {1530-0358},
abstract = {BACKGROUND: Alterations in the gastrointestinal microbiome have been associated with increased anastomotic leak risk. Oral antibiotics and bowel preparations may both reduce anastomotic leaks rates.

OBJECTIVE: Within patients undergoing colorectal surgery, we aimed to examine the impact of oral antibiotic use, bowel preparation and other perioperative factors on the mucosa associated microbiota and investigated association with anastomotic leak rates.

DESIGN: We opportunistically sampled Australian patients undergoing colorectal resection for any indication with anastomosis, mucosal swabs were taken from the proximal and distal extent of the resected specimen immediately after extraction.

SETTINGS: A single site, public tertiary referral hospital of 694 beds with an accredited specialist colorectal unit in Newcastle, Australia.

PATIENTS: Of 192 patients; 31 patients were identified as receiving oral antibiotics pre-surgery. Thirty-one patients received mechanical preparation and 58 received enema pre-surgery.

MAIN OUTCOME MEASURES: The influence of patient factors on mucosa-associated microbiota composition and associations to rate of anastomotic leaks.

RESULTS: The leak rate was 15% (N = 28/192). Preoperative oral antibiotic manipulation and bowel preparation minimally affected the mucosa-associated microbiota, but neither were associated with anastomotic leaks. Erythromycin (N = 14/192) had the greatest impact on the mucosa-associated microbiota. Of the different bowel preparation regimes, excluding patients given antibiotics, only fleet enemas (N = 58/161) had a significant impact on the mucosa-associated microbiota. Bowel preparation was not associated with occurrence of anastomotic leaks. There were only subtle differences observed in the mucosa-associated microbiota between anastomotic leaks and non-anastomotic leaks patients.

LIMITATIONS: Antibiotic recipient numbers included were modest.

CONCLUSIONS: This is the largest series of routine colorectal anastomoses for which the mucosa-associated microbiota adjacent the anastomoses was examined. We show that antibiotics and bowel preparation in the preoperative period exert only limited effects on the mucosa-associated microbiota and conclude that there are no obvious mucosa-associated microbiota characteristics that are predictive for an anastomotic leak.},
}

@article {pmid40213471,
year = {2025},
author = {Kurz, C and Arbeeva, L and Azcarate-Peril, MA and Stewart, DA and Lascelles, BDX and Loeser, RF and Nelson, AE},
title = {Exploring associations among pro-inflammatory cytokines, osteoarthritis, and gut microbiome composition in individuals with obesity using machine learning.},
journal = {Osteoarthritis and cartilage open},
volume = {7},
number = {2},
pages = {100603},
pmid = {40213471},
issn = {2665-9131},
abstract = {OBJECTIVE: To investigate potentially novel and modifiable mechanisms of the effects of gut microbiome composition on obesity-related osteoarthritis (OA), focusing on cross-sectional relationships between microbiota, cytokines, and lipopolysaccharide (LPS).

DESIGN: Johnston County OA Project participants (n ​= ​64) with (cases) and without (controls) OA in hands and knees, with age ≥55 years and obesity (BMI ≥30 ​kg/m[2]), provided samples for multiplex cytokine, LPS, and fecal microbiota analysis. Latent Dirichlet Allocation (LDA), a machine learning method to detect latent groups within data, was used to identify microbial enterotypes. LDA regression models were used to evaluate associations of enterotypes with demographics, cytokines associated with OA, and LPS.

RESULTS: We identified 5 enterotypes. Enterotypes 3, 4 (most prevalent in our sample), and 5, dominated respectively by genera Akkermansia, Bacteroides, Ruminococcus/Phascolarctobacterium, were positively associated with control status, and inversely associated with levels of at least two cytokines associated with OA in our sample. We observed no associations of enterotypes with LPS levels. Enterotype 3 was inversely associated with thrombopoietin and IL-4 levels (b [95 ​% CIs] -0.19 [-0.43, 0.05] and -0.17 [-0.42, 0.08]), enterotype 5 with osteopontin and thrombopoietin (-0.23 [-0.49, 0.03] and -0.24 [-0.51, 0.04]), and enterotype 4 was inversely associated with all 3 of these cytokines (b -0.20 to -0.35).

CONCLUSION: Three of five identified enterotypes were inversely associated with OA status and levels of OA associated cytokines. These exploratory analyses revealed associations between the gut microbiome, cytokines, and OA outcomes, suggesting potentially cytokine-mediated mechanisms of the effects of gut composition on OA in obese individuals, and providing a basis for further investigation of the underlying causal mechanisms.},
}

@article {pmid40213273,
year = {2025},
author = {Subedi, S and Dang, UJ},
title = {Multivariate Poisson lognormal distribution for modeling counts from modern biological data: An overview.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {1255-1264},
pmid = {40213273},
issn = {2001-0370},
abstract = {Modern biological data are often multivariate discrete counts, and there has been a dearth of statistical distributions to directly model such counts in an efficient manner. While mixed Poisson distributions, e.g., negative binomial distribution, are often the distribution of choice for univariate data, multivariate statistical distributions and their algorithmic implementations tend to have different drawbacks, e.g., non-tractable distributions, non-closed form solutions for parameter estimates, constrained correlation structures, and slow convergence during iterative parameter estimation. Herein, we provide an overview of the Poisson lognormal and multivariate Poisson lognormal distributions. These distributions can be written in an hierarchical fashion. An efficient variational approximation-based parameter estimation strategy as well as a hybrid approach for full Bayesian posterior estimation is available for such models, allowing for scaling up and modeling high-dimensional data. We provide comparisons of the univariate Poisson, the negative binomial, and the Poisson lognormal distributions in terms of the estimated mean-variance relationships using simulations and example real datasets. We also discuss the properties of the multivariate Poisson lognormal distribution, and ability to directly model count data including zero counts, over-dispersion, both positive and negative covariance elements, and the mapping from correlations in the latent space vs. the observed space. Finally, we illustrate their use through two model-based clustering examples using a mixtures of distributions approach in RNA-seq and microbiome data.},
}

@article {pmid40213158,
year = {2025},
author = {Wang, Y and Cheng, N and Zhang, Q and Chang, F and Wang, T and Kan, M and Han, Y and Zhai, B and Huang, K and He, X},
title = {Longitudinal multi-omics analysis of the gut-liver axis: Unraveling the molecular mechanisms of metabolic homeostasis regulation by Pd@Pt nanozymes.},
journal = {Materials today. Bio},
volume = {32},
number = {},
pages = {101685},
pmid = {40213158},
issn = {2590-0064},
abstract = {Recently, the nanozyme Pd@Pt has garnered attention due to its notable specific surface area and superior enzyme-like catalytic activity, leading to extensive examination and application in previous studies. However, the comprehensive impact of Pd@Pt nanozyme on treating metabolic disorders, such as diabetes and its associated conditions, remains largely unexplored. This research aimed to clarify how Pd@Pt influences metabolic balance at both the transcriptome and microbiome levels and to explore the interactions between microbiota and genes. We conducted an examination of mice subjected to a high-fat diet (HFD) following treatment with Pd@Pt. Transcriptome analysis was performed to identify differentially expressed genes (DEGs), and microbiome analysis was conducted to identify significant bacterial correlations associated with Pd@Pt exposure. The results indicated enhancements in glucose metabolism dysfunctions in the treated mice. Transcriptome analysis revealed that DEGs after Pd@Pt administration were enriched in the PI3K-Akt, NF-κB, and MAPK signaling pathways in the liver. Microbiome analysis identified four significant bacteria that exhibited a strong negative correlation with Pd@Pt exposure, while ten bacteria showed a positive correlation. Furthermore, a correlation network established among the gut microbiota, metabolites, and DEGs demonstrated a robust association. This research enhances our understanding of the mechanisms by which Pd@Pt affects the regulation of metabolic diseases in HFD-exposed environments and proposes a novel strategy for utilizing nanozymes in human health management.},
}

@article {pmid40212922,
year = {2025},
author = {Wang, C and Li, C and You, F and Zhou, Y and Tu, G and Liu, R and Yi, P and Wu, X and Nie, H},
title = {Multi-Omics Analysis of Gut Microbiome and Host Metabolism in Different Populations of Chinese Alligators (alligator sinensis) During Various Reintroduction Phases.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71221},
pmid = {40212922},
issn = {2045-7758},
abstract = {Reintroduction plays a significant role in the self-maintenance and reconstruction of wild animal populations, serving as a communication bridge between captive and wild animals. The Chinese alligator (Alligator sinensis) is a distinct and endangered reptile species found in China. The mechanisms by which artificially bred Chinese alligators adapt following their release into the wild remain poorly understood. This study aims to elucidate the alterations in gut microbiomes and metabolic phenotypes of Chinese alligators during their reintroduction. During the Chinese alligator's reintroduction, Fusobacterium and Cetobacterium became more abundant, while typical pathogens declined significantly. The gut type of the Chinese alligator changed from Acinetobacter to Cetobacterium. The construction of the gut microbial community was dominated by neutral (random) processes and shifted towards deterministic processes with the progression of reintroduction. In terms of species function, reintroduction significantly upregulated the expression of host immune-related genes and significantly decreased the expression of gut bacterial pathogenic genes and antibiotic resistance genes. Metagenomic and metabolomic KEGG enrichment analyses indicate that glucoside hydrolase families 13 and 23-alongside glycolysis and gluconeogenesis pathways-may play pivotal roles in energy metabolism, host-pathogen interactions, and homeostasis maintenance for Chinese alligators. Differential metabolite analysis identified significant upregulation of metabolites related to neuroendocrine immune modulation and significant down-regulation of anti-inflammatory metabolites during Chinese alligator reintroduction. Association analysis showed that there were significant co-metabolic effects between microorganisms and metabolites, which coordinated host adaptive interaction. This study provides insights into the synergistic mechanisms of host adaptation and wild environment adaptation for Chinese alligators.},
}

@article {pmid40212761,
year = {2024},
author = {Moysidou, CM and van Niekerk, DC and Stoeger, V and Pitsalidis, C and Draper, LA and Withers, AM and Hughes, K and McCoy, R and Acharya, R and Hill, C and Owens, RM},
title = {Modelling Human Gut-Microbiome Interactions in a 3D Bioelectronic Platform.},
journal = {Small science},
volume = {4},
number = {6},
pages = {2300349},
pmid = {40212761},
issn = {2688-4046},
abstract = {The role of the gut microbiome in various aspects of health and disease is now a well-established concept in modern biomedicine. Numerous studies have revealed links between host health and microbial activity, spanning from digestion and metabolism to autoimmune disorders, stress and neuroinflammation. However, the exact mechanisms underlying this complex cross-talk still remain a mystery. Conventionally, studies examining host-microbiome interactions rely on animal models, but translation of such findings into human systems is challenging. Bioengineered models represent a highly promisingapproach for tackling such challenges. Here, a bioelectronic platform, the e-transmembrane, is used to establish a 3D model of human intestine, to study the effects of microbiota on gut barrier integrity. More specifically, how postbiotics and live bacteria impact the morphology and function of the intestinal barrier is evaluated. e-Transmembrane devices provide a means for in-line and label-free continuous monitoring of host-microbe cross-talk using electrochemical impedance spectroscopy, revealing distinct patterns that emerge over 24 hours. Microscopy and quantification of molecular biomarkers further validate the differential effects of each bacterial intervention on the host tissue. In addition, a framework to better study and screen drug candidates and potential therapeutic/dietary interventions, such as postbiotics and probiotics, in more physiologically relevant human models is provided.},
}

@article {pmid40212655,
year = {2025},
author = {Iriarte-Mesa, C and Bergen, J and Danielyan, K and Crudo, F and Marko, D and Kählig, H and Del Favero, G and Kleitz, F},
title = {Functionalization of Silica Nanoparticles for Tailored Interactions with Intestinal Cells and Chemical Modulation of Paracellular Permeability.},
journal = {Small science},
volume = {5},
number = {1},
pages = {2400112},
pmid = {40212655},
issn = {2688-4046},
abstract = {The intestinal compartment confines the gut microbiome while enabling food passage and absorption of active molecules. For the rational design of oral formulations aiming to overcome physiological barriers of the gut, it is crucial to understand how cells respond to the presence of nanoparticulate materials. Taking advantage of the versatility and biocompatibility of dendritic mesoporous silica nanoparticles (DMSNs), several post-grafting strategies are developed to diversify the surface properties of spherical DMSNs and then probe interactions with the intestinal coculture cell model Caco-2/HT29-MTX-E12. Herein, the functionalization of DMSNs with polyethylene glycol, phosphonate, methyl, and farnesol moieties enables the investigation of both particle penetration through the mucus layer and pathways relevant to intracellular uptake. Contributions of surface chemistry, charge, and colloidal stability are correlated with the modulation of particle movement through the mucus and the organization of cell-cell junctions. Hydrophilic and negative functionalities favor particle distribution toward the intestinal monolayer. Instead, hydrophobic DMSNs are hindered by the mucus, possibly limiting cell contact. Hybrid surfaces, combining phosphonate and long carbon chain functions, support diffusion through the mucus and foster the paracellular permeability as well as the transient barrier relapse, as indicated by increased cell-cell distances and reorganization of tight junctions.},
}

@article {pmid40212495,
year = {2025},
author = {Mouselimis, D and Özcan, F and Wiech, T and Lüring, C},
title = {A Revision of an Infected Total Hip Arthroplasty leading to Oxalate Nephropathy: A Case Report.},
journal = {Journal of orthopaedic case reports},
volume = {15},
number = {4},
pages = {90-94},
pmid = {40212495},
issn = {2250-0685},
abstract = {INTRODUCTION: Although one of the most successful orthopedic procedures, total hip arthroplasty (THA) conveys a not negligible risk for complications.

CASE REPORT: A 72-year-old patient after a THA received an operative revision 2 times due to persistent hematoma and early periprothetic infection. Post-operative renal failure requiring hemodialysis has been caused by a histologically confirmed oxalate nephropathy (ON). Post-operative antibiotic treatment altering the gut microbiome has been assumed as the most likely cause of ON. It is the first presented case of ON as a post-operative complication after a hip arthroplasty revising operation.

CONCLUSION: Acute post-operative renal injury conveys significant danger for the patients. An interdisciplinary approach is needed as many cases require complex diagnostic and therapeutical procedures offered by experts on the field.},
}

@article {pmid40212383,
year = {2025},
author = {Yu, Y and Geng, S and Bu, C and Cao, G and Han, Y and Xie, D and Hong, Y},
title = {Dry ginger and Schisandra chinensis modulate intestinal flora and bile acid metabolism to treatment asthma.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1541335},
pmid = {40212383},
issn = {1664-302X},
abstract = {BACKGROUND AND AIMS: Zingiber officinale Rosc (Dry ginger) and Schisandra chinensis (Turcz.) Baill (Schisandra chinensis) drug pairs (DSP) are often used as drug pairs for the treatment of asthma, and these two traditional Chinese medicines (TCM) are also the core components of multiple TCM. However, its specific pharmacological mechanism needs further research. The aim of this study is to investigate the effects of DSP on intestinal flora and bile acid metabolism in rats with asthma caused by cold, and to provide experimental evidence for its clinical application.

MATERIALS AND METHODS: Sixty male rats are divided into five groups, 12 rats per group. Except for control groups, other groups of rats use the method of "abdominal injection of "OVA + ice water swimming" to establish cold cough rats models. After the administration cycle is over, an optical microscope count method is used to detect eosinophils (EOS) and neutrophils (Neu) in bronchoalveolar lavage fluid (BALF); Enzyme-Linked Immunosorbent Assay (ELISA) method detects Immunoglobulin E (IgE), Interleukin-13 (IL-13), Interleukin-4 (IL-4), Tumor Necrosis Factor-α (TNF-α), Interferon-γ (INF-γ); Western Blot (WB) and Reverse Transcription-Polymerase Chain Reaction (RT-PCR) analysis was used to detect Forkhead box protein P3 (Foxp3) and Transforming Growth Factor-beta 1 (TGF-β1) proteins expression. In addition, Using 16S rDNA sequencing reveal the role of intestinal flora in asthma and the effect on the gut microbiome after DSP treatment. We also examined Farnesoid X Receptor (FXR) proteins expression, and finally used ultra performance UPLC-MS/MS to analyze bile acids (BAs) contentin in rats.

RESULTS: DSP inhibits asthma inflammation. It alleviates inflammatory factors, suppresses the inflammatory response in asthmatic rats by regulating FOXP3 and TGF-β1 in Treg cells, and reduces tissue damage. After DSP treatment, intestinal flora changed: harmful bacteria like Streptococcus decreased, while beneficial bacteria such as Candidatus - Arthromitus and Ligilactobacillus increased. These changes can be potential markers for DSP-intervened asthma. Also, DSP increased FXR protein expression and changed the bile acid spectrum: Deoxycholic acid (DCA) increased, allocholic acid (ACA), glycolithocholic acid (GLCA), glycochenodeoxycholic acid (GCDCA) andglycoursodeoxycholic acid (GUDCA) decreased.

CONCLUSION: This study has preliminarily revealed that DSP has the effect of alleviating inflammation levels, also regulate the expression of FOXP3 and TGF-β1 proteins, and has an impact on the gut microbiota and bile acid metabolism, thereby exerting an improving effect on asthma and providing a reference for the clinical application of traditional Chinese medicine in the treatment of asthma.},
}

@article {pmid40212372,
year = {2025},
author = {Kang, Y and Sun, Y and Cui, J and Song, Y and Sun, Z and Li, H and Niu, R and Qiao, H},
title = {Combined microbiome and metabolomics analysis of yupingfeng san fermented by Bacillus coagulans: insights into probiotic and herbal interactions.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19206},
pmid = {40212372},
issn = {2167-8359},
mesh = {*Fermentation ; *Probiotics/metabolism ; *Metabolomics ; *Drugs, Chinese Herbal/metabolism ; *Bacillus coagulans/metabolism ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Yupingfeng san is a traditional Chinese medicine formula composed of siler, atractylodes, and astragalus. The herbal medicine fermentation process relies on the role of probiotics. Bacillus coagulans is a probiotic commonly used to ferment food and drugs. It produces a variety of beneficial metabolites during fermentation. However, the study on the interaction between B. coagulans and yupingfeng san is still blank.

METHODS: During solid-state fermentation of yupingfeng san, we used metabolomics technology and 16S rDNA sequencing to analyze the differential metabolites and microbial flora of B. coagulans at 0, 3, 7, 11, and 15 d, which corresponded to groups A0, B3, B7, B11, and B15, respectively. This research explored the correlation between microorganisms and metabolites in fermented compound Chinese medicine.

RESULTS: The results revealed a significant difference in species β diversity between group A0 and the B groups (P < 0.01). At the phylum level, in fermentation groups B3, B7, B11, and B15, the Cyanobacteria relative abundance decreased by 6.69%, 9.09%, 5.74%, and 2.24%, respectively (P < 0.05). The Firmicutes relative abundance increased by 39.73%, 35.65%, 49.09%, and 68.66% (P < 0.05), respectively. The Proteobacteria relative abundance decreased by 39.86% and 26.70%, respectively, in groups B11 and B15 (P < 0.05). The relative abundance of Actinobacteria increased initially with extended fermentation time, and then gradually decreased after reaching its peak in group B7. At the genus level, compared with group A0, the relative abundance of Actinobacteria increased to its highest level of 21.12% in fermentation group B3 and decreased to 9.51% after a fermentation time of 15 d. The abundance of Leuconostoc in fermentation groups B3, B7, and B11 was significantly higher than in group A0 (20.93%, 20.73%, and 21.00%, respectively, P < 0.05). Pediococcus in fermentation groups B3, B7, B11, and B15 was also significantly higher than in group A0 (4.20%, 2.35%, 18.84%, and 52.01%, P < 0.05). Both Pediococcus and Leuconostoc, which belong to lactic acid bacteria, increased fivefold, accounting for a total abundance of 62%. After yupingfeng san fermentation, using nontargeted metabolomics, we identified 315 differential metabolites. This results showed a decrease in the content of alkene and an increase in the contents of acids, lipids, ketones, and amino acids. In addition, in group B3, the contents of quercetin, paeoniflorin-3-O-glucoside, netin, iristin, anthocyanin, caffeic acid, rosmarinic acid, liquiritin, and isoliquiritin were significantly upregulated.

CONCLUSION: In this study, the composition and metabolic profile of yupingfeng san after the fermentation of B. coagulans were studied, and it was found that the fermentation group showed rich species diversity, in which the abundance of Leuconostoc and Weisseria increased significantly, while the opportunistic pathogens such as Pseudomonas aeruginosa and Enterobacter decreased significantly. The analysis of metabolic products showed that the contents of acids, lipids and ketones were significantly increased, rich in a variety of beneficial microorganisms and small molecular compounds with antibacterial effects, and these changes worked together to inhibit the growth of pathogens and maintain intestinal health. The study not only helps to elucidate the assembly mechanism and functional expression of microorganisms after Chinese traditional medicine fermentation, but also provides a solid scientific basis for the development of efficient and safe micro-ecological feed additives.},
}

*Fermentation
*Probiotics/metabolism
*Metabolomics
*Drugs, Chinese Herbal/metabolism
*Bacillus coagulans/metabolism
*Microbiota
RNA, Ribosomal, 16S/genetics

@article {pmid40212280,
year = {2025},
author = {Agranyoni, O and Rowley, T and Johnson, SB and Volk, H and Schleif, W and Hernandez, RG and Klein, LM and Yolken, RH and Sabunciyan, S},
title = {Oral microbiome composition is associated with depressive symptoms during pregnancy.},
journal = {Brain, behavior, & immunity - health},
volume = {45},
number = {},
pages = {100978},
pmid = {40212280},
issn = {2666-3546},
abstract = {BACKGROUND: Oral microbiome dysbiosis has been linked to systemic disease with an underlying inflammatory etiology. However, the possible association of the oral microbiome in antenatal depression has received little attention.

METHODS: Participants were pregnant women in the PREDICT prenatal cohort study (n = 400) who provided saliva during pregnancy. Using 16S rRNA sequencing, we determined the association between composition of the salivary microbiome and a continuous measure of depressive symptoms (Center for Epidemiological Studies-Depression Scale (CES-D): 0-60) as well as clinically significant depressive symptoms during pregnancy (CES-D score> 16, n = 46) compared with women without clinically significant symptoms (n = 327).

RESULTS: CES-D scores were associated with differences in bacterial levels in the salivary microbiome. Women with clinically significant depressive symptoms (CES-D≥16) had significantly lower abundance in nine bacterial taxa, including the Neisseria genus, which has previously been positively associated with oral health and negatively correlated with pro-inflammatory cytokines, mental health, and infant birth weight. Findings were not explained by body mass index, smoking, antibiotic administration, oral health problems, or gestational week. Prediction tools based on 16S sequences indicated that significantly lower levels of several pathways related to the biosynthesis of Menaquinol, Ectoine biosynthesis, and D-glucarate degradation, were associated with women with depressive symptoms.

CONCLUSIONS: Our findings underscore the potential relationship between the oral microbiome and antenatal depression, highlighting microbiome measures as a promising source of biomarkers for maternal mental health. This study suggests previously unexplored aspects for understanding the microbiome's composition in women with mental health problems, emphasizing the need for further longitudinal investigations to elucidate the temporal dynamics of the oral microbiome in pregnancy.},
}

@article {pmid40212162,
year = {2025},
author = {Aleali, MS and Mahapatro, A and Maddineni, G and Paladiya, R and Jeanty, H and Mohanty, E and Mirchandani, M and Jahanshahi, A and Devulapally, P and Alizadehasl, A and Tariq, MD and Hosseini Jebelli, SF and Aliabadi, AY and Hashemi, SM and Amini-Salehi, E},
title = {The impact of gut microbiome modulation on anthropometric indices in metabolic syndrome: an umbrella review.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {4},
pages = {2263-2277},
pmid = {40212162},
issn = {2049-0801},
abstract = {BACKGROUND: Metabolic syndrome (MetS) is a complex disorder characterized by a cluster of metabolic risk factors. Recent research highlights the gut microbiome's role in metabolic regulation, suggesting that modulation through probiotics, prebiotics, and synbiotics may provide a novel approach to managing MetS. This umbrella review aims to integrate insights from existing meta-analyses to explore how changes in gut microbiota influence key body measurement indicators in individuals with MetS.

METHODS: A systematic search of PubMed, Scopus, and Web of Science databases identified meta-analyses that assessed the impact of probiotics, prebiotics, or synbiotics on anthropometric indices in MetS patients.

RESULTS: The results indicated that microbial therapy leads to a significant reduction in body mass index (BMI) (SMD: -0.22; 95% CI: -0.35 to -0.09; P < 0.01) and waist circumference (WC) (SMD: -0.47; 95% CI: -0.80 to -0.15; P < 0.01). However, microbial therapy did not significantly affect body fat mass (SMD: -0.30; 95% CI: -0.64 to 0.02; P = 0.06), body fat percentage (SMD: -0.29; 95% CI: -0.62 to 0.03; P = 0.07), waist-to-hip ratio (SMD: -0.09; 95% CI: -0.46 to 0.28; P = 0.63), and weight (SMD: -0.06; 95% CI: -0.21 to 0.08; P = 0.37).

CONCLUSIONS: Gut microbial modulation, mainly through probiotics and synbiotics, shows promise in reducing BMI and WC in MetS patients. However, its effects on other anthropometric indices remain uncertain, warranting further high-quality research to fully understand microbial interventions' therapeutic potential.},
}

@article {pmid40212158,
year = {2025},
author = {Abbas, AH and Haji, MR and Shimal, AA and Kurmasha, YH and Al-Janabi, AAH and Azeez, ZT and Al-Ali, ARS and Al-Najati, HMH and Al-Waeli, ARA and Abdulhadi, NASA and Al-Tuaama, AZH and Al-Ashtary, MM and Hussin, OA},
title = {A multidisciplinary review of long COVID to address the challenges in diagnosis and updated management guidelines.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {4},
pages = {2105-2117},
pmid = {40212158},
issn = {2049-0801},
abstract = {Long COVID has emerged as a significant challenge since the COVID-19 pandemic, which was declared as an outbreak in March 2020, marked by diverse symptoms and prolonged duration of disease. Defined by the WHO as symptoms persisting or emerging for at least two months post-SARS-CoV-2 infection without an alternative cause, its prevalence varies globally, with estimates of 10-20% in Europe, 7.3% in the USA, and 3.0% in the UK. The condition's etiology remains unclear, involving factors, such as renin-angiotensin system overactivation, persistent viral reservoirs, immune dysregulation, and autoantibodies. Reactivated viruses, like EBV and HSV-6, alongside epigenetic alterations, exacerbate mitochondrial dysfunction and energy imbalance. Emerging evidence links SARS-CoV-2 to chromatin and gut microbiome changes, further influencing long-term health impacts. Diagnosis of long COVID requires detailed systemic evaluation through medical history and physical examination. Management is highly individualized, focusing mainly on the patient's symptoms and affected systems. A multidisciplinary approach is essential, integrating diverse perspectives to address systemic manifestations, underlying mechanisms, and therapeutic strategies. Enhanced understanding of long COVID's pathophysiology and clinical features is critical to improving patient outcomes and quality of life. With a growing number of cases expected globally, advancing research and disseminating knowledge on long COVID remain vital for developing effective diagnostic and management frameworks, ultimately supporting better care for affected individuals.},
}

@article {pmid40212131,
year = {2025},
author = {Mubeen, M and Shazad, A and Aziz, M and Poudel, S},
title = {Role of gut microbiota and trimethylamine N-oxide in preeclampsia: pathophysiological insights and therapeutic opportunities.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {4},
pages = {1790-1793},
pmid = {40212131},
issn = {2049-0801},
abstract = {Preeclampsia (PE) is a condition where a sudden rise in blood pressure (>140/90 mmHg) after the 20th week of gestation poses a significant threat to maternal as well as fetal health. PE causes maternal organ damage and several fetal abnormalities which may prove fatal, leading to a high mortality rate. Several studies have been conducted on the role of the gut microbiome, linking its connection to the development of various diseases including PE. One such derivative of gut microbiota is trimethylamine N-oxide (TMAO), a metabolite shown to be involved in the progression of PE by disrupting the normal microbiome, promoting inflammation and oxidative stress. The objective of this editorial is to provide a general overview of PE, assess the negative effect of TMAO leading to diseases such as PE, and provide an outline for its potential exploitation as a treatment strategy. Although the current findings offer important insights into the mechanisms related to TMAO, further trials can confirm its clinical relevance and investigate its potential as a diagnostic biomarker and a therapeutic target.},
}

@article {pmid40212081,
year = {2024},
author = {Tuerhongjiang, G and Guo, M and Qiao, X and Liu, J and Xi, W and Wei, Y and Liu, P and Lou, B and Wang, C and Sun, L and Yuan, X and Liu, H and Xiong, Y and Ma, Y and Li, H and Zhou, B and Li, L and Yuan, Z and Wu, Y and She, J},
title = {Gut Microbiota Regulate Saturated Free Fatty Acid Metabolism in Heart Failure.},
journal = {Small science},
volume = {4},
number = {9},
pages = {2300337},
pmid = {40212081},
issn = {2688-4046},
abstract = {AIMS: Heart failure (HF) is associated with profound changes in cardiac metabolism. At present, there is still a lack of relevant research to explore the key microbiome and their metabolites affecting the progression of HF. Herein, the interaction of gut microbiota and circulating free fatty acid (FFA) in HF patients and mice is investigated.

METHODS AND RESULTS: In HF patients, by applying metagenomics analysis and targeted FFA metabolomics, enriched abundance of Clostridium sporogenes (C.sp) in early and late stage of HF patients, which negatively correlated to saturated free fatty acid (SFA) levels, is identified. KEGG analysis further indicates microbiota gene enrichment in FFA degradation in early HF, and decreased gene expression in FFA synthesis in late HF. In HF mice (C57BL/6J) induced by isoproterenol (ISO), impaired intestinal permeability is observed, and decreased fecal C.sp and increased SFA are further validated. At last, by supplementing C.sp to ISO-induced HF mice, the cardiac function, fibrosis, and myocardial size are partially rescued, together with decreased circulating SFA levels.

CONCLUSIONS: Clostridium abundance is increased in HF, compensating cardiac function deterioration via downregulation of circulating SFA levels. The results demonstrate that the gut microbiota-SFA axis plays an important role in HF protection, which may provide a strategic advantage for the probiotic therapy development in HF.},
}

@article {pmid40211980,
year = {2025},
author = {Elena Schmitz, J and Rahmann, S},
title = {A comprehensive review and evaluation of species richness estimation.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf158},
pmid = {40211980},
issn = {1477-4054},
mesh = {*Biodiversity ; Computer Simulation ; Animals ; Computational Biology/methods ; Algorithms ; },
abstract = {MOTIVATION: The statistical problem of estimating the total number of distinct species in a population (or distinct elements in a multiset), given only a small sample, occurs in various areas, ranging from the unseen species problem in ecology to estimating the diversity of immune repertoires. Accurately estimating the true richness from very small samples is challenging, in particular for highly diverse populations with many rare species. Depending on the application, different estimation strategies have been proposed that incorporate explicit or implicit assumptions about either the species distribution or about the sampling process. These methods are scattered across the literature, and an extensive overview of their assumptions, methodology, and performance is currently lacking.

RESULTS: We comprehensively review and evaluate a variety of existing methods on real and simulated data with different compositions of rare and abundant species. Our evaluation shows that, depending on species composition, different methods provide the most accurate richness estimates. Simple methods based on the observed number of singletons yield accurate asymptotic lower bounds for several of the tested simulated species compositions, but tend to underestimate the true richness for heterogeneous populations and small samples containing 1% to 5% of the population. When the population size is known, upsampling (extrapolating) estimators such as PreSeq and RichnEst yield accurate estimates of the total species richness in a sample that is up to 10 times larger than the observed sample.

AVAILABILITY: Source code for data simulation and richness estimation is available at https://gitlab.com/rahmannlab/speciesrichness.},
}

*Biodiversity
Computer Simulation
Animals
Computational Biology/methods
Algorithms

@article {pmid40211775,
year = {2025},
author = {Kumar, N and Das, A and Kumari, N and Jain, U and Singh, G and Pandey, DP and Bodakhe, SH},
title = {"Preventive Role of Intermittent Fasting and Vitamin E in Mitigating Propylthiouracil-Induced Hypothyroidism Progression in Rat Model".},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1-25},
doi = {10.1017/S0007114525000832},
pmid = {40211775},
issn = {1475-2662},
abstract = {Thyroid disorders are increasingly prevalent globally and are considered metabolic-lifestyle diseases. While medications can manage thyroid dysfunction, they are usually lifelong, costly, and not always practical. Intermittent fasting (IF), a highly adaptable dietary regimen, has been shown to influence lifestyle, gut microbiome, and circadian rhythms. Our study hypothesized that IF, combined with vitamin supplementation, could reduce the risk of thyroid disorders due to their antioxidant effects. In this study, experimental animals were divided into five groups: Euthyroid, hypothyroidism control, IF + vitamin E, vitamin E, and IF. Hypothyroidism was induced using propylthiouracil (PTU) over 24 days, and IF and vitamin E (66 mg/ml) were administered based on the experimental group. The hypothyroid animals exhibited increased anxiety, weight gain, lipid peroxidation, and a significant reduction in thyroid hormone levels, locomotor activity, and antioxidant levels-clear signs of thyroid dysfunction's impact on metabolism and overall health. Our proposed therapies IF and vitamin E effectively mitigated thyroid damage. Drawing inspiration from ancient Ayurveda and modern healthcare strategies, these cost-effective and practical regimens offer a promising solution to managing thyroid disorders globally.},
}

@article {pmid40211688,
year = {2025},
author = {Ge, SX and Niu, YM and Ren, LL and Zong, SX},
title = {Inheritance or Recruitment? The Assembly Mechanisms and Functional Dynamics of Microbial Communities in the Life Cycle of a Wood-Feeding Beetle.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17751},
doi = {10.1111/mec.17751},
pmid = {40211688},
issn = {1365-294X},
support = {2021YFD1400900//National Key R&D Program of China/ ; },
abstract = {Microbial partners enhance the metabolic capabilities of insects, enabling their adaptation to diverse ecological niches. Xylophagous insects have larvae that can digest lignocellulose and cope with plant secondary metabolites (PSMs). However, there is little information in terms of microbiome sources, dynamics and species contributions. This limits our understanding of the interaction between xylophagous insects and the microbiome. Monochamus saltuarius (Cerambycidae) is a significant borer of conifers. We used combined qPCR, host genomic and microbiome metagenomic datasets, as well as in vitro validation experiments to study the dynamics of the associated microbiome and its interactions with M. saltuarius. We evaluated microbial metabolic/biosynthetic contributions and validated their related functions. Our findings revealed that insect growth and development altered the quantity and community composition of associated bacteria and fungi. The egg microbiome was particularly susceptible to alteration due to oviposition pits. Bacterial transmission largely persisted between developmental stages, while fungal re-acquisition primarily originated from the external environment. By reconstructing community pathway maps, we identified the cooperative interactions between the insect and its gut microbiome. As larvae transitioned from phloem to xylem feeding, the functional role of the gut microbiome in various pathways was weakened. Remarkably, high-contribution bacterial species largely overlapped across different functional roles, and these species also showed considerable overlap between phloem and xylem feeding periods. Overall, our study highlights the unique interaction between xylophagous insects and their microbiome, which enhances their ability in lignocellulose digestion, PSMs degradation and the acquisition of essential amino acids, as well as vitamins.},
}

@article {pmid40211685,
year = {2025},
author = {Kim, JW and Choi, EC and Lee, KJ},
title = {Standardizing the approach to clinical-based human microbiome research: from clinical information collection to microbiome profiling and human resource utilization.},
journal = {Osong public health and research perspectives},
volume = {},
number = {},
pages = {},
doi = {10.24171/j.phrp.2024.0319},
pmid = {40211685},
issn = {2210-9099},
abstract = {OBJECTIVES: This study presents the standardized protocols developed by the Clinical-Based Human Microbiome Research and Development Project (cHMP) in the Republic of Korea.

METHODS: It addresses clinical metadata collection, specimen handling, DNA extraction, sequencing methods, and quality control measures for microbiome research.

RESULTS: The cHMP involves collecting samples from healthy individuals and patients across various body sites, including the gastrointestinal tract, oral cavity, respiratory system, urogenital tract, and skin. These standardized procedures ensure consistent data quality through controlled specimen collection, storage, transportation, DNA extraction, and sequencing. Sequencing encompasses both amplicon and whole metagenome methods, followed by stringent quality checks. The protocols conform to international guidelines, ensuring that the data generated are both reliable and comparable across microbiome studies.

CONCLUSION: The cHMP underscores the importance of methodological standardization in enhancing data integrity, reproducibility, and advancing microbiome-based research with potential applications for improving human health outcomes.},
}

@article {pmid40211627,
year = {2025},
author = {Yakubu, I and Yeon, E and Kong, HG},
title = {Microbial Community Responses to Alternate Wetting and Drying in the System of Rice Intensification.},
journal = {The plant pathology journal},
volume = {41},
number = {2},
pages = {231-239},
doi = {10.5423/PPJ.NT.01.2025.0001},
pmid = {40211627},
issn = {1598-2254},
support = {//Chungbuk National University/ ; },
abstract = {Continuous flooding in rice production presents significant challenges, such as increased labor intensity and soil degradation. However, when properly implemented, alternate wetting and drying can mitigate these issues. Despite its potential advantages, the effects of different water management practices on the soil microbiome are not well understood. This study explored how intermittent flooding and drying influence the soil microbiome by analyzing microbial communities under varying moisture conditions using Illumina sequencing. The results showed notable shifts in the abundance of Bacillota and Actinomycetota in response to fluctuations in water levels, although the overall microbial abundance returned to its original state under stable moisture conditions. In contrast, the abundance of Chloroflexota, which increased during waterlogging, remained elevated even under dry conditions. Additionally, microbial interactions were more pronounced during waterlogging compared to both moist and dry conditions. Overall, this research underscores the significant role of water management in shaping soil bacterial communities.},
}

@article {pmid40211625,
year = {2025},
author = {Lee, SM and Tae, HS and Kong, HG and Lee, B and Chang, YK and Ryu, CM},
title = {Foliar Application of Chlorella Supernatant Protects Turfgrass against Clarireedia jacksonii by Eliciting Induced Resistance and Modulating the Rhizosphere Microbiota.},
journal = {The plant pathology journal},
volume = {41},
number = {2},
pages = {210-224},
doi = {10.5423/PPJ.FT.01.2025.0009},
pmid = {40211625},
issn = {1598-2254},
support = {ABC-2010-0029728//Ministry of Science, ICT and Future Planning/ ; 918017-4//Ministry of Agriculture, Food and Rural Affairs/ ; RS-2023-00249410//National Research Foundation of Korea/ ; //Korea Reseach Institute of Bioscience & BioTechnology/ ; },
abstract = {Large-scale culture of the microalga Chlorella produces valuable products. Cultivation also generates tons of supernatant waste that require detoxification and disposal. Recent research has focused on recycling waste supernatant as a plant protectant and biofertilizer, although, to date, most studies have considered its use as a biological control of pathogens infecting dicot plants. By contrast, the current study evaluated whether Chlorella supernatant could protect turfgrass (Agrostis stolonifera), a monocot plant widely used as a turfgrass, against dollar spot disease caused by the fungal pathogen Clarireedia jacksonii (formerly Sclerotinia homoeocarpa) under greenhouse and field conditions. Foliar application of supernatants from Chlorella sp. ABC001 and HS2 cultures reduced the incidence of dollar spot disease in turfgrass under both greenhouse and field conditions without directly inhibiting growth. The effects of supernatant application on the rhizosphere microbiome were investigated using 16S rRNA amplicon sequencing. Application of ABC001 and HS2 supernatants modulated the structure of the rhizosphere microbiome and enriched specific microbial taxa that improved turfgrass health in the presence of C. jacksonii. The application of waste Chlorella supernatant therefore offers an alternative method for protecting monocot plants against fungal pathogens, while also enhancing the composition of soil microbes in the rhizosphere.},
}

@article {pmid40211604,
year = {2025},
author = {Rajczewski, AT and Blakeley-Ruiz, JA and Meyer, A and Vintila, S and McIlvin, MR and Van Den Bossche, T and Searle, BC and Griffin, TJ and Saito, MA and Kleiner, M and Jagtap, PD},
title = {Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e202400187},
doi = {10.1002/pmic.202400187},
pmid = {40211604},
issn = {1615-9861},
support = {R35GM138362/NH/NIH HHS/United States ; R01GM135709/GM/NIGMS NIH HHS/United States ; OCE-2123055//National Science Foundation/ ; 2021-67013-34537//U.S. Department of Agriculture National Institute of Food and Agriculture/ ; [1286824N]//Research Foundation Flanders/ ; T32DK007737//National Institute of Diabetes and Digestive and Kidney Diseases:/ ; },
abstract = {Mass spectrometry (MS)-based metaproteomics is used to identify and quantify proteins in microbiome samples, with the frequently used methodology being data-dependent acquisition mass spectrometry (DDA-MS). However, DDA-MS is limited in its ability to reproducibly identify and quantify lower abundant peptides and proteins. To address DDA-MS deficiencies, proteomics researchers have started using Data-independent acquisition mass spectrometry (DIA-MS) for reproducible detection and quantification of peptides and proteins. We sought to evaluate the reproducibility and accuracy of DIA-MS metaproteomic measurements relative to DDA-MS using a mock community of known taxonomic composition. Artificial microbial communities of known composition were analyzed independently in three laboratories using DDA- and DIA-MS acquisition methods. In this study, DIA-MS yielded more protein and peptide identifications than DDA-MS in each laboratory for the particular instruments and software parameters chosen. In addition, the protein and peptide identifications were more reproducible in all laboratories and provided an accurate quantification of proteins and taxonomic groups in the samples. We also identified some limitations of current DIA tools when applied to metaproteomic data, highlighting specific needs to improve DIA tools enabling analysis of metaproteomic datasets from complex microbiomes. Ultimately, DIA-MS represents a promising strategy for MS-based metaproteomics due to its large number of detected proteins and peptides, reproducibility, deep sequencing capabilities, and accurate quantitation.},
}

@article {pmid40211528,
year = {2025},
author = {Liu, Y and Feng, D and Zhang, H and Wang, L},
title = {Dissecting Causal Relationships Between Gut Microbiota, 1400 Blood Metabolites, and Intervertebral Disc Degeneration.},
journal = {Neurospine},
volume = {22},
number = {1},
pages = {211-221},
doi = {10.14245/ns.2449172.586},
pmid = {40211528},
issn = {2586-6583},
abstract = {OBJECTIVE: The precise mechanisms driving intervertebral disc degeneration (IVDD) development remain unclear, but evidence suggests a significant involvement of gut microbiota (GM) and blood metabolites. We aimed to investigate the causal relationships between GM, IVDD, and blood metabolites using Mendelian randomization (MR) analysis.

METHODS: We utilized the summary statistics of GM from the MiBioGen consortium, 1400 blood metabolites from the genome-wide association studies (GWAS) Catalog, and IVDD data from the FinnGen repository, which are sourced from the largest GWAS conducted to date. Employing bidirectional MR analyses, we investigated the causal relationships between GM and IVDD. Additionally, we conducted 2 mediation analyses, 2-step MR and multivariable MR (MVMR), to identify potential mediating metabolites.

RESULTS: Five bacterial genera were causally associated with IVDD, while IVDD did not show a significant causal effect on GM. In the 2-step MR analysis, Eubacteriumfissicatenagroup, RuminococcaceaeUCG003, Lachnoclostridium, and Marvinbryantia genera, along with metabolites X-24949, Pimeloylcarnitine/3-methyladipoylcarnitine (C7-DC), X-24456, histidine, 2-methylserine, Phosphocholine, and N-delta-acetylornithine, were all significantly associated with IVDD (all p < 0.05). MVMR analysis revealed that the associations between Eubacteriumfissicatenagroup genus and IVDD were mediated by X-24949 (8.1%, p = 0.024); Lachnoclostridium genus and IVDD were mediated by histidine (18.1%, p = 0.013); and RuminococcaceaeUCG003 genus and IVDD were mediated by C7-DC (-7.5%, p = 0.041).

CONCLUSION: The present MR study offers evidence supporting the causal relationships between several specific GM taxa and IVDD, as well as identifying potential mediating metabolites.},
}

@article {pmid40211458,
year = {2025},
author = {Akagawa, S and Tsuji, S and Nakai, Y and Urakami, C and Yamagishi, M and Akagawa, Y and Kaneko, K},
title = {Faecalibacterium in the Gut Microbiota Predicts Tolerance Acquisition in Pediatric Hen's Egg Allergy.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16556},
pmid = {40211458},
issn = {1398-9995},
support = {//Nipponham Foundation for the Future of Food/ ; //Kansai Medical University/ ; },
}

@article {pmid40211390,
year = {2025},
author = {Wang, Z and Gao, X and Ji, H and Shao, M and Ni, B and Fei, S and Sun, L and Chen, H and Tan, R and Du, M and Gu, M},
title = {Characterization of gut microbiota and metabolites in renal transplant recipients during COVID-19 and prediction of one-year allograft function.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {420},
pmid = {40211390},
issn = {1479-5876},
support = {82170769//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Kidney Transplantation ; *COVID-19/metabolism/microbiology/complications ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Middle Aged ; Adult ; *Metabolome ; SARS-CoV-2 ; Allografts ; Transplant Recipients ; Feces/microbiology ; Aged ; },
abstract = {BACKGROUND: The gut-lung-kidney axis is pivotal in immune-related kidney diseases, with gut dysbiosis potentially exacerbating the severity of Coronavirus disease 2019 (COVID-19) in recipients of kidney transplant. This study aimed to characterize the gut microbiome and metabolome in renal transplant recipients with COVID-19 pneumonia over a one-year follow-up period.

METHODS: A total of 30 renal transplant recipients were enrolled, comprising 17 with COVID-19 pneumonia, six with mild COVID-19, and seven without COVID-19. Fecal samples were collected at the onset of infection for gut microbiome and metabolome analysis. Generalized Estimating Equations (GEE) model and Latent Class Growth Mixed Model (LCGMM) were employed to dissect the relationships among clinical characteristics, laboratory tests, and gut microbiota and metabolites.

RESULTS: Four microbial phyla (Deferribacteres, TM7, Fusobacteria, and Gemmatimonadetes) and 13 genera were significantly enriched across three recipients groups, correlating with baseline inflammatory response and allograft function. Additionally, 52 differentially expressed metabolites were identified, with seven significantly correlating with eight altered microbiota genera. LCGMM revealed two distinct classes of recipients, with those suffering from COVID-19 pneumonia exhibiting significantly elevated serum creatinine (Scr) trajectories over the one-year period. GEE further identified 12 genera and 181 metabolites closely associated with these trajectories; a multivariable model incorporating gut metabolites of 1-Caffeoylquinic Acid and PMK was found to effectively predict one-year allograft function.

CONCLUSIONS: Our study indicates a possible interaction between the composition of the gut microbiota and metabolites community and COVID-19 in renal transplant recipients, particularly in relation to disease severity and the prediction of one-year allograft function.},
}

Humans
*Kidney Transplantation
*COVID-19/metabolism/microbiology/complications
*Gastrointestinal Microbiome/physiology
Female
Male
Middle Aged
Adult
*Metabolome
SARS-CoV-2
Allografts
Transplant Recipients
Feces/microbiology
Aged

@article {pmid40211330,
year = {2025},
author = {Zhang, Z and Jiang, C and Xing, YQ and Yang, T and Zou, L and Jia, Z and Zhao, L and Han, X and Qu, X and Zhang, Z and Zong, J and Wang, S},
title = {Unveiling the interplay among skin microbiota, cytokines, and T2DM: an insightful Mendelian randomization study.},
journal = {Nutrition & metabolism},
volume = {22},
number = {1},
pages = {29},
pmid = {40211330},
issn = {1743-7075},
support = {82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; },
abstract = {BACKGROUND: Previous observational studies have indicated a correlation between the skin microbiome and Type 2 diabetes (T2DM). It is hypothesized that this causal relationship may be influenced by inflammatory responses. However, these factors as determinants of T2DM remain largely unexplored.

METHOD: This study incorporated data from the GWAS database on the skin microbiome, 91 types of inflammatory cytokines, and T2DM. We employed two-sample MR and multivariable MR methods to assess the correlation between the skin microbiome and T2DM, and to investigate whether this correlation is affected by inflammatory cytokines.

RESULTS: The results of the two-sample MR analysis indicate that within the skin microbiome, genetically predicted genus: Acinetobacter, class: Alphaproteobacteria, genus: Bacteroides, ASV005[Propionibacterium granulosum], and ASV072[Rothia mucilaginosa] are associated with an increased risk of T2DM, while phylum: Proteobacteria, genus: Enhydrobacter, family: Clostridiales, ASV006[Staphylococcus hominis] serve as protective factors against T2DM. Among the inflammatory cytokines, levels of Macrophage colony-stimulating factor 1, Tumor necrosis factor receptor superfamily member 9, Urokinase-type plasminogen activator, and C-C motif chemokine 28 are associated with an increased risk of T2DM. Multivariable MR analysis further revealed that Macrophage colony-stimulating factor 1 levels act as a mediating factor between ASV072[Rothia mucilaginosa] and T2DM.

CONCLUSION: In this study, we found a connection between the skin microbiome and T2DM, with inflammatory cytokines playing a key role in this relationship. This research helps us better understand this complex link and shows that addressing inflammation is important for preventing and treating diabetes. This could greatly benefit public health by reducing the impact of diabetes and its complications. Our results suggest that future studies should explore the specific biological interactions between the skin microbiome and diabetes to develop more effective risk management and treatment strategies from a microbial perspective.},
}

@article {pmid40211272,
year = {2025},
author = {Li, N and Wang, Y and Zhang, H and Ma, L and Huang, X and Qiao, Y and Li, H and Zhao, H and Li, P},
title = {Urobiome of patients with diabetic kidney disease in different stages is revealed by 2bRAD-M.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {414},
pmid = {40211272},
issn = {1479-5876},
support = {82104601//The National Natural Science Foundation of China/ ; 82174144//National Natural Science Foundation of China/ ; U23A20504//National Natural Science Foundation of China/ ; 82174296//National Natural Science Foundation of China/ ; 2023-NHLHCRFDJMS-05//National High Level Hospital Clinical Research Funding/ ; ZRJY2024-GG11//Elite Medical Professionals project of China-Japan Friendship Hospital/ ; },
mesh = {Humans ; *Diabetic Nephropathies/microbiology/urine ; *Microbiota/genetics ; Male ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Diabetes Mellitus, Type 2/microbiology ; Bacteria/genetics ; Case-Control Studies ; Aged ; },
abstract = {BACKGROUND: Knowledge of the urinary microbiome (urobiome) in diabetic kidney disease (DKD) remains limited. The most commonly used 16S rRNA sequencing technique can only provide bacterial identification at the genus level. As a novel technique, 2bRAD sequencing for microbiome (2bRAD-M) can be used to identify the low-biomass microbiome at the species level. In this study, we used 2bRAD-M to compare the urobiome composition of patients with DKD at different stages with healthy individuals and those with type 2 diabetes mellitus (T2DM), with the expectation that we would find discriminative species correlated with DKD.

METHOD: Healthy controls, patients with DKD with microalbuminuria (DKD1 group) or macroalbuminuria (DKD2 group), and patients with T2DM were recruited (n = 20 for each group). The first-morning urine was collected for 2bRAD-M testing. The albumin-to-creatinine ratio (ACR) was also measured with urine samples. Serum samples were collected for detecting clinical indicators. The microbial diversity and composition based on abundance were calculated. Differential bacteria for different groups were identified. Besides, the correlation between discriminative bacteria and clinical indices was also analyzed.

RESULTS: Urobiome diversity was significantly reduced in the DKD groups. In the DKD1 group, was the dominant genus, followed by Pseudomonas_E, whereas in the DKD2 group, Pseudomonas_E became the dominant genus and Escherichia was notably reduced. Both Bifidobacterium and Streptococcus, which were the top genera in the control group, were substantially decreased in the DKD groups. The discriminative species for DKD1 included Escherichia coli and Acinetobacter johnsonii, while for DKD2, Pseudomonas_E oleovorans, Enterococcus faecalis, and Morganella morganii were identified. Pseudomonas_E, Enterococcus and Morganella showed a strong correlation with renal function indicators and urinary protein levels.

CONCLUSION: The urobiome diversity and composition in patients with DKD were markedly different from those in healthy individuals and T2DM patients. These findings provide valuable insights into the onset and progression of DKD, driven by changes in the urinary bacterial community structure.},
}

Humans
*Diabetic Nephropathies/microbiology/urine
*Microbiota/genetics
Male
Female
Middle Aged
RNA, Ribosomal, 16S/genetics
Diabetes Mellitus, Type 2/microbiology
Bacteria/genetics
Case-Control Studies
Aged

@article {pmid40211121,
year = {2025},
author = {Polizel, GHG and Diniz, WJS and Cesar, ASM and Ramírez-Zamudio, GD and Cánovas, A and Dias, EFF and Fernandes, AC and Prati, BCT and Furlan, É and Pombo, GDV and Santana, MHA},
title = {Impacts of prenatal nutrition on metabolic pathways in beef cattle: an integrative approach using metabolomics and metagenomics.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {359},
pmid = {40211121},
issn = {1471-2164},
support = {2021/03265-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/12105-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 307593/2021-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {Animals ; Cattle ; Female ; *Metabolomics/methods ; Pregnancy ; *Metabolic Networks and Pathways ; *Metagenomics/methods ; Male ; Metabolome ; Rumen/microbiology ; Microbiota ; *Prenatal Nutritional Physiological Phenomena ; *Animal Nutritional Physiological Phenomena ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: This study assessed the long-term metabolic effects of prenatal nutrition in Nelore bulls through an integrated analysis of metabolome and microbiome data to elucidate the interconnected host-microbe metabolic pathways. To this end, a total of 126 cows were assigned to three supplementation strategies during pregnancy: NP (control)- only mineral supplementation; PP- protein-energy supplementation during the last trimester; and FP- protein-energy supplementation throughout pregnancy. At the end of the finishing phase, blood, fecal, and ruminal fluid samples were collected from 63 male offspring. The plasma underwent targeted metabolomics analysis, and fecal and ruminal fluid samples were used to perform 16 S rRNA gene sequencing. Metabolite and ASV (amplicon sequence variant) co-abundance networks were constructed for each treatment using the weighted gene correlation network analysis (WGCNA) framework. Significant modules (p ≤ 0.1) were selected for over-representation analyses to assess the metabolic pathways underlying the metabolome (MetaboAnalyst 6.0) and the microbiome (MicrobiomeProfiler). To explore the metabolome-metagenome interplay, correlation analyses between host metabolome and microbiome were performed. Additionally, a holistic integration of metabolic pathways was performed (MicrobiomeAnalyst 2.0).

RESULTS: A total of one and two metabolite modules associated with the NP and FP were identified, respectively. Regarding fecal microbiome, three, one, and two modules for the NP, PP, and FP were identified, respectively. The rumen microbiome demonstrated two modules correlated with each of the groups under study. Metabolite and microbiome enrichment analyses revealed the main metabolic pathways associated with lipid and protein metabolism, and regulatory mechanisms. The correlation analyses performed between the host metabolome and fecal ASVs revealed 13 and 12 significant correlations for NP and FP, respectively. Regarding the rumen, 16 and 17 significant correlations were found for NP and FP, respectively. The NP holistic analysis was mainly associated with amino acid and methane metabolism. Glycerophospholipid and polyunsaturated fatty acid metabolism were over-represented in the FP group.

CONCLUSIONS: Prenatal nutrition significantly affected the plasma metabolome, fecal microbiome, and ruminal fluid microbiome of Nelore bulls, providing insights into key pathways in protein, lipid, and methane metabolism. These findings offer novel discoveries about the molecular mechanisms underlying the effects of prenatal nutrition.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Animals
Cattle
Female
*Metabolomics/methods
Pregnancy
*Metabolic Networks and Pathways
*Metagenomics/methods
Male
Metabolome
Rumen/microbiology
Microbiota
*Prenatal Nutritional Physiological Phenomena
*Animal Nutritional Physiological Phenomena
Gastrointestinal Microbiome

@article {pmid40211032,
year = {2025},
author = {Hindson, J},
title = {Diet-driven microbiome restoration associated with cardiometabolic benefits.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {40211032},
issn = {1759-5053},
}

@article {pmid40210899,
year = {2025},
author = {Ni Lochlainn, M and Bowyer, RCE and Moll, JM and García, MP and Wadge, S and Baleanu, AF and Nessa, A and Sheedy, A and Akdag, G and Hart, D and Raffaele, G and Seed, PT and Murphy, C and Harridge, SDR and Welch, AA and Greig, C and Whelan, K and Steves, CJ},
title = {Author Correction: Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3393},
doi = {10.1038/s41467-025-58771-w},
pmid = {40210899},
issn = {2041-1723},
}

@article {pmid40210877,
year = {2025},
author = {Wagner, J and Handley, A and Donato, CM and Lyons, EA and Pavlic, D and Ong, DS and Bonnici, R and Bogdanovic-Sakran, N and Parker, EPK and Bronowski, C and Thobari, JA and Satria, CD and Nirwati, H and Witte, D and Jere, KC and Mpakiza, A and Watts, E and Turner, A and Boniface, K and Mandolo, J and Justice, F and Bar-Zeev, N and Iturriza-Gomara, M and Buttery, JP and Cunliffe, NA and Soenarto, Y and Bines, JE},
title = {Early-life gut microbiome associates with positive vaccine take and shedding in neonatal schedule of the human neonatal rotavirus vaccine RV3-BB.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3432},
pmid = {40210877},
issn = {2041-1723},
support = {1164384//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1058454//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1164384//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1111055//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1058454//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1164384//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1111055//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1058454//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1164384//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1111055//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1054584//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1164384//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1111055//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1058454//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1111055//Bill and Melinda Gates Institute for Population and Reproductive Health (Gates Institute)/ ; 1012425//Department of Health | National Health and Medical Research Council (NHMRC)/ ; 1012425//Department of Health | National Health and Medical Research Council (NHMRC)/ ; 1012425//Department of Health | National Health and Medical Research Council (NHMRC)/ ; 1012425//Department of Health | National Health and Medical Research Council (NHMRC)/ ; 1012425//Department of Health | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Rotavirus Vaccines/immunology/administration & dosage ; *Rotavirus Infections/prevention & control/immunology/virology ; Infant ; Infant, Newborn ; Rotavirus/immunology ; Female ; Immunoglobulin A/immunology ; Feces/virology/microbiology ; Virus Shedding/immunology ; Male ; Vaccines, Attenuated/immunology/administration & dosage ; Antibodies, Viral/immunology/blood ; Immunization Schedule ; Malawi ; Indonesia ; Seroconversion ; Vaccination ; },
abstract = {Rotavirus vaccines are less effective in high mortality regions. A rotavirus vaccine administered at birth may overcome challenges to vaccine uptake posed by a complex gut microbiome. We investigated the association between the microbiome and vaccine responses following RV3-BB vaccine (G3P[6]) administered in a neonatal schedule (dose 1: 0-5 days), or infant schedule (dose 1: 6-8 weeks) in Indonesia (Phase 2b efficacy study) (n = 478 samples/193 infants) (ACTRN12612001282875) and in Malawi (Immunigenicity study) (n = 355 samples/186 infants) (NCT03483116). Vaccine responses assessed using anti-rotavirus IgA seroconversion (IgA), stool shedding of vaccine virus and vaccine take (IgA seroconversion and/or shedding). Here we report, high alpha diversity, beta diversity differences and high abundance of Bacteroides is associated with positive vaccine take and shedding following RV3-BB administered in the neonatal schedule, but not with IgA seroconversion, or in the infant schedule. Higher alpha diversity was associated with shedding after three doses of RV3-BB in the neonatal schedule compared to non-shedders, or the placebo group. High abundance of Streptococcus and Staphylococcus is associated with no shedding in the neonatal schedule group. RV3-BB vaccine administered in a neonatal schedule modulates the early microbiome environment and presents a window of opportunity to optimise protection from rotavirus disease.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Rotavirus Vaccines/immunology/administration & dosage
*Rotavirus Infections/prevention & control/immunology/virology
Infant
Infant, Newborn
Rotavirus/immunology
Female
Immunoglobulin A/immunology
Feces/virology/microbiology
Virus Shedding/immunology
Male
Vaccines, Attenuated/immunology/administration & dosage
Antibodies, Viral/immunology/blood
Immunization Schedule
Malawi
Indonesia
Seroconversion
Vaccination

@article {pmid40210868,
year = {2025},
author = {Fu, Y and Guzior, DV and Okros, M and Bridges, C and Rosset, SL and González, CT and Martin, C and Karunarathne, H and Watson, VE and Quinn, RA},
title = {Balance between bile acid conjugation and hydrolysis activity can alter outcomes of gut inflammation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3434},
pmid = {40210868},
issn = {2041-1723},
support = {1R01DK140854//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; },
mesh = {Animals ; *Bile Acids and Salts/metabolism ; Humans ; Gastrointestinal Microbiome/genetics ; Mice, Knockout ; Mice ; Amidohydrolases/metabolism/genetics ; Hydrolysis ; Acyltransferases/genetics/metabolism ; Taurocholic Acid/pharmacology/metabolism ; Disease Models, Animal ; *Colitis/metabolism/pathology/microbiology ; Male ; Inflammatory Bowel Diseases/metabolism/microbiology ; Female ; Mice, Inbred C57BL ; Clostridiales/metabolism/genetics ; Crohn Disease/metabolism/microbiology/genetics ; },
abstract = {Conjugated bile acids (BAs) are multi-functional detergents in the gastrointestinal (GI) tract produced by the liver enzyme bile acid-CoA:amino acid N-acyltransferase (BAAT) and by the microbiome from the acyltransferase activity of bile salt hydrolase (BSH). Humans with inflammatory bowel disease (IBD) have an enrichment in both host and microbially conjugated BAs (MCBAs), but their impacts on GI inflammation are not well understood. We investigated the role of host-conjugated BAs in a mouse model of colitis using a BAAT knockout background. Baat[-/-] KO mice have severe phenotypes in the colitis model that were rescued by supplementation with taurocholate (TCA). Gene expression and histology showed that this rescue was due to an improved epithelial barrier integrity and goblet cell function. However, metabolomics also showed that TCA supplementation resulted in extensive metabolism to secondary BAs. We therefore investigated the BSH activity of diverse gut bacteria on a panel of conjugated BAs and found broad hydrolytic capacity depending on the bacterium and the amino acid conjugate. The complexity of this microbial BA hydrolysis led to the exploration of bsh genes in metagenomic data from human IBD patients. Certain bsh sequences were enriched in people with Crohn's disease particularly that from Ruminococcus gnavus. This study shows that both host and microbially conjugated BAs may provide benefits to those with IBD, but this is dictated by a delicate balance between BA conjugation/deconjugation based on the bsh genes present.},
}

Animals
*Bile Acids and Salts/metabolism
Humans
Gastrointestinal Microbiome/genetics
Mice, Knockout
Mice
Amidohydrolases/metabolism/genetics
Hydrolysis
Acyltransferases/genetics/metabolism
Taurocholic Acid/pharmacology/metabolism
Disease Models, Animal
*Colitis/metabolism/pathology/microbiology
Male
Inflammatory Bowel Diseases/metabolism/microbiology
Female
Mice, Inbred C57BL
Clostridiales/metabolism/genetics
Crohn Disease/metabolism/microbiology/genetics

@article {pmid40210576,
year = {2025},
author = {Park, DE and Aziz, M and Salazar, JE and Pham, T and Nelson, SG and Villani, J and Weber, NO and Price, LB and Hungate, BA and Liu, CM},
title = {The nasal microbiome modulates risk for SARS-CoV-2 infection.},
journal = {EBioMedicine},
volume = {},
number = {},
pages = {105660},
doi = {10.1016/j.ebiom.2025.105660},
pmid = {40210576},
issn = {2352-3964},
abstract = {BACKGROUND: The nasal microbiome may influence host risk for COVID-19 by modulating the expression of key proteins that facilitate SARS-CoV-2 entry, including angiotensin-converting enzyme 2 (ACE2), which binds the virus, and transmembrane serine protease 2 (TMPRSS2), which activates viral entry into nasal epithelial cells. This study examined whether the expression levels of ACE2 and TMPRSS2 in the nasal cavity predict the risk of SARS-CoV-2 infection and whether the host nasal microbiome modulates their expression.

METHODS: Using 1548 self-collected nasal swabs from a population-based surveillance testing of community-dwelling adults in Washington D.C., we conducted two retrospective case-control studies (cross-sectional: n = 111 cases and 343 controls; longitudinal: n = 97 cases, 286 controls) and a nasal microbiome study (n = 428). Cases, defined as individuals with a positive SARS-CoV-2 test, were matched with controls based on age and test date. Pre-infection samples were analysed. We measured nasal ACE2/TMPRSS2 expression using RT-qPCR and characterized the nasal microbiome using 16S rRNA gene-based qPCR and sequencing. We used machine learning and regression analysis to determine if nasal ACE2/TMPRSS2 expression predicts SARS-CoV-2 infection and whether the nasal microbiome influences their expression.

FINDINGS: Elevated nasal ACE2/TMPRSS2 expression was associated with 3.6-fold increased risk of contracting COVID-19 (95% CI = 1.71-7.47) compared to those with no detectable levels of ACE2 or TMPRSS2. Before testing positive for SARS-CoV-2, cases also had significantly higher and more unstable ACE2/TMPRSS2 expression in their nasal cavity than controls. Having high densities of Staphylococcus aureus, Haemophilus influenzae, or Moraxella catarrhalis/nonliquefaciens was linked to increased nasal ACE2/TMPRSS2 expression. In contrast, having high densities of Dolosigranulum pigrum was associated with decreased nasal ACE2/TMPRSS2 expression.

INTERPRETATION: These results suggest that natural variation in the nasal microbiome significantly impacts ACE2/TMPRSS2 expression in the nasal cavity and the near-term risk of SARS-CoV-2 infection in adults. Modifying the nasal microbiome could potentially reduce COVID-19 risk.

FUNDING: Research reported in this article was supported by the Milken Institute School of Public Health, the George Washington University and the National Institute of Allergy and Infectious Diseases, National Institutes of Health under award number R01AI168182. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.},
}

@article {pmid40210439,
year = {2025},
author = {Smith, BJ and Zhao, C and Dubinkina, V and Jin, X and Zahavi, L and Shoer, S and Moltzau-Anderson, J and Segal, E and Pollard, KS},
title = {Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279543.124},
pmid = {40210439},
issn = {1549-5469},
abstract = {Metagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity of bacterial species within and across individuals. Even within a single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, and virulence. Methods that harness metagenomic data to resolve strain-level differences in functional potential are crucial for understanding the causes and consequences of this intraspecific diversity. The enormous size of pangenome references, strain mixing within samples, and inconsistent sequencing depth present challenges for existing tools that analyze samples one at a time. To address this gap, we updated the MIDAS pangenome profiler, now released as version 3, and developed StrainPGC, an approach to strain-specific gene content estimation that combines strain tracking and correlations across multiple samples. We validate our integrated analysis using a complex synthetic community of strains from the human gut and find that StrainPGC outperforms existing approaches. Analyzing a large, publicly available metagenome collection from inflammatory bowel disease patients and healthy controls, we catalog the functional repertoires of thousands of strains across hundreds of species, capturing extensive diversity missing from reference databases. Finally, we apply StrainPGC to metagenomes from a clinical trial of fecal microbiota transplantation for the treatment of ulcerative colitis. We identify two Escherichia coli strains, from two different donors, that are both frequently transmitted to patients but have notable differences in functional potential. StrainPGC and MIDAS v3 together enable precise, intraspecific pangenomic investigations using large collections of metagenomic data without microbial isolation or de novo assembly.},
}

@article {pmid40210403,
year = {2025},
author = {Africa, AJ and Setati, ME and Hitzeroth, AC and Blancquaert, EH},
title = {Exploring the evolution of microbial communities from the phyllosphere and carposphere to the grape must of Vitis vinifera L. cv's Chardonnay and Pinot noir.},
journal = {Food microbiology},
volume = {130},
number = {},
pages = {104780},
doi = {10.1016/j.fm.2025.104780},
pmid = {40210403},
issn = {1095-9998},
mesh = {*Vitis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Fungi/classification/genetics/isolation & purification ; *Plant Leaves/microbiology ; *Fruit/microbiology ; Wine/microbiology/analysis ; South Africa ; },
abstract = {Microbial communities associated with the grapevine phyllosphere and carposhere are a fundamental determinant of grape and wine quality. High throughput amplicon sequencing was used to profile the fungal and bacterial communities on the associated phylloplane and carposphere of Vitis vinifera L. cv's Chardonnay and Pinot noir in the Elgin and Hemel-en-Aarde wine districts of South Africa in the 2021-2022 growing season. The subsequent grape must was analysed to determine the prevalent microbiome. The most abundant bacterial and fungal genera found in both the phylloplane and carposphere of Chardonnay and Pinot noir were Pseudomonas and Filobasidium. The LEfSe (Linear discriminant analysis Effect Size) revealed significant differences in fungal and bacterial biomarkers from leaf, berry and grape must samples; however, no biomarkers were identified for cultivar nor location. Fungal β-diversity was significantly similar at different phenological stages, whereas bacterial β-diversity was significantly similar regardless of the site of colonisation. However, skin integrity of the grapes was may have influenced the microbial diversity.},
}

*Vitis/microbiology
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Fungi/classification/genetics/isolation & purification
*Plant Leaves/microbiology
*Fruit/microbiology
Wine/microbiology/analysis
South Africa

@article {pmid40210182,
year = {2025},
author = {Chen, Y and Bi, S and Zhang, X and Chen, J and Xin, J and Liu, Z and Guan, Q and Qiu, P and Wang, P and Liu, J},
title = {Engineered probiotics remodel the intestinal epithelial barrier and enhance bacteriotherapy for inflammatory bowel diseases.},
journal = {Acta biomaterialia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.actbio.2025.04.016},
pmid = {40210182},
issn = {1878-7568},
abstract = {Inflammatory bowel diseases (IBDs) are often associated with compromised epithelial barriers and dysregulated gut microbiota. In this study, we revealed the synergistic effect that zinc and indole-3-carbinol (I3C) have in restoring the epithelial barrier, and co-localized them on a ZI platform, which was further conjugated to the surface of Escherichia coli Nissle 1917 (EcN). The ZI@EcN formulation effectively delivered ZI to colon tissues and extended its retention in the intestines due to the colonic colonization effect of EcN, thereby promoting the sustained release of zinc and I3C for optimal synergistic effects on epithelial barrier remodeling. The restored epithelium acts as a protective barrier, preventing the infiltration of toxins and pathogens, which significantly reduces inflammation in colonic tissues. Additionally, EcN enriched the gut microbiome, increasing the abundance of beneficial bacteria while reducing that of pathogens, demonstrating its significant efficacy in gut microbiome regulation. In dextran sulfate sodium-induced mouse colitis models, ZI@EcN exhibited substantially improved prophylactic and therapeutic efficacy with favorable safety profiles, highlighting its potential for clinical applications. STATEMENT OF SIGNIFICANCE: This study highlighted the synergistic effects that zinc and indole-3-carbinol, both derived from dietary sources, have on restoring integrity of the intestinal epithelial barrier. A platform (ZI@EcN) was also developed for the targeted delivery and sustained release of zinc and indole-3-carbinol, specifically in colonic tissues, for colitis treatment. This platform not only restores the compromised intestinal epithelial barrier but also regulates the dysbiotic gut microbiota, promoting the recovery of a healthy intestinal microenvironment and showing promise in alleviating complex symptoms in a single formulation. Furthermore, the formulation demonstrated potent prophylactic and therapeutic efficacy against colitis, with favorable safety profiles, and a strong potential for clinical applications.},
}

@article {pmid40209775,
year = {2025},
author = {Jiang, Y and Yao, Q and Zhao, Y and Kong, Y and Yu, T and Wang, Y and Yang, F and Mo, W},
title = {Abundance and Composition of the Meconium Microbiota in Preterm Infants with Infections, Feeding Intolerance, or Necrotizing Enterocolitis.},
journal = {Clinical laboratory},
volume = {71},
number = {4},
pages = {},
doi = {10.7754/Clin.Lab.2024.240911},
pmid = {40209775},
issn = {1433-6510},
mesh = {Humans ; *Meconium/microbiology ; *Enterocolitis, Necrotizing/microbiology/diagnosis ; Infant, Newborn ; *Infant, Premature ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Gestational Age ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification/isolation & purification ; *Food Intolerance/microbiology ; Case-Control Studies ; },
abstract = {BACKGROUND: The role of the microbial flora of the gut of a newborn is of scientific and practical interest. The aim of this study was to assess the abundance and composition of the meconium microbiota in preterm infants with infections, feeding intolerance, or necrotizing enterocolitis (NEC).

METHODS: Eighty-four preterm infants born by cesarean section were prospectively enrolled in this study. Out of the 28 diseased infants, 23 developed infections, including 8 cases of sepsis, 10 cases of pneumonia, 1 case of enterocolitis, and 4 cases of NEC. Fifty-six (66.67%) preterm infants without these characteristics served as control group. General clinical information (gender, gestational age, birth weight, presence of preterm rupture of mem-branes, Apgar 1-minute score, and duration of hospitalization) was collected. First-pass meconium samples were collected for 16S rRNA microbiological analysis.

RESULTS: Compared with the control group, the diseased infants had a lower gestational age (p < 0.001) and lower body weight (p = 0.014). In addition, the hospitalization time of the diseased infants was longer than that of the control group (p < 0.001). On the α-diversity measure, there was no difference in species abundance and diversity between the two groups; on the β-diversity measure, the differences in the microbial composition of the two groups were subjected to PCoA analyses, which showed that there was a difference between the disease group and the control group. At the phylum level, the dominant phylum in both groups was p_Proteobacteria, with higher abundance of p_Firmicutes in the disease group. At the genus level, the dominant genus in both groups was g_Novosphingobium. Microbiome phenotype prediction by BugBase revealed that microbial phenotypes 'Gram-positive' and 'Anaerobic' were abundantly increased in the disease group; microbial function prediction did not differ between the two groups in terms of significant function.

CONCLUSIONS: The impact of infections, feeding intolerance, and NEC on a host is complex. Preterm infants delivered by cesarean section have p_Proteobacteria as the dominant phylum, with a higher abundance of p_Firmicutes in the disease group, a difference contributed by g_Peptoniphilus.},
}

Humans
*Meconium/microbiology
*Enterocolitis, Necrotizing/microbiology/diagnosis
Infant, Newborn
*Infant, Premature
Female
Male
RNA, Ribosomal, 16S/genetics
Prospective Studies
Gestational Age
*Gastrointestinal Microbiome
*Bacteria/genetics/classification/isolation & purification
*Food Intolerance/microbiology
Case-Control Studies

@article {pmid40209684,
year = {2025},
author = {Indrio, F and Szajewska, H},
title = {Preface.},
journal = {Annals of nutrition & metabolism},
volume = {},
number = {},
pages = {1-2},
doi = {10.1159/000540495},
pmid = {40209684},
issn = {1421-9697},
}

@article {pmid40209676,
year = {2025},
author = {Schell, LD and Carmody, RN},
title = {An energetic framework for gut microbiome-mediated obesity induced by early-life exposure to antibiotics.},
journal = {Cell host & microbe},
volume = {33},
number = {4},
pages = {470-483},
doi = {10.1016/j.chom.2025.03.009},
pmid = {40209676},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/adverse effects/pharmacology ; *Obesity/chemically induced/microbiology/etiology/metabolism ; Animals ; Humans ; *Energy Metabolism/drug effects ; Female ; Mice ; Male ; },
abstract = {Early-life antibiotic (ELA) exposure has garnered attention for its potential role in modulating obesity risk, although outcomes from mouse experiments and human epidemiological studies often vary based on dosage and sex. Low-dose (subtherapeutic) antibiotics can enhance energy availability through moderate alterations in gut microbiome profile, while high-dose (therapeutic) antibiotics substantially deplete the gut microbiota, thereby contributing to short-term negative energy balance. In this perspective, we propose a framework to understand how these distinct impacts of antibiotics on the gut microbiome during critical developmental windows shape long-term obesity risk through their influence on host energy balance. Using this framework, we then propose several hypotheses to explain variation in ELA-induced obesity outcomes across males and females. We conclude by discussing the evolutionary implications of ELAs, positing that the response of the gut microbiome to ELAs may signal energy availability and environmental volatility, influencing metabolic programming and adaptive traits across generations.},
}

*Gastrointestinal Microbiome/drug effects
*Anti-Bacterial Agents/adverse effects/pharmacology
*Obesity/chemically induced/microbiology/etiology/metabolism
Animals
Humans
*Energy Metabolism/drug effects
Female
Mice
Male

@article {pmid40209653,
year = {2025},
author = {Inokuchi, T and Tomiyama, K and Okuda, T and Tsutsumi, K and Yama, K and Fujii, Y and Ohara, K and Chikazawa, T and Kakizawa, Y and Mukai, Y},
title = {Phellodendron bark extract and berberine chloride suppress microbiome dysbiosis in a saliva-derived in vitro microcosm biofilm model.},
journal = {Archives of oral biology},
volume = {174},
number = {},
pages = {106231},
doi = {10.1016/j.archoralbio.2025.106231},
pmid = {40209653},
issn = {1879-1506},
abstract = {OBJECTIVE: Preventing oral microbiome dysbiosis is crucial for averting the onset and progression of periodontal diseases. Phellodendron bark extract (PBE) and its active component berberine exhibit antibacterial properties against periodontal pathogenic bacteria. Although they inhibit Porphyromonas gingivalis (P. gingivalis)-induced dysbiosis in vitro in multiple species of saliva-derived planktonic cultures, their effects on microcosm biofilm models remain unclear. In this study, we aimed to elucidate the dysbiosis-suppressive effects of PBE and berberine chloride (BC) on biofilm formation.

DESIGN: PBE or BC was added during the formation of in vitro microcosm biofilms containing saliva and P. gingivalis, which were anaerobically cultured for one week. Next-generation sequencing was performed to assess microbiota composition, while quantitative real-time PCR was used to measure bacterial concentrations. Additionally, the butyrate concentration in the culture supernatant was assessed as biofilm pathogenicity.

RESULTS: PBE and BC treatments reduced the relative abundance of periodontal pathogenic bacteria, including P. gingivalis, and significantly increased the relative abundance of the genus Streptococcus and nitrate-reducing bacteria, including the genera of Neisseria and Haemophilus. Moreover, the treatment groups exhibited significantly decreased butyrate concentrations.

CONCLUSIONS: Our findings suggest that PBE and BC could suppress dysbiosis triggered by P. gingivalis in microcosm biofilms in vitro by decreasing the relative abundance and amount of periodontal pathogenic bacteria and enhancing those of nitrate-reducing bacteria that have a high relative abundance in orally healthy individuals. In summary, PBE and BC may contribute to the prevention of periodontal disease through their dysbiosis-suppressive and anti-inflammatory effects.},
}

@article {pmid40209638,
year = {2025},
author = {Garlanda, C and Dambra, M and Magrini, E},
title = {Interplay between the complement system and other immune pathways in the tumor microenvironment.},
journal = {Seminars in immunology},
volume = {78},
number = {},
pages = {101951},
doi = {10.1016/j.smim.2025.101951},
pmid = {40209638},
issn = {1096-3618},
abstract = {Tumor growth and spread are sustained by the tumor microenvironment. Inflammatory cells and pathways have a fundamental role in the tumor microenvironment, driving or conditioning the functional activation of other leukocyte subsets and favoring evasion of anti-tumor immunity. One of the inflammatory pathways contributing to cancer-related inflammation is the complement system. Complement has long been considered an immune mechanism associated with immunosurveillance. More recently it emerged as a tumor promoting pathway, due to direct effects on cancer cells or indirect effects via immunosuppression driven by myeloid cells. The role of complement in cancer is complex and ambiguous, and depends on the tumor type and stage, as well as other factors including oncogenic drivers, leukocyte infiltration, interactions with other tumor microenvironment components or tumor cells. Other factors of complexity include the source of complement molecules, its canonical or non-canonical extracellular functions, its potential intracellular activation, and the interaction with other systems, such as the coagulation or the microbiome. Preclinical studies generally demonstrate the involvement of complement activation in smouldering inflammation in cancer and promotion of an immunosuppressive environment. These studies paved the way for clinical trials aimed at enhancing the potential of immunotherapy, in particular by targeting complement-dependent myeloid-sustained immunosuppression. However, the complex role of complement in cancer and the multiplicity of complement players may represent stumbling blocks and account for failures of clinical trials, and suggest that further studies are required to identify patient subsets who may benefit from specific complement molecule targeting in combination with conventional therapies or immunotherapy. Here, we will discuss the anti- or pro-tumor role of complement activation in cancer, focusing on the interactions of complement with immune cells within the tumor microenvironment, in particular the myeloid compartment. Furthermore, we will examine the potential of complement targeting in cancer treatment, particularly in the context of macrophage reprogramming.},
}

@article {pmid40209382,
year = {2025},
author = {Su, C and Kang, J and Liu, S and Li, C},
title = {Exploring the influence of fruit ripeness on the microbiome, bioactive components, and flavor profiles of naturally fermented noni (Morinda citrifolia L.) juice.},
journal = {Food chemistry},
volume = {482},
number = {},
pages = {144192},
doi = {10.1016/j.foodchem.2025.144192},
pmid = {40209382},
issn = {1873-7072},
abstract = {Raw fruit ripeness is an important factor affecting fermented noni fruit juice (FNJ). This study investigated the physicochemical properties, active and volatile components, microbiota, and functional characteristics of FNJ prepared from noni fruits at varying ripening stages. The results showed that deacetylasperulosidic acid (203.54-805.89 mg/L) and asperulosidic acid (102.78-393.41 mg/L) were detected across in all FNJs during fermentation. As noni fruit ripens, the levels of octanoic acid and hexanoic acid in FNJs gradually decreased, while the content of esters significantly increased, particularly during the final stage of ripeness. Metagenomic analysis revealed that Acetobacter sp. and Gluconobacter sp. were core microbes responsible for FNJs, primarily contributing to fatty acid metabolism. Correlation analysis further indicated that the fruit's ripeness significantly influenced its functional properties and volatile components of FNJs. This study offered new insights into selecting the optimal ripeness of noni fruits for the preparation of FNJ and its potential industrial applications.},
}

@article {pmid40209373,
year = {2025},
author = {Wang, L and Pei, H and Xing, T and Chen, D and Chen, Y and Hao, Z and Tian, Y and Ding, J},
title = {Gut bacteria and host metabolism: The keys to sea cucumber (Apostichopus japonicus) quality traits.},
journal = {Food chemistry},
volume = {482},
number = {},
pages = {144178},
doi = {10.1016/j.foodchem.2025.144178},
pmid = {40209373},
issn = {1873-7072},
abstract = {Gut bacteria have a significant impact on modern genetics and contribute to the improvement of aquatic germplasm, which is a key focus for breeders. However, the effects of complex interactions between gut bacteria community and phenotypic trait of aquatic products remain largely unknown. Here, we unravel the association between phenotypic trait, gut microbiota and host metabolic variables of 216 sea cucumbers (Apostichopus japonicus) by Metagenome-wide association studies (MWAS) and Weighted correlation network analysis (WGCNA) methods. Our findings reveal that a total of 14 microbial biomarkers and 201 metabolic markers considered being associated with polysaccharide and collagen content. Among them, Desulfobacterota has the capacity to facilitate the synthesis of octopamine within the neuroactive ligand-receptor metabolic pathway, subsequently influencing polysaccharide content. Additionally, the Lachnospiraceae_NK4A136_group was shown to enhance collagen content through the facilitation of glycine synthesis. In conclusion, this research indicating that precision microbiome management could be a strategy for develop strategies for cultivating high-quality aquatic germplasm.},
}

@article {pmid40209092,
year = {2025},
author = {Jiang, M and Jia, Y and Ma, C and Zeng, Z and Wu, Y and Gan, H and Zhang, H},
title = {Akkermansia muciniphila Protects Against Trinitrobenzene Sulfonic Acid Induced Colitis by Inhibiting IL6/STAT3 Pathway.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf057},
pmid = {40209092},
issn = {1536-4844},
support = {2023YFS0279//Sichuan Province Science and Technology Support Program/ ; },
abstract = {BACKGROUND: Inflammatory bowel disease is a long-standing inflammatory disorder that influences the intestinal tract. The intent of this research is to explore whether the relative abundance of Akkermansia muciniphila is related to the IL6/STAT3 pathway and the fundamental molecular mechanisms of A. muciniphila on a trinitrobenzene sulfonic acid (TNBS)-induced enteritis mouse model, including the expression of inflammatory cytokines and proteins in the IL6/STAT3 signaling pathway.

METHODS: The association between the A. muciniphila and IL6/STAT3 was investigated by using mucosal biopsies and fecal samples. TNBS-induced colitis mouse models were performed to elucidate the underlying mechanisms. The alteration of intestinal microbiota was organized by 16s rRNA sequencing.

RESULTS: In Crohn's disease patients, the level of STAT3 and IL-6 presented a negative relationship with A. muciniphila. The expression of IL-6, p-STAT3, and STAT3 was downregulated in A.m+TNBS group, indicating A. muciniphila may inhibit the IL6/STAT3 pathway in TNBS-induced enteritis in vivo. To investigate the potential defensive role of A. muciniphila supplementation in vivo with TNBS-induced enteritis, 16S rRNA sequencing was performed to analyze changes in the intestinal microbiota composition. The results revealed a marked increase in microbial diversity and abundance within the A. muciniphila-treated group, suggesting a beneficial modulation of the gut microbiome associated with the supplementation.

CONCLUSIONS: Our findings declared that A. muciniphila supplementation alleviates gastrointestinal inflammation through IL-6/STAT3 signaling pathway. This protective effect was mediated by the downregulation of the IL-6 and STAT3, highlighting a potential mechanism by which A. muciniphila modulates inflammatory responses. This work disclosed that A. muciniphila demonstrates a defensive influence against TNBS-induced enteritis in vivo, proposing it qualified as a unique therapeutic focusing on modulating IL-6, STAT3, or p-STAT3 in the treatment of colitis.},
}

@article {pmid40208926,
year = {2025},
author = {Dalman, JM and Blaustein, ER and van Solingen, C},
title = {Gut Instincts: The Gut Microbiome-Cardiovascular Inflammation Axis.},
journal = {Circulation research},
volume = {136},
number = {8},
pages = {806-808},
doi = {10.1161/CIRCRESAHA.125.326363},
pmid = {40208926},
issn = {1524-4571},
}

@article {pmid40208670,
year = {2025},
author = {Jouve, T},
title = {[The highlights of kidney transplantation in 2024].},
journal = {Nephrologie & therapeutique},
volume = {21},
number = {S1},
pages = {18-23},
doi = {10.1684/ndt.2025.111},
pmid = {40208670},
issn = {1872-9177},
abstract = {The year 2024 of kidney transplantation was rich in communications in five main selected fields: immunomonitoring biomarkers, therapeutic innovation with anti-CD38 antibodies, tele-monitoring opportunities, patients’ quality of life and health equity considerations. Two biomarkers were consecrated in 2024: the TorqueTenoVirus (TTV) viral load and donor-derived cell-free DNA (dd-cfDNA). Antibodies directed against CD38 both in the field of desensitization and treatment of antibody-mediated rejection showed promising results and promise further upcoming clinical trials. Tele-monitoring of transplanted patients, with the use of dedicated smartphone applications, suggests new ways to improve the logistic of care together with the quality of care. This notion of patient-reported quality of life is gathering importance in the field. It is associated with the patient’s microbiome, opening new potential treatment opportunities. Finally, ethical considerations bring us to think of quality of care in female kidney transplant recipients: as of 2024, this quality remains insufficient when compared to male recipients.},
}

@article {pmid40208663,
year = {2025},
author = {Seifert, A and Ingram, K and Eko, EN and Nunziato, J and Ahrens, M and Howell, BR},
title = {Impact of maternal obesity and mode of delivery on the newborn skin and oral microbiomes.},
journal = {Journal of medical microbiology},
volume = {74},
number = {4},
pages = {},
doi = {10.1099/jmm.0.002000},
pmid = {40208663},
issn = {1473-5644},
mesh = {Humans ; Female ; Pregnancy ; Infant, Newborn ; *Skin/microbiology ; *Mouth/microbiology ; *Microbiota ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Cesarean Section ; *Delivery, Obstetric/methods ; *Obesity/microbiology ; RNA, Ribosomal, 16S/genetics ; *Pregnancy in Obesity/microbiology ; *Pregnancy Complications/microbiology ; Dysbiosis/microbiology ; Young Adult ; },
abstract = {Introduction. Previous studies have shown vast differences in the skin and oral microbiomes of newborns based on delivery method [Caesarean section (C-section) vs vaginal]. Exposure to or absence of certain bacteria during delivery can impact the neonate's future susceptibility to infections, allergies or autoimmunity by altering immune functions. Few studies have focused on the impact of maternal obesity on the variations of newborn skin and oral microbiomes. Obese pregnant women typically have a higher vaginal microbiome diversity, and their pregnancies are at higher risk for adverse outcomes and complications.Hypothesis. We hypothesized that the skin and oral microbiomes of newborns born to obese mothers would include more diverse, potentially pathogenic bacteria and that the skin and oral microbiome in C-section delivered newborns would be less diverse than vaginally delivered newborns.Aim. We aim to begin to establish maternal obesity and mode of delivery as factors contributing to increased risk for negative newborn outcomes through impacts on newborn bacterial dysbiosis.Methodology. A skin swab was collected immediately following delivery of 39 newborns from 13 healthy weight body mass index (BMI 18.50-24.99), 11 overweight (BMI 25.0-29.99) and 15 obese (BMI ≥30.00) pregnant participants. An oral swab was collected immediately following delivery for 38 of these newborns from 13 healthy weight, 10 overweight and 15 obese pregnant participants. Bacterial genera were identified via 16S rRNA amplicon sequencing.Results. The newborn skin microbiome was comprised of typical skin bacteria (i.e. Corynebacterium). Newborns of obese participants had a higher relative abundance of Peptoniphilus in their skin microbiome compared to newborns of healthy weight participants (P=0.007). Neonates born via C-section had a higher relative abundance of Ureaplasma in their oral microbiome compared to neonates delivered vaginally (P=0.046).Conclusion. We identified differences in the newborn skin and oral microbiomes based on pre-pregnancy BMI and method of delivery. These differences could be linked to an increased risk of allergies, autoimmune disease and infections. Future longitudinal studies will be crucial in determining the long-term impact of these specific genera on newborn outcomes. Understanding these connections could lead to targeted interventions that reduce the risk of adverse outcomes and improve overall health trajectory.},
}

Humans
Female
Pregnancy
Infant, Newborn
*Skin/microbiology
*Mouth/microbiology
*Microbiota
Adult
*Bacteria/classification/genetics/isolation & purification
Cesarean Section
*Delivery, Obstetric/methods
*Obesity/microbiology
RNA, Ribosomal, 16S/genetics
*Pregnancy in Obesity/microbiology
*Pregnancy Complications/microbiology
Dysbiosis/microbiology
Young Adult

@article {pmid40208412,
year = {2025},
author = {Sandu, AM and Chifiriuc, MC and Vrancianu, CO and Cristian, RE and Alistar, CF and Constantin, M and Paun, M and Alistar, A and Popa, LG and Popa, MI and Tantu, AC and Sidoroff, ME and Mihai, MM and Marcu, A and Popescu, G and Tantu, MM},
title = {Healthcare-Associated Infections: The Role of Microbial and Environmental Factors in Infection Control-A Narrative Review.},
journal = {Infectious diseases and therapy},
volume = {},
number = {},
pages = {},
pmid = {40208412},
issn = {2193-8229},
support = {CNFIS-FDI-2024-F-0484 INOVEX//University of Bucharest/ ; Pillar III//Ministry of Research, Innovation and Digitalization through the National Recovery and Resilience Plan (PNRR) of Romania/ ; Component C9/Investment no. 8 (I8) - contract CF 68//Ministry of Research, Innovation and Digitalization through the National Recovery and Resilience Plan (PNRR) of Romania/ ; Project No. RO1567-IBB05/2023//Institute of Biology Bucharest of the Romanian Academy/ ; project no. 23020101//The core program within the National Research Development and Innovation Plan, 2022-2027', carried out with the support of the Ministry of Research, Innovation and Digitalization (MCID),/ ; Contract no. 7N from 3 January 2023//The core program within the National Research Development and Innovation Plan, 2022-2027', carried out with the support of the Ministry of Research, Innovation and Digitalization (MCID),/ ; Dezvoltarea cercetării genomice în România - ROGEN" (Development of genomic research in Romania -ROGEN).//ROGEN/ ; },
abstract = {Healthcare-associated infections (HAIs), previously known as nosocomial infections, represent a significant threat to healthcare systems worldwide, prolonging patient hospital stays and the duration of antimicrobial therapy. One of the most serious consequences of HAIs is the increase in the rate of antibiotic resistance (AR) generated by the prolonged, frequent, and sometimes incorrect use of antibiotics, which leads to the selection of resistant bacteria, making treatment difficult and expensive, with direct consequences for the safety of patients and healthcare personnel. Therefore, timely and accurate diagnosis of HAIs is mandatory to develop appropriate infection prevention and control practices (IPC) and new therapeutic strategies. This review aimed to present the prevalence, risk factors, current diagnosis, including artificial intelligence (AI) and machine learning approaches, future perspectives in combating HAIs causative bacteria (phage therapy, microbiome-based interventions, and vaccination), and HAIs surveillance strategies. Also, we discussed the latest findings regarding the relationships of AR with climate change and environmental pollution in the context of the One Health approach. Phage therapy is an emerging option that can offer an alternative to ineffective antibiotic treatments for antibiotic-resistant bacteria causing HAIs. Clinical trials dealing with vaccine development for resistant bacteria have yielded conflicting results. Two promising strategies, fecal microbiota transplantation and probiotic therapy, proved highly effective against recurrent Clostridium difficile infections and have been shown to reduce HAI incidence in hospitalized patients undergoing antibiotic therapy. Artificial intelligence and machine learning systems offer promising predictive capabilities in processing large volumes of clinical, microbiological, and patient data but require robust data integration. Our paper argues that HAIs are still a global challenge, requiring stringent IPC policies, computer vision, and AI-powered tools. Despite promising avenues like integrated One Health approaches, optimized phage therapy, microbiome-based interventions, and targeted vaccine development, several knowledge gaps in clinical efficacy, standardization, and pathogen complexity remain to be answered.},
}

@article {pmid40208342,
year = {2025},
author = {Zubiria-Barrera, C and Yamba, LY and Klassert, TE and Bos, M and Ahl, J and Wasserstrom, L and Slevogt, H and Riesbeck, K},
title = {Profiling the nasopharyngeal Microbiome in patients with community-acquired pneumonia caused by Streptococcus pneumoniae: diagnostic challenges and ecological insights.},
journal = {Medical microbiology and immunology},
volume = {214},
number = {1},
pages = {19},
pmid = {40208342},
issn = {1432-1831},
mesh = {Humans ; *Nasopharynx/microbiology ; *Community-Acquired Infections/microbiology/diagnosis ; Male ; *Microbiota ; Female ; *Streptococcus pneumoniae/isolation & purification/genetics ; Middle Aged ; Aged ; RNA, Ribosomal, 16S/genetics ; *Pneumonia, Pneumococcal/microbiology/diagnosis ; Adult ; Aged, 80 and over ; DNA, Bacterial/genetics/chemistry ; Community-Acquired Pneumonia ; },
abstract = {Community-acquired pneumonia (CAP) is a significant health threat for adults. Although conjugate vaccines have reduced pneumococcal CAP incidence in children, Streptococcus pneumoniae-related CAP remains prevalent among older adults. The nasopharynx acts as a reservoir for S. pneumoniae, yet the interplay between this pathogen and the nasopharyngeal microbiome during and after pneumonia remains poorly understood. This study included 61 adult patients diagnosed with pneumococcal CAP and 61 matched healthy controls. An S. pneumoniae-specific PCR, urine antigen tests and bacterial cultures were performed. Nasopharyngeal swabs collected at admission and three months post-infection were analyzed for microbiome dynamics through 16 S rRNA gene amplicon sequencing. 16 S rRNA gene amplicon sequencing revealed Streptococcus spp. in the majority of all nasopharyngeal samples during infection compared to the other diagnostic test performed. While overall bacterial biomass did not differ between groups, patients exhibited higher alpha diversity (p = 0.012) and lower microbiome stability post-infection. Beta diversity analysis distinguished infection from healthy status (p = 0.002). Taxonomic analysis showed similar core microbiota across groups, but Streptococcus spp. was significantly more abundant during infection, particularly in those patients with viral co-infections. Notably, unique significant bacterial interactions were identified both during and after infection, as well as in healthy states. A negative correlation was observed between Corynebacterium and Streptococcus spp. in infected patients, suggesting a potential antagonistic interaction between these taxa. The nasopharyngeal microbiome in patients with pneumococcal CAP demonstrates persistent disruption post-infection, characterized by lower resilience three months after acute illness. Additionally, we identified specific bacterial interplays during and after infection that differed from those in healthy donors. These bacterial dynamics might play critical roles in pathogen colonization resistance and infection prevention. Thus, our findings highlight the need for further investigation into microbial interactions and potential microbiome-based therapies for respiratory infections, particularly in vulnerable populations.},
}

Humans
*Nasopharynx/microbiology
*Community-Acquired Infections/microbiology/diagnosis
Male
*Microbiota
Female
*Streptococcus pneumoniae/isolation & purification/genetics
Middle Aged
Aged
RNA, Ribosomal, 16S/genetics
*Pneumonia, Pneumococcal/microbiology/diagnosis
Adult
Aged, 80 and over
DNA, Bacterial/genetics/chemistry
Community-Acquired Pneumonia

@article {pmid40208254,
year = {2025},
author = {Bush, A and Schaub, B},
title = {Approaches to reduce the risk of severe asthma in children with preschool wheeze.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2025.2491722},
pmid = {40208254},
issn = {1747-6356},
abstract = {INTRODUCTION: Asthma is a common, serious condition. We can treat the symptoms of mild-moderate disease, but severe asthma is life-threatening despite treatment. We cannot cure asthma and have no specific preventive strategies.

AREAS COVERED: We performed a PubMed search using the terms 'Severe asthma' and 'Prevention' and 'Preschool wheeze' limited to children, humans and English language over the previous five years. We searched the bibliographies of relevant references and also our personal archives. We cover transgenerational, antenatal and early life factors which increase the risk of pre-school wheeze; the factors promoting or protecting the pre-school wheezer from developing school age asthma; and the factors leading to one of the three types of severe asthma defined by WHO (untreated, difficult to treat, and treatment resistant).

EXPERT OPINION: Currently we have no pharmacological preventive strategies. Risk can be reduced by public health measures such as reduction in smoking and environmental pollution, and there are tantalizing hints from comparison of farming to other environments that exploring how environmental modulation may lead to more specific, personalized strategies. The effects of new RSV prevention strategies are awaited. We need better understanding of the pathways driving disease progression, and biomarkers of risk.

Asthma is one of the commonest non-communicable diseases worldwide and is incurable. We can often treat the symptoms of mild to moderate asthma effectively, but severe asthma may be refractory and severely impair quality of life. Prevention would therefore be optimal. Prevention of severe asthma could be via preventing asthma developing at all or preventing progression to severe disease. The roots of asthma are transgenerational, antenatal and in the early years, and we describe possible ways of intervening to prevent asthma across the developmental spectrum. Significant risk reduction can be achieved by public health measures such as reductions in smoking, air pollution and child poverty but we have no specific personalized therapies to reduce risk. The most promising avenue arises from the observation that babies born on cattle or poultry farms have a low risk of allergies and asthma, perhaps related to increased bacterial and fungal diversity in the environment, and early innate immune stimulation, but more work is needed. If mild-moderate asthma is not to become severe, active, which may be subclinical inflammation needs to be treated aggressively. Also important is education to get the basic management steps, and, especially in low resource settings, ensuring that essential asthma medications are made available.},
}

@article {pmid40208053,
year = {2025},
author = {Xu, K and Motiwala, Z and Corona-Avila, I and Makhanasa, D and Alkahalifeh, L and Khan, MW},
title = {The Gut Microbiome and Its Multifaceted Role in Cancer Metabolism, Initiation, and Progression: Insights and Therapeutic Implications.},
journal = {Technology in cancer research & treatment},
volume = {24},
number = {},
pages = {15330338251331960},
doi = {10.1177/15330338251331960},
pmid = {40208053},
issn = {1533-0338},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Neoplasms/metabolism/therapy/etiology/pathology/microbiology ; Disease Progression ; Animals ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; },
abstract = {This review summarizes the intricate relationship between the microbiome and cancer initiation and development. Microbiome alterations impact metabolic pathways, immune responses, and gene expression, which can accelerate or mitigate cancer progression. We examine how dysbiosis affects tumor growth, metastasis, and treatment resistance. Additionally, we discuss the potential of microbiome-targeted therapies, such as probiotics and fecal microbiota transplants, to modulate cancer metabolism. These interventions offer the possibility of reversing or controlling cancer progression, enhancing the efficacy of traditional treatments like chemotherapy and immunotherapy. Despite promising developments, challenges remain in identifying key microbial species and pathways and validating microbiome-targeted therapies through large-scale clinical trials. Nonetheless, the intersection of microbiome research and cancer initiation and development presents an exciting frontier for innovative therapies. This review offers a fresh perspective on cancer initiation and development by integrating microbiome insights, highlighting the potential for interdisciplinary research to enhance our understanding of cancer progression and treatment strategies.},
}

Humans
*Gastrointestinal Microbiome
*Neoplasms/metabolism/therapy/etiology/pathology/microbiology
Disease Progression
Animals
Dysbiosis/microbiology
Probiotics/therapeutic use
Fecal Microbiota Transplantation

@article {pmid40207973,
year = {2025},
author = {Jamerlan, AM and An, SSA and Hulme, JP},
title = {Microbial diversity and fitness in the gut-brain axis: influences on developmental risk for Alzheimer's disease.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2486518},
doi = {10.1080/19490976.2025.2486518},
pmid = {40207973},
issn = {1949-0984},
mesh = {Humans ; *Alzheimer Disease/microbiology ; *Gastrointestinal Microbiome ; Probiotics/administration & dosage ; *Dysbiosis/microbiology ; *Brain ; Animals ; *Brain-Gut Axis ; *Gastrointestinal Tract/microbiology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {The gut-brain axis (GBA) denotes the dynamic and bidirectional communication system that connects the gastrointestinal tract and the central nervous system (CNS). This review explored this axis, focusing on the role of microbial diversity and fitness in maintaining gastrointestinal health and preventing neurodegeneration, particularly in Alzheimer's disease (AD). Gut dysbiosis, characterized by the imbalance in populations of beneficial and harmful bacteria, has been associated with increased systemic inflammation, neuroinflammation, and the progression of AD through pathogenic mechanisms involving amyloid deposition, tauopathy, and increased blood-brain barrier (BBB) permeability. Emerging evidence highlighted the therapeutic potential of probiotics, dietary interventions, and intermittent fasting in restoring microbial balance, reducing inflammation, and minimizing neurodegenerative risks. Probiotics and synbiotics are promising in helping improve cognitive function and metabolic health, while dietary patterns like the Mediterranean diet were linked to decreased neuroinflammation and enhanced gut-brain communication. Despite significant advancement, further research is needed to elucidate the specific microbial strains, metabolites, and mechanisms influencing brain health. Future studies employing longitudinal designs and advanced omics technologies are essential to developing targeted microbiome-based therapies for managing AD-related disorders.},
}

Humans
*Alzheimer Disease/microbiology
*Gastrointestinal Microbiome
Probiotics/administration & dosage
*Dysbiosis/microbiology
*Brain
Animals
*Brain-Gut Axis
*Gastrointestinal Tract/microbiology
Bacteria/classification/genetics/isolation & purification

@article {pmid40207948,
year = {2025},
author = {Kularatne, BMDN and Hill, JE},
title = {Transformation of Gardnerella vaginalis with a Bifidobacterium-Escherichia coli shuttle vector plasmid.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0048125},
doi = {10.1128/spectrum.00481-25},
pmid = {40207948},
issn = {2165-0497},
abstract = {UNLABELLED: Gardnerella spp. significantly influence female reproductive health and are indicators of bacterial vaginosis, a common gynecological disorder. Lack of genetic tools for Gardnerella spp. is a hindrance to fully understanding their role in the vaginal microbiome, and no naturally occurring plasmids have yet been identified in these organisms. The aim of this study was to transform Gardnerella vaginalis and characterize transformants carrying Bifidobacterium-E. coli shuttle vector pKO403-lacZ'-Sp. G. vaginalis ATCC 49145 was selected for protocol development based on its high growth rate, lack of restriction activity, and susceptibility to spectinomycin. Low efficiency (~10[2] cfu/µg of plasmid DNA) but reproducible transformation was achieved. The expression of the spectinomycin resistance gene and the β-galactosidase gene of pKO403-lacZ'-Sp in G. vaginalis ATCC 49145 resulted in an increase in spectinomycin tolerance from 2 µg/mL (MIC) to >512 µg/mL, and an appreciable increase in β-galactosidase activity compared with the wild type. Plasmid copy number was determined to be ~3 per genome copy. Plasmid was lost rapidly in the absence of spectinomycin selection, with only ~5% of colony-forming units retaining the resistant phenotype after 24 h of growth without selection. These results demonstrate that G. vaginalis can be transformed by electroporation and that pKO403-lacZ'-Sp can be maintained and its genes expressed in this host, offering a starting point for the development of genetic tools for mechanistic studies of this important member of the vaginal microbiome.

IMPORTANCE: The healthy human vaginal microbiome is mainly dominated by Lactobacillus spp. An imbalance or shift in this population can lead to a gynecological disorder known as bacterial vaginosis (BV). In BV, there is a reduction in Lactobacillus spp. and an overgrowth of mixed anaerobes and facultative bacteria including Gardnerella spp. The reason for this increase in the Gardnerella population and associated changes in the vaginal microbiota composition is yet not understood, and a lack of genetic tools is one of the major barriers to performing mechanistic research to study the biology of these clinically significant organisms. The first step in developing genetic tools is introducing foreign DNA. In this study, we have developed a protocol for transformation and identified a plasmid that can be maintained in G. vaginalis.},
}

@article {pmid40207944,
year = {2025},
author = {Koestler, BJ},
title = {Reply to "Overcoming barriers to nicotine-degrading bacteria isolation in oral microbiome research".},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0005425},
doi = {10.1128/jmbe.00054-25},
pmid = {40207944},
issn = {1935-7877},
}

@article {pmid40207943,
year = {2025},
author = {Goyal, H and Mehta, N and Gupta, A and Shrivastava, R and Gautam, V},
title = {Overcoming barriers to nicotine-degrading bacteria isolation in oral microbiome research.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0023924},
doi = {10.1128/jmbe.00239-24},
pmid = {40207943},
issn = {1935-7877},
}

@article {pmid40207941,
year = {2025},
author = {Townsend, EC and Xu, K and De La Cruz, K and Huang, L and Sandstrom, S and Arend, D and Gromek, O and Scarborough, J and Huttenlocher, A and Gibson, ALF and Kalan, LR},
title = {Still not sterile: viability-based assessment of the skin microbiome following pre-surgical application of a broad-spectrum antiseptic reveals transient pathogen enrichment and long-term recovery.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0287324},
doi = {10.1128/spectrum.02873-24},
pmid = {40207941},
issn = {2165-0497},
abstract = {Broad-spectrum antiseptics such as chlorhexidine gluconate (CHG) have widespread use as pre-surgical tools to lower skin microbial burden and reduce the risk of surgical site infection. However, the short- and long-term effects of CHG on healthy skin microbial communities remain undefined due to the confounding effects of CHG binding with persistent bacterial DNA on the skin surface. Here, we aim to accurately characterize the immediate and long-term impact of pre-surgical preparation with CHG-based antiseptics on the human skin microbiome. Twenty-eight patients undergoing elective surgeries were enrolled. Swabs of the surgical site and a control site skin microbiome were collected at multiple time points before and up to 2 weeks after surgery. A propidium monoazide (PMAxx)-based viability assay was optimized to selectively evaluate DNA from live microbes in complex skin microbial communities with viability-qPCR and viable 16S ribosomal RNA gene profiling. Pre-operative CHG induces a measurable reduction in the viable microbial bioburden at the surgical site. On the day of surgery, surgical sites displayed a significant increase in the relative abundance of several SSI-associated bacterial genera including Acinetobacter, Bacillus, Escherichia-Shigella, and Pseudomonas compared to baseline. Bacillus species isolated from subjects at baseline also demonstrate resistance to CHG with minimum inhibitory concentrations exceeding 1,000 µg/mL. Although there are major skin microbiome shifts upon exposure to CHG, we also find that these shifts are largely transient. For the majority of individuals, skin microbial bioburden and community structure recover to near baseline by post-surgical follow-up.IMPORTANCESurgical site infections continue to occur despite widespread adoption of surgical antiseptics. Before surgery, patients often wash their whole body multiple times with chlorhexidine gluconate (CHG)-based antiseptic soap and have CHG applied to the surgical site in the operating room. However, the effects of CHG antiseptics on the healthy skin microbiome are undefined due to CHG persisting and binding DNA from dead cells on the skin. We optimized a viability assay to selectively target DNA from live microbes on the skin before and after exposure to CHG. Our findings demonstrate that pre-surgical application of CHG significantly reduces the bioburden on skin; however, potentially pathogenic bacteria remain. Post-surgery, the skin microbiome eventually recovers to resemble its pre-CHG exposed state. Collectively, these findings identify tangible avenues for improving antiseptic formulations and further support that the skin microbiome is viable, stable, and resilient to chemical perturbation.},
}

@article {pmid40207938,
year = {2025},
author = {Zhao, D and Salas-Leiva, DE and Williams, SK and Dunn, KA and Shao, JD and Roger, AJ},
title = {Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data.},
journal = {mBio},
volume = {},
number = {},
pages = {e0069925},
doi = {10.1128/mbio.00699-25},
pmid = {40207938},
issn = {2150-7511},
abstract = {UNLABELLED: Whole-genome shotgun (WGS) metagenomic sequencing of microbial communities enables the discovery of the functions, physiologies, and evolutionary histories of prokaryotic and eukaryotic microbes. However, metagenomic studies of microbial eukaryotes lag due to challenges in identifying and assembling high-quality genomes from WGS data. To address this problem, we developed Eukfinder, a bioinformatics pipeline that identifies potential eukaryotic sequences from WGS metagenomic data, with a complementary binning workflow for recovering nuclear and mitochondrial genomes. Eukfinder uses two specialized databases for read/contig classification, customizable to specific data sets or environments. We tested Eukfinder on simulated gut microbiome data sets which included varying numbers of reads from the protist Blastocystis, a human gut commensal. We also applied Eukfinder to previously published human gut microbiome WGS metagenomic data to recover new genomes of Blastocystis. Compared to other workflows, Eukfinder offers the potential to recover high-quality, near-complete genomes of diverse eukaryotes, including different Blastocystis subtypes, without relying on a reference genome. With sufficient sequencing depth, Eukfinder outperforms similar tools for recovering eukaryotic genomes from metagenomic data. Eukfinder is a valuable tool for reference-independent and cultivation-free studies of eukaryotic microbial genomes from environmental WGS metagenomic samples.

IMPORTANCE: Advancements in next-generation sequencing have made whole-genome shotgun (WGS) metagenomic sequencing an efficient method for de novo reconstruction of microbial genomes from various environments. Thousands of new prokaryotic genomes have been characterized; however, the large size and complexity of protistan genomes have hindered the use of WGS metagenomics to sample microbial eukaryotic diversity. Eukfinder enables the recovery of eukaryotic microbial genomes from environmental WGS metagenomic samples. Retrieval of high-quality protistan genomes from diverse metagenomic samples increases the number of reference genomes available. This aids future metagenomic investigations into the functions, physiologies, and evolutionary histories of eukaryotic microbes in the gut microbiome and other ecosystems.},
}

@article {pmid40207924,
year = {2025},
author = {Hendricks, A and Philips, TK and Engl, T and Plarre, R( and Martinson, VG},
title = {The bacterial microbiome in spider beetles and deathwatch beetles.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0198124},
doi = {10.1128/spectrum.01981-24},
pmid = {40207924},
issn = {2165-0497},
abstract = {UNLABELLED: The beetle family Ptinidae contains a number of economically important pests, such as the cigarette beetle Lasioderma serricorne, the drugstore beetle Stegobium paniceum, and the diverse spider beetles. Many of these species are stored product pests, which target a diverse range of food sources, from dried tobacco to books made with organic materials. Despite the threat that the 2,200 species of Ptinidae beetles pose, fewer than 50 have been surveyed for microbial symbionts, and only a handful have been screened using contemporary genomic methods. In this study, we screen 116 individual specimens that cover most subfamilies of Ptinidae, with outgroup beetles from closely related families Dermestidae, Endecatomidae, and Bostrichidae. We used 16S ribosomal RNA gene amplicon data to characterize the bacterial microbiomes of these specimens. The majority of these species had never been screened for microbes. We found that, unlike in their sister family, Bostrichidae, that has two mutualistic bacteria seen in most species, there are no consistent bacterial members of ptinid microbiomes. For specimens which had Wolbachia infections, we did additional screening using multilocus sequence typing and showed that our populations have different strains of Wolbachia than noted in previous publications.

IMPORTANCE: Ptinid beetles are both household pests of pantry goods and economic pests of dried goods warehouses and cultural archives, such as libraries and museums. Currently, the most common pest control measures for ptinid beetles are phosphine and/or heat treatments. Many ptinid beetles have been observed to have increasing resistance to phosphine, and heat treatments are not appropriate for many of the goods commonly infested by ptinids. Pest control techniques focused on symbiotic bacteria have been shown to significantly decrease populations and often have the beneficial side effect of being more specific than other pest control techniques. This survey provides foundational information about the bacteria associated with diverse ptinid species, which may be used for future control efforts.},
}

@article {pmid40207916,
year = {2025},
author = {Lebrun-Corbin, M and Cheung, BH and Hullahalli, K and Dailey, KG and Bailey, K and Waldor, MK and Wunderink, RG and Bachta, KER and Hauser, AR},
title = {Pseudomonas aeruginosa population dynamics in a vancomycin-induced murine model of gastrointestinal carriage.},
journal = {mBio},
volume = {},
number = {},
pages = {e0313624},
doi = {10.1128/mbio.03136-24},
pmid = {40207916},
issn = {2150-7511},
abstract = {UNLABELLED: Pseudomonas aeruginosa is a common nosocomial pathogen and a major cause of morbidity and mortality in hospitalized patients. Multiple reports highlight that P. aeruginosa gastrointestinal colonization may precede systemic infections by this pathogen. Gaining a deeper insight into the dynamics of P. aeruginosa gastrointestinal carriage is an essential step in managing gastrointestinal colonization and could contribute to preventing bacterial transmission and progression to systemic infection. Here, we present a clinically relevant mouse model relying on parenteral vancomycin pretreatment and a single orogastric gavage of a controlled dose of P. aeruginosa. Robust carriage was observed with multiple clinical isolates, and carriage persisted for up to 60 days. Histological and microbiological examination of mice indicated that this model indeed represented carriage and not infection. We then used a barcoded P. aeruginosa library along with the sequence tag-based analysis of microbial populations (STAMPR) analytic pipeline to quantify bacterial population dynamics and bottlenecks during the establishment of the gastrointestinal carriage. Analysis indicated that most of the P. aeruginosa population was rapidly eliminated in the stomach, but the few bacteria that moved to the small intestine and the cecum expanded rapidly. Hence, the stomach constitutes a significant barrier against gastrointestinal carriage of P. aeruginosa, which may have clinical implications for hospitalized patients.

IMPORTANCE: While Pseudomonas aeruginosa is rarely part of the normal human microbiome, carriage of the bacterium is quite frequent in hospitalized patients and residents of long-term care facilities. P. aeruginosa carriage is a precursor to infection. Options for treating infections caused by difficult-to-treat P. aeruginosa strains are dwindling, underscoring the urgency to better understand and impede pre-infection stages, such as colonization. Here, we use vancomycin-treated mice to model antibiotic-treated patients who become colonized with P. aeruginosa in their gastrointestinal tracts. We identify the stomach as a major barrier to the establishment of gastrointestinal carriage. These findings suggest that efforts to prevent gastrointestinal colonization should focus not only on judicious use of antibiotics but also on investigation into how the stomach eliminates orally ingested P. aeruginosa.},
}

@article {pmid40207909,
year = {2025},
author = {Spiegelhauer, MR and Offersen, SM and Mao, X and Gambino, M and Sandris Nielsen, D and Nguyen, DN and Brunse, A},
title = {Protection against experimental necrotizing enterocolitis by fecal filtrate transfer requires an active donor virome.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2486517},
doi = {10.1080/19490976.2025.2486517},
pmid = {40207909},
issn = {1949-0984},
mesh = {Animals ; *Enterocolitis, Necrotizing/prevention & control/therapy/microbiology/pathology ; Swine ; Gastrointestinal Microbiome ; *Feces/virology ; *Virome/radiation effects ; *Fecal Microbiota Transplantation/methods ; Disease Models, Animal ; Animals, Newborn ; Virus Inactivation/radiation effects ; Ultraviolet Rays ; Clostridium perfringens ; Humans ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Necrotizing enterocolitis (NEC) remains a frequent catastrophic disease in preterm infants, and fecal filtrate transfer (FFT) has emerged as a promising prophylactic therapy. This study explored the role of virome viability for the protective effect of FFT. Using ultraviolet (UV) irradiation, we established a viral inactivation protocol and administered FFT, UV-inactivated FFT (iFFT) or sterile saline orally to preterm piglets at risk for experimental NEC. The gut pathology and barrier properties were assessed, while the microbiome was explored by 16S rRNA amplicon and metavirome sequencing. Like in prior studies, FFT reduced NEC severity and intestinal inflammation, while these effects were absent in the iFFT group. Unexpectedly, piglets receiving FFT exhibited mild side effects in the form of early-onset diarrhea. The FFT also converged the gut colonization by increased viral heterogeneity and a reduced abundance of pathobionts like Clostridium perfringens and Escherichia. In contrast, the gut microbiome of iFFT recipients diverged from both FFT and the controls. These findings highlight the clear distinction between the ability of active and inactivate viromes to modulate gut microbiota and decrease pathology. The efficacy of FFT may be driven by active bacteriophages, and loss of virome activity could have consequences for the treatment efficacy.},
}

Animals
*Enterocolitis, Necrotizing/prevention & control/therapy/microbiology/pathology
Swine
Gastrointestinal Microbiome
*Feces/virology
*Virome/radiation effects
*Fecal Microbiota Transplantation/methods
Disease Models, Animal
Animals, Newborn
Virus Inactivation/radiation effects
Ultraviolet Rays
Clostridium perfringens
Humans
Bacteria/classification/genetics/isolation & purification

@article {pmid40207877,
year = {2025},
author = {Huang, L and Chen, C and Meng, J and Yan, Q and Luo, G and Sha, S and Xing, Y and Liu, C and Xu, M and Zhao, L and Guo, S and Wu, X and Chen, H and Ma, J and You, W and Zhang, Y and Guo, R and Li, S and Yao, X and Ma, W and Kong, X and Zhou, P and Sun, W},
title = {Metagenome-Based Characterization of the Gut Virome Signatures in Patients With Gout.},
journal = {Journal of medical virology},
volume = {97},
number = {4},
pages = {e70336},
doi = {10.1002/jmv.70336},
pmid = {40207877},
issn = {1096-9071},
support = {//This study was supported by 2024 High-quality Development Project of Shenzhen Bao'an Public Hospital (BAGZL2024138 and BAGZL2024130), National Natural Science Foundation of China (82370563), Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding (JCH22023017), the Key Laboratory of Guizhou Provincial Education Department (Guizhou Education Technology [2023] No. 017), National and Provincial Science and Technology Innovation Talent Team Cultivation Program of Guizhou University of Traditional Chinese Medicine (GZUTCM-TD[2022]004)./ ; },
mesh = {Humans ; *Virome ; *Gastrointestinal Microbiome ; *Gout/virology ; Male ; Middle Aged ; Feces/virology ; Female ; *Metagenome ; Metagenomics ; *Viruses/classification/genetics/isolation & purification ; Adult ; Aged ; Longitudinal Studies ; },
abstract = {The gut microbiome has been implicated in the development of autoimmune diseases, including gout. However, the role of the gut virome in gout pathogenesis remains underexplored. We employed a reference-dependent virome approach to analyze fecal metagenomic data from 102 gout patients (77 in the discovery cohort and 25 in the validation cohort) and 86 healthy controls (HCs) (63 and 23 in each cohort). A subset of gout patients in the discovery cohort provided longitudinal samples at Weeks 2, 4, and 24. Our analysis revealed significant alterations in the gut virome of gout patients, including reduced viral richness and shifts in viral family composition. Notably, Siphoviridae, Myoviridae, and Podoviridae were depleted, while Quimbyviridae, Retroviridae, and Schitoviridae were enriched in gout patients. We identified 359 viral operational taxonomic units (vOTUs) associated with gout. Enriched vOTUs in gout patients predominantly consisted of Fusobacteriaceae, Bacteroidaceae, and Selenomonadaceae phages, while control-enriched vOTUs included Ruminococcaceae, Oscillospiraceae, and Enterobacteriaceae phages. Longitudinal analysis revealed that a substantial proportion of these virome signatures remained stable over 6 months. Functional profiling highlighted the enrichment of viral auxiliary metabolic genes, suggesting potential metabolic interactions between viruses and host bacteria. Notably, gut virome signatures effectively discriminated gout patients from HCs, with high classification performance in the validation cohort. This study provides the first comprehensive characterization of the gut virome in gout, revealing its potential role in disease pathogenesis and highlighting virome-based signatures as promising biomarkers for gout diagnosis and future therapeutic strategies.},
}

Humans
*Virome
*Gastrointestinal Microbiome
*Gout/virology
Male
Middle Aged
Feces/virology
Female
*Metagenome
Metagenomics
*Viruses/classification/genetics/isolation & purification
Adult
Aged
Longitudinal Studies

@article {pmid40207768,
year = {2025},
author = {Phatak, M and Nair, B and Soni, U and Pujari, R},
title = {Exploring the Gut-Brain Axis: Microbiome Contributions to Pathophysiology of Attention Deficit Hyperactivity Disorder and Potential Therapeutic Strategies.},
journal = {Current drug metabolism},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892002361676250325082424},
pmid = {40207768},
issn = {1875-5453},
abstract = {Attention Deficit Hyperactivity Disorder (ADHD) is a prevalent neurodevelopmental disorder characterized by symptoms of hyperactivity, inattention, and impulsivity, significantly impacting individuals' daily functioning and quality of life. This manuscript explores the intricate relationship between the gut microbiome and ADHD, emphasizing the role of the gut-brain axis, a bidirectional communication pathway linking the central nervous system (CNS) and the gastrointestinal tract (GIT). The composition of gut microbiota influences several physiological processes, including immune function, metabolism, and the production of neuroactive metabolites, which are critical for cognitive functions such as memory and decision-making. The review discusses alternative therapeutic options, including dietary modifications, synbiotics, and specific diets like the ketogenic diet, which may offer promising outcomes in managing ADHD symptoms. Further research is necessary to establish the efficacy and mechanisms of action of synbiotics and dietary interventions, despite preliminary studies suggesting their potential benefits. This review article aims to provide a comprehensive overview of the current understanding of the gut microbiome's impact on ADHD, highlighting the need for continued investigation into innovative treatment strategies that leverage the gut-brain connection.},
}

@article {pmid40207766,
year = {2025},
author = {Kumar, M and Mehan, S and Sharma, T and Kumar, A and Khan, Z and Sharma, AK and Kumar, N and Gupta, GD},
title = {Integrating Gut-Brain Axis: Exploring the Neurogastrointestinal Interactions and Therapeutic Potentials in Autism Spectrum Disorder.},
journal = {Endocrine, metabolic & immune disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715303369166250325110016},
pmid = {40207766},
issn = {2212-3873},
abstract = {This comprehensive review critically examines the gut-brain axis (GBA) and its implications in autism spectrum disorder (ASD). The GBA is a complex, bidirectional communication network that integrates the gastrointestinal tract, the central nervous system, and the gut microbiota. This axis is mediated through various physiological pathways, including the enteric nervous system (ENS), the vagus nerve, immune responses, and metabolic activities of gut microorganisms. ASD, a developmental disorder marked by social impairments and repetitive behaviors, presents with notable neurological irregularities. The review highlights the increased prevalence of gastrointestinal (GI) disturbances in individuals with ASD, suggesting a potential link between GI symptoms and the severity of ASD-related behaviors. This correlation is supported by evidence of altered gut microbiota composition in ASD, indicating significant interactions between the gut environment and neurological health. Moreover, the pathophysiology of ASD is explored with an emphasis on genetic and environmental contributions to neurodevelopmental impairments. Key topics include synaptic dysfunction, the roles of neurotransmitters like GABA and serotonin, and the impact of gut-brain interactions on ASD progression. Specifically, this review addresses how gut microbiota may influence metabolic alterations, immune dysregulation, oxidative stress, mitochondrial function, and neurotransmitter production in ASD. Emerging research on microbiome-based therapies for ASD is discussed, focusing on the potential of probiotics, prebiotics, and faecal microbiota transplantation (FMT) as novel interventions. Ethical considerations in this burgeoning field are also considered, highlighting the necessity for rigorous scientific inquiry and ethical oversight. The review advocates for a multidisciplinary approach to understanding and addressing the complexities of ASD. By integrating insights from genetics, neuroscience, psychology, and gastroenterology, a more comprehensive understanding of the role of GBA in ASD can be achieved. This interdisciplinary perspective is crucial for developing effective, individualized treatments and improving the quality of life for individuals with ASD.},
}

@article {pmid40207754,
year = {2025},
author = {V S, S and Prasad, C and Panicker, SP},
title = {Exploring the Role of Non-Coding RNAs in the Gut and Skin Microbiome: Implications for Colorectal Cancer and Healthy Longevity.},
journal = {MicroRNA (Shariqah, United Arab Emirates)},
volume = {},
number = {},
pages = {},
doi = {10.2174/0122115366342509250401043719},
pmid = {40207754},
issn = {2211-5374},
abstract = {In the last forty years, cancer mortality rates have risen by more than 40%, with colo-rectal cancer (CRC) ranking as the third most common kind worldwide, significantly affected by dietary factors. Restricted access to sophisticated medical treatment and insufficient comprehen-sion of colorectal cancer's biology contribute to its elevated occurrence. Researchers have recog-nized dysbiosis of the gut microbiome as a critical contributor to the development of colorectal cancer, as it influences the expression of non-coding RNAs (ncRNAs) and subsequent molecular pathways essential for tumor proliferation. Moreover, interactions between gut and skin microbi-ota can impact systemic health and ncRNA regulation, influencing CRC advancement. This study shows how important the gut-skin microbiome axis is in developing colorectal cancer. It suggests that targeting this axis may lead to new treatments, such as changing the microbiome through probiotics, prebiotics, or fecal microbiota transplantation. Nonetheless, we must address obstacles such as population heterogeneity and intricate microbiome-host interactions to facilitate the tran-sition of these medicines into clinical practice. This study seeks to elucidate the roles of dietary treatments, microbiomes, and ncRNAs in the etiology and prevention of colorectal cancer (CRC).},
}

@article {pmid40207751,
year = {2025},
author = {Huang, Y and Guo, H and Liu, Y and Jin, W and Palanisamy, CP and Pei, J and Oz, F and Abd El-Aty, AM},
title = {Effects of Natural Polysaccharides on the Gut Microbiota Related to Human Metabolic Health.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e202400792},
doi = {10.1002/mnfr.202400792},
pmid = {40207751},
issn = {1613-4133},
support = {2023-JC-ZD-13//Key Basic Research Project of Shaanxi Provinci-al Department of Science and Technology / ; JP//Special Support Plan for High-Level Talent in Shaanxi Province/ ; //Foreign Expert Project of the Ministry of Science and Technology/ ; },
abstract = {Natural polysaccharides (NPs) are sugar chains bound by glycosidic bonds that are composed of at least 10 monosaccharides and have broad biological activity. The human body microbiome is a complex ecosystem that plays a role in host metabolism, immunity, and other important life activities. Numerous studies have demonstrated an obvious relationship between the gut flora and the occurrence of many human diseases. Many studies have reviewed and investigated the effects of polysaccharides on the microbiome, but the underlying mechanisms remain unclear. Most of these studies have focused on the effects of NPs on microbes, as they are important "foods" for the intestinal flora. However, polysaccharides can also affect microbes by improving gut homeostasis. Therefore, the purpose of this review is to introduce recent research that looks at how NPs affect microbiomes by directly acting as fermentation substrates and enhancing gut homeostasis. In addition, this study provides a succinct summary of NP extraction, purification, and structural characteristics, as well as a discussion of their structure‒activity correlations. This study also sheds light on future directions and obstacles in the use of NPs with protective properties, with the aim of providing insights into their potential applications in disease treatment.},
}

@article {pmid40207550,
year = {2025},
author = {Pletsch, EA and Dawson, HD and Cheung, L and Ragonese, JS and Chen, CT and Smith, AD},
title = {A type 4 resistant potato starch alters the cecal microbiome, gene expression and resistance to colitis in mice fed a Western diet based on NHANES data.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo04697h},
pmid = {40207550},
issn = {2042-650X},
abstract = {Four major types of resistant starch (RS1-4) are present in foods and can be fermented to produce short-chain fatty acids (SCFAs), alter the microbiome and modulate post-prandial glucose metabolism. While studies in rodents have examined the effects of RS4 consumption on the microbiome, fewer have examined its effect on gene expression in the cecum or colon or resistance to bacterial-induced colitis, and those that have, use diets that do not reflect what is typically consumed by humans. Here we fed mice a Total Western Diet (TWD), based on National Health and Nutrition Examination Survey (NHANES) data for 6-7 weeks and then supplemented their diet with 0, 2, 5, or 10% of the RS4, Versafibe 1490™ (VF), a phosphorylated and cross-linked potato starch. After three weeks, mice were infected with Citrobacter rodentium (Cr) to induce colitis. Infected mice fed the 10% VF diet had the highest levels of Cr fecal excretion at days 4, 7 and 11 post-infection. Infected mice fed the 5% and 10%VF diets had increased hyperplasia and colonic damage compared with the control. Changes in bacterial genera relative abundance, and alpha and beta diversity due to diet were most evident in mice fed 10% VF. Cr infection also resulted in specific changes to the microbiome and gene expression both in the cecum and the colon compared with diet alone, including the expression of multiple antimicrobial genes, Reg3b, Reg3g, NOS2 and Ifng. These results demonstrate that VF, a RS4, alters cecal and colonic gene expression, the microbiome composition and resistance to bacterial-induced colitis.},
}

@article {pmid40207496,
year = {2025},
author = {Patra, S and Chaudhary, S and Samal, SC and Ayyanar, P and Padhi, S and Nayak, HK and Satapathy, AK and Nayak, S and Sahu, A and Parida, T and Shahin, M},
title = {FoxP3-positive T regulatory cells and its effector mechanisms in Crohn's disease: an immunohistochemical and image morphometric analysis on endoscopic mucosal biopsies.},
journal = {European journal of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MEG.0000000000002971},
pmid = {40207496},
issn = {1473-5687},
abstract = {OBJECTIVE: Crohn's disease (CD) is an immune inflammatory disorder of the gastrointestinal tract arising from a complex interplay of genetic, environmental, microbiome, and immune factors. Regulatory T cells (Tregs), characterized by FoxP3 expression, are crucial for maintaining immune homeostasis through PD-1/PD-L1 interaction, interleukin (IL)-10 release, and granzyme (GrB) production. This study aimed to elucidate the role of FoxP3 positive (+) Tregs in CD.

METHODS: Segmental colonoscopic biopsies from 46 treatment-naive CD cases (34 adults and 12 children) categorized into noninflamed [n = 32; Nancy histologic index (NHI) 0, 1] and inflamed (n = 100; NHI 2-4) mucosae using NHI. CD4, FoxP3, PD-1, IL-10, and GrB immunoexpression were analyzed by eyeballing and image morphometry. Findings were correlated with activity, granulomas, and skip lesions; and compared with site-matched non-inflammatory bowel disease (IBD) controls (n = 30).

RESULTS: FoxP3+ Tregs, IL-10, PD-1, and GrB expressions were significantly higher in NHI 3-4 mucosae than in NHI 0-1 and controls (P < 0.05). No significant differences were observed between adults and children, whereas those with granulomas had increased expression (P = 0.045). The FoxP3 : CD4 ratio positively correlated with IL-10 (Spearman, r = 0.307, P = 0.002), GrB (r = 0.302, P = 0.002), but not with PD-1 (r = 0.98, P = 0.33).

CONCLUSIONS: Our findings point to the possibility of a qualitative defect in FoxP3+ Tregs in CD. The functional arms of Tregs in CD need to be elucidated further in larger prospective cohorts to validate our observations and pave the way for future immunotherapy.},
}

@article {pmid40207282,
year = {2025},
author = {Stuivenberg, GA and Poon, A and Burton, JP and Spence, JD},
title = {Potential effects of probiotics on atherosclerosis.},
journal = {Microbiome research reports},
volume = {4},
number = {1},
pages = {11},
pmid = {40207282},
issn = {2771-5965},
abstract = {The rising global incidence of atherosclerosis highlights the inadequacies in our understanding of the pathophysiology and treatment of the disease. Increasing evidence outlines the importance of the intestinal microbiome in atherosclerosis, wherein gut-derived uremic toxins (GDUTs) may be of concern. Plasma levels of the GDUTs trimethylamine n-oxide (TMAO), p-cresyl sulfate, and indoxyl sulfate are associated with accelerated renal function decline and increased cardiovascular risk. Thus, reducing the amount of GDUTs in circulation is expected to benefit patients with atherosclerosis. Because some beneficial bacteria can clear GDUTs in vitro and in vivo, orally administered probiotics targeting the intestinal tract represent a promising way to bring about these changes. Atherosclerosis such, this perspective reviews the potential use of probiotics to treat atherosclerosis, particularly in patients with non-traditional risk factors and/or impaired renal function.},
}

@article {pmid40207280,
year = {2025},
author = {Abbas, M and Tangney, M},
title = {The oncobiome; what, so what, now what?.},
journal = {Microbiome research reports},
volume = {4},
number = {1},
pages = {16},
pmid = {40207280},
issn = {2771-5965},
abstract = {Microbial communities inhabiting various body sites play critical roles in the initiation, progression, and treatment of cancer. The gut microbiota, a highly diverse microbial ecosystem, interacts with immune cells to modulate inflammation and immune surveillance, influencing cancer risk and therapeutic outcomes. Local tissue microbiota may impact the transition from premalignant states to malignancy. Characterization of the intratumoral microbiota increasingly reveals distinct microbiomes that may influence tumor growth, immune responses, and treatment efficacy. Various bacteria species have been reported to modulate cancer therapies through mechanisms such as altering drug metabolism and shaping the tumor microenvironment (TME). For instance, gut or intratumoral bacterial enzymatic activity can convert prodrugs into active forms, enhancing therapeutic effects or, conversely, inactivating small-molecule chemotherapeutics. Specific bacterial species have also been linked to improved responses to immunotherapy, underscoring the microbiome's role in treatment outcomes. Furthermore, unique microbial signatures in cancer patients, compared with healthy individuals, demonstrate the diagnostic potential of microbiota. Beyond the gut, tumor-associated and local microbiomes also affect therapy by influencing inflammation, tumor progression, and drug resistance. This review explores the multifaceted relationships between microbiomes and cancer, focusing on their roles in modulating the TME, immune activation, and treatment efficacy. The diagnostic and therapeutic potential of bacterial members of microbiota represents a promising avenue for advancing precision oncology and improving patient outcomes. By leveraging microbial biomarkers and interventions, new strategies can be developed to optimize cancer diagnosis and treatment.},
}

@article {pmid40207278,
year = {2025},
author = {Bocchio, F and Mancabelli, L and Milani, C and Lugli, GA and Tarracchini, C and Longhi, G and Conto, F and Turroni, F and Ventura, M},
title = {Compendium of Bifidobacterium-based probiotics: characteristics and therapeutic impact on human diseases.},
journal = {Microbiome research reports},
volume = {4},
number = {1},
pages = {2},
pmid = {40207278},
issn = {2771-5965},
abstract = {The human microbiota, a complex community of microorganisms residing in and on the human body, plays a crucial role in maintaining health and preventing disease. Bifidobacterium species have shown remarkable therapeutic potential across a range of health conditions, thus being considered optimal probiotic bacteria. This review provides insights into the concept of probiotics and explores the impact of bifidobacteria on human health, focusing on the gastrointestinal, respiratory, skeletal, muscular, and nervous systems. It also integrates information on the available genetic bases underlying the beneficial effects of each bifidobacterial probiotic species on different aspects of human physiology. Notably, Bifidobacterium-based probiotics have proven effective in managing gastrointestinal conditions such as constipation, antibiotic-associated diarrhea, irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and Helicobacter pylori infections. These benefits are achieved by modulating the intestinal microbiota, boosting immune responses, and strengthening the gut barrier. Moreover, Bifidobacterium species have been reported to reduce respiratory infections and asthma severity. Additionally, these probiotic bacteria offer benefits for skeletal and muscular health, as evidenced by Bifidobacterium adolescentis and Bifidobacterium breve, which have shown anti-inflammatory effects and symptom relief in arthritis models, suggesting potential in treating conditions like rheumatoid arthritis. Furthermore, probiotic therapies based on bifidobacterial species have shown promising effects in alleviating anxiety and depression, reducing stress, and enhancing cognitive function. Overall, this review integrates the extensive scientific literature now available that supports the health-promoting applications of probiotic Bifidobacterium species and underscores the need for further research to confirm their clinical efficacy across different body systems.},
}

@article {pmid40207277,
year = {2025},
author = {Rachmühl, C and Lacroix, C and Ferragamo, A and Giorgetti, A and Stoffel, NU and Zimmermann, MB and Brittenham, GM and Geirnaert, A},
title = {Galacto-oligosaccharides alone and combined with lactoferrin impact the Kenyan infant gut microbiota and epithelial barrier integrity during iron supplementation in vitro.},
journal = {Microbiome research reports},
volume = {4},
number = {1},
pages = {9},
pmid = {40207277},
issn = {2771-5965},
abstract = {Aim: Iron supplementation to African weaning infants was associated with increased enteropathogen levels. While cohort studies demonstrated that specific prebiotics inhibit enteropathogens during iron supplementation, their mechanisms remain elusive. Here, we investigated the in vitro impact of galacto-oligosaccharides (GOS) and iron-sequestering bovine lactoferrin (bLF) alone and combined on the gut microbiota of Kenyan infants during low-dose iron supplementation. Methods: Different doses of iron, GOS, and bLF were first screened during batch fermentations (n = 3), and the effect of these factors was studied on microbiota community structure and activity in the new Kenyan infant continuous intestinal PolyFermS model. The impact of different fermentation treatments on barrier integrity, enterotoxigenic Escherichia coli (ETEC) infection, and inflammatory response was assessed using a transwell co-culture of epithelial and immune cells. Results: A dose-dependent increase in short-chain fatty acid (SCFA) production, Bifidobacterium and Lactobacillus/Leuconostoc/Pediococcus (LLP) growth was detected with GOS alone and combined with bLF during iron supplementation in batches. This was confirmed in the continuous PolyFermS model, which also showed a treatment-induced inhibition of opportunistic pathogens C. difficile and C. perfringens. In all tests, supplementation of iron alone and combined with bLF did not have a significant effect on microbiota composition and activity. We observed a strengthening of the epithelial barrier and a decrease in cell death and pro-inflammatory response during ETEC infection with microbiota fermentation supernatants from iron + GOS, iron + bLF, and iron + GOS + bLF treatments compared to iron alone. Conclusion: Overall, beneficial effects on infant gut microbiota were shown using advanced in vitro models for GOS alone and combined with bLF during low-dose iron supplementation.},
}

@article {pmid40207275,
year = {2025},
author = {Horwell, E and Bearn, P and Cutting, SM},
title = {A microbial symphony: a literature review of the factors that orchestrate the colonization dynamics of the human colonic microbiome during infancy and implications for future health.},
journal = {Microbiome research reports},
volume = {4},
number = {1},
pages = {1},
pmid = {40207275},
issn = {2771-5965},
abstract = {Since the advent of new sequencing and bioinformatic technologies, our understanding of the human microbiome has expanded rapidly over recent years. Numerous studies have indicated causal links between alterations to the microbiome and a range of pathological conditions. Furthermore, a large body of epidemiological data is starting to suggest that exposure, or lack thereof, to specific microbial species during the first five years of life has key implications for long-term health outcomes. These include chronic inflammatory and metabolic conditions such as diabetes, asthma, inflammatory bowel disease (IBD), and obesity, with the effects lasting into adulthood. Human microbial colonisation during these first five years of life is a highly dynamic process, with multiple environmental exposures recently being characterised to have influence before the microbiome stabilises and resembles that of an adult at 3-5 years. This short period of time, known as the window of opportunity, appears to "prime" immunoregulation for later life. Understanding and appreciating this aspect of human physiology is therefore crucial for clinicians, scientists, and public health officials. This review outlines the most recent evidence for the pre- and post-natal environments that order the development of the microbiome, how these influences metabolic and immunoregulatory pathways, and their associated health outcomes. It also discusses the limitations of the current knowledge base, and describes the potential microbiome-mediated interventions and public health measures that may have therapeutic potential in the future.},
}

@article {pmid40207273,
year = {2025},
author = {van Beek, N and Katavisto, I and Lehto, M and Kolho, KL and de Vos, WM and Salonen, A and Korpela, K},
title = {Host-microbiota interactions in the infant gut revealed by daily faecal sample time series.},
journal = {Microbiome research reports},
volume = {4},
number = {1},
pages = {13},
pmid = {40207273},
issn = {2771-5965},
abstract = {Aim: This study aims to explore the interplay between host immune factors and gut microbiota in human infants in vivo using time-series daily stool samples and identify biomarkers of host-microbe interactions. Methods: 216 faecal samples collected from infants aged 5-6 or 11-12 months were analysed for gut microbiota composition, total bacterial load, and biomarkers of immune function. Results: We identified indications of microbial stimulation of eosinophil cationic protein (ECP), IgA, calprotectin (Cal), intestinal alkaline phosphatase (IAP), and Bactericidal/permeability-increasing protein (BPI) at 6 and 12 months, as well as stimulation of lipocalin 2 (LCN2), lactoferrin (LTF), and alpha-defensin-5 only at 6 months. The associations between biomarker concentrations and bacterial population growth were primarily positive at 6 months and mostly negative at 12 months, suggesting increasing host regulation of the microbiota with age. The exceptions were IAP, which was predictive of declining bacterial populations at both time points, and Cal, whose associations changed from negative at 6 months to positive at 12 months. Conclusion: There is an age-associated development in the correlation pattern between bacterial population growth and the biomarker concentrations, suggesting that host-microbe interactions change during early development. Albumin appeared as a potential marker of gut permeability, while LCN2 seemed to correlate with gut transit time. Mucin degradation appeared to decrease with age. Mucin2 and IAP emerged as potentially important regulators of the bacterial populations in the infant gut. The study demonstrates the utility of biomarker and bacteria profiling from daily stool samples for analysing in vivo associations between the immune system and the gut microbiota and provides evidence of host regulation of the microbiota in infants.},
}

@article {pmid40207272,
year = {2025},
author = {Kreuze, K and Friman, VP and Vatanen, T},
title = {Mobile genetic elements: the hidden puppet masters underlying infant gut microbiome assembly?.},
journal = {Microbiome research reports},
volume = {4},
number = {1},
pages = {7},
pmid = {40207272},
issn = {2771-5965},
abstract = {The gut microbiota is important for healthy infant development. Part of the initial colonizing microbial strains originate from the maternal gut, and undergo a selective event, termed the "colonization bottleneck". While vertical mother-to-infant inheritance and subsequent colonization of bacteria have previously been studied, the role of mobile genetic elements (MGEs) in the infant gut microbiota assembly is unclear. In this perspective article, we discuss how horizontally and vertically transmitted phages and conjugative elements potentially have important roles in infant gut microbiota assembly and colonization through parasitic and mutualistic interactions with their bacterial hosts. While some of these MGEs are likely to be detrimental to their host survival, in other contexts, they may help bacteria colonize new niches, antagonize other bacteria, or protect themselves from other parasitic MGEs in the infant gut. As a result, the horizontal transfer of MGEs likely occurs at high rates in the infant gut, contributing to gene transfer between bacteria and affecting which bacteria can pass the colonization bottleneck. We conclude by highlighting the potential in silico, in vitro, and in vivo methodological approaches that could be employed to study the transmission and colonization dynamics of MGEs and bacteria in the infant gut.},
}

@article {pmid40207271,
year = {2025},
author = {Chen, J and van Wesemael, AJ and Denswil, NP and Niemarkt, HJ and van Goudoever, JB and Muncan, V and de Meij, TGJ and van den Akker, CHP},
title = {Impact of mother's own milk vs. donor human milk on gut microbiota colonization in preterm infants: a systematic review.},
journal = {Microbiome research reports},
volume = {4},
number = {1},
pages = {8},
pmid = {40207271},
issn = {2771-5965},
abstract = {Background: Nutritional intake in preterm infants is associated with short- and long-term outcomes. The favorable outcomes of preterm infants who predominantly receive their mother's own milk (MOM) are thought to be mediated partly through beneficial effects on the gut microbiome. When MOM is not available, donor human milk (DHM) is recommended as the best alternative. However, DHM is less effective in preventing adverse outcomes, which may be explained by compositional differences between MOM and DHM, resulting in different microbiome development. This systematic review focuses on the effects of predominant DHM vs. MOM feeding on the gut microbiota composition in preterm infants. Methods: A comprehensive search was conducted across MEDLINE, Embase, and Cochrane databases. Eight out of the 717 publications identified were included. Data on gut microbiota composition, alpha diversity, and taxonomic differences between DHM- and MOM-fed preterm infants were extracted and analyzed. Results: The microbiome composition was distinct between the two feeding groups. Alpha diversity measures were lower in DHM-fed infants, particularly when preterm formula (PF) was also provided. DHM-fed infants showed higher abundances of Staphylococcaceae and Clostridiaceae, and lower abundances of Bacteroidetes and Bifidobacterium. Conclusion: The observed gut microbiome differences in DHM-fed preterm infants have previously been linked to adverse health outcomes. This underlines the importance of increasing the awareness of MOM intake in preterm infants. Further studies should explore the mechanisms through which human milk affects health outcomes.},
}

@article {pmid40207154,
year = {2025},
author = {Ahn, JS and Han, EJ and Chung, HJ},
title = {Comparison of metagenomic analysis of fecal and gastrointestinal tract samples for identifying beneficial gut microorganisms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1533580},
pmid = {40207154},
issn = {1664-302X},
abstract = {INTRODUCTION: Previous research on the gut microbiome has primarily focused on fecal microbiota, raising concerns about whether fecal samples accurately represent the entire intestinal microbiota. Studies have shown that microbial communities across the gastrointestinal (GI) tract are more diverse than those in feces, suggesting that microbial composition may vary depending on the sampling method. Additionally, analyzing the broader diversity of microbial communities in the GI tract may enhance the identification of potentially beneficial microbiota.

METHODS: In this study, we compare gut microbiome datasets obtained from fecal samples and GI samples (collected by pooling luminal contents and mucosal scrapings from the stomach to the end of the colon) of 6-month-old mice using 16S rRNA sequencing. We further investigate the associations between gut microbiota and motor, cognitive, and emotional functions in mice, examining differences between the two sample types. To assess these variations, we apply DESeq2 analysis to identify microbial species enriched in high-functioning groups and evaluate how their selection may differ depending on the sampling approach.

RESULTS: Our findings reveal notable differences in microbial composition between fecal and GI samples, suggesting that sampling methods may influence the identification of beneficial bacteria.

DISCUSSION: These results highlight the importance of selecting an appropriate sampling approach in microbiome research to ensure a comprehensive understanding of gut microbiota-host interactions.},
}

@article {pmid40207016,
year = {2025},
author = {Zhou, X and Tian, W and Gu, S and Rabinovitch, M and Nicolls, MR and Snyder, MP},
title = {Microbiome-Immune Interaction in Pulmonary Arterial Hypertension: What Have We Missed?.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0669},
pmid = {40207016},
issn = {2639-5274},
abstract = {Pulmonary arterial hypertension (PAH) is a devastating disease characterized by perivascular inflammation, immune dysregulation, and vascular remodeling. Recent studies have unveiled a potential link between the gut microbiome and PAH pathogenesis, suggesting that microbial dysbiosis and increased intestinal permeability may contribute to the inflammatory pathology in PAH and ultimately disease progression. This perspective highlights the emerging evidence of the role of leaky gut in PAH, the interplay between microbiota-induced immune responses, and the activation of endogenous retroviruses like human endogenous retrovirus K. Understanding these complex interactions opens new interdisciplinary avenues for research and therapeutic interventions, potentially transforming PAH management through microbiome-targeted strategies.},
}

@article {pmid40206877,
year = {2025},
author = {Shi, M and Qin, T and Pu, Z and Yang, Z and Lim, KJ and Yang, M and Wang, Z},
title = {Salt stress alters the selectivity of mature pecan for the rhizosphere community and its associated functional traits.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1473473},
pmid = {40206877},
issn = {1664-462X},
abstract = {INTRODUCTION: Salt stress is a major global environmental factor limiting plant growth. Rhizosphere bacteria, recruited from bulk soil, play a pivotal role in enhancing salt stress resistance in herbaceous and crop species. However, whether the rhizosphere bacterial community of a mature tree can respond to salt stress, particularly in saline-alkalitolerant trees, remains unexplored. Pecan (Carya illinoinensis), an important commercially cultivated nut tree, is considered saline-alkali tolerant.

METHODS: Pecan trees (12 years) were subjected to different NaCl concentrations for 12 weeks. Collected samples included bulk soil, rhizosphere soil, roots, leaves, and fruit. Amplicon sequencing data and shotgun metagenomic sequencing data obtained from the samples were investigated: 1) microbial communities in various ecological niches of mature pecan trees; 2) the characteristic of the rhizosphere bacteria community and the associated functional traits when pecan suffered from salt stress.

RESULTS AND DISCUSSION: We characterized the mature pecan-associated microbiome (i.e., fruit, leaf, root, and rhizosphere soil) for the first time. These findings suggest that niche-based processes, such as habitat selection, drive bacterial and fungal community assembly in pecan tissues. Salt stress reduced bacterial diversity, altered community composition, and shifted pecan's selective pressure on Proteobacteria and Actinobacteria. Shotgun metagenomic sequencing further revealed functional traits of the rhizosphere microbiome in response to salt stress. This study enhances our understanding of mature tree-associated microbiomes and supports the theory that shaping the rhizosphere microbiome may be a strategy for saline-alkali-tolerant mature trees to resist salt stress. These findings provide insights into salt tolerance in mature trees and suggest potential applications, such as the development of bio-inoculants, for managing saline environments in agricultural and ecological contexts.},
}

@article {pmid40206649,
year = {2025},
author = {Gao, T and Xiang, H and Wu, QN and Zhu, LS and Pei, WJ and Fu, WJ and Chou, TS},
title = {Advances in the research of comorbid insomnia and depression: mechanisms, impacts, and interventions.},
journal = {Frontiers in psychiatry},
volume = {16},
number = {},
pages = {1468212},
pmid = {40206649},
issn = {1664-0640},
abstract = {Insomnia and depression, both significantly impacting public health, are common psychosomatic illnesses that frequently co-occur in the same individual. Not only do these two conditions commonly co-occur, but they also exhibit a bidirectional link, where the existence of one may heighten the risk for the other. Latest research offers compelling evidence of significant overlap in biological, psychological, and sociological aspects in the comorbidity of insomnia and depression. Building on this, we aim to examine the pathophysiology of insomnia and depression, along with their comorbid mechanisms, encompassing biological routes (like genetics, HPA axis, immune-inflammatory activation, neuroendocrine regulation, microbiome alterations, and neural circuits integrating sleep and emotion regulation), as well as psychosocial routes. Consequently, proposing a self-perpetuating and mutually reinforcing "snowball effect" model of comorbid insomnia and depression, and examining corresponding preventative intervention strategies to rectify associated imbalances. Finally, this article encapsulates the challenges in this field of study and the directions for future research. Finally, the paper points out the limitations of current research (cross-sectional data being dominant, and the mechanism of multi-omics dynamics being unknown) and the future direction (longitudinal cohort combined with computational modeling to resolve temporal interactions), which will provide a theoretical basis for precision interventions.},
}

@article {pmid40206504,
year = {2025},
author = {Cummings, CL and Landreville, KD and Kuzma, J},
title = {Natural vs. genetically engineered microbiomes: understanding public attitudes for indoor applications and pathways for future engagement.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1560601},
pmid = {40206504},
issn = {1664-8021},
abstract = {This study examines public preferences for natural microbiomes and support for genetically engineered (GE) microbiomes in the built environment, focusing on the demographic, sociographic, and attitudinal factors that influence these preferences. Using data from a nationally representative survey of 1,000 U.S. adults, we employed hierarchical regression analyses to assess the relative contribution of these variables. While demographic and sociographic factors explained limited variance, topic-specific attitudes, including positive perceptions of microbiome engineering's potential to improve quality of life, were the most significant predictors of support. Conversely, age, distrust in science, and perceived knowledge negatively influenced support for GE microbiomes, reflecting skepticism among some audiences. The findings highlight the potential of the Responsible Research and Innovation (RRI) framework to align the development of microbiome engineering with societal values and to address diverse public perspectives. This research provides actionable insights for policymakers, researchers, and communicators seeking to navigate the complexities of public engagement with emerging biotechnologies.},
}

@article {pmid40206278,
year = {2025},
author = {Cresci, GAM and Liu, Q and Sangwan, N and Liu, D and Grove, D and Shapiro, D and Ali, K and Cazzaniga, B and Prete, LD and Miller, C and Hashimoto, K and Quintini, C},
title = {The Impact of Liver Graft Preservation Method on Longitudinal Gut Microbiome Changes Following Liver Transplant: A Proof-of-concept Study.},
journal = {Journal of clinical and translational hepatology},
volume = {13},
number = {4},
pages = {284-294},
pmid = {40206278},
issn = {2310-8819},
abstract = {BACKGROUND AND AIMS: End-stage liver disease is associated with disruptions in gut microbiota composition and function, which may facilitate gut-to-liver bacterial translocation, impacting liver graft integrity and clinical outcomes following liver transplantation. This study aimed to assess the impact of two liver graft preservation methods on fecal microbiota and changes in fecal and breath organic acids following liver transplantation.

METHODS: This single-center, non-randomized prospective pilot study enrolled liver transplant patients whose grafts were preserved using either static cold storage or ex situ normothermic machine perfusion (NMP). Fresh stool and breath samples were collected immediately before surgery and at postoperative months 3, 6, and 12. Stool microbiota was profiled via 16S rRNA gene sequencing, stool short-chain fatty acids were measured using gas chromatography/-mass spectrometry, and breath volatile organic compounds (VOCs) were analyzed with selected-ion flow-tube mass spectrometry.

RESULTS: Both cohorts experienced a loss of microbiota diversity and dominance by single taxa. The NMP cohort demonstrated enrichment of several beneficial gut taxa, while the static cold storage cohort showed depletion of such taxa. Various gut bacteria were found to correlate with stool short-chain fatty acids (e.g., lactic acid, butyric acid) and several VOCs.

CONCLUSIONS: Fecal microbiota alterations associated with end-stage liver disease do not fully normalize to a healthy control profile following liver transplantation. However, notable differences in microbiota composition and function were observed between liver graft preservation methods. Future research with larger randomized cohorts is needed to explore whether the NMP-associated shift in gut microbiota impacts clinical outcomes and if breath VOCs could serve as biomarkers of the clinical trajectory in liver transplant patients.},
}

@article {pmid40206252,
year = {2025},
author = {Wang, L and Qu, M and Li, L and Mei, W and Zhang, F and Hu, Z and Li, G and Xu, L and Liang, H},
title = {Effects of glycyrrhetinic acid on production performance, serum biochemical indexes, ruminal parameters, and rumen microflora of beef cattle.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1529383},
pmid = {40206252},
issn = {2297-1769},
abstract = {This research was carried out to assess the impact of supplementing with glycyrrhetinic acid (GA) on production performance, serum biochemical indexes, ruminal parameters, and rumen bacterial flora of beef cattle. Twenty-four Simmental bulls were randomly assigned to two dietary treatments (n = 12 per treatment): the control treatment (basal ration, CON) and the GA treatment (basal ration supplemented with GA at 0.1% DM). After an 87-day feeding trial (7-day adaptation period and 80-day period dedicated to data and sample collection), feces, blood, and rumen fluid samples were collected on day 87. The GA addition significantly increased the average daily gain of beef cattle (p < 0.05). The GA treatment exhibited significantly greater apparent digestibility of crude protein, neutral detergent fiber, and acid detergent fiber than the control treatment (p < 0.05). Total volatile fatty acid concentration, microbial protein concentration, and propionic acid concentration in the rumen fluid were significantly increased by GA addition (p < 0.05). Compared with the control group, the interleukin-4 concentration was significantly higher in GA treatment (p < 0.05). The indices, including operational taxonomic units (OTUs), Sobs, Shannon, Ace, and Chao1, were found to be greater in the GA treatment. At the phyla level, GA addition (p < 0.05) significantly decreased the relative abundance of Bacteroidetes and increased the relative abundance of Firmicutes, while also significantly decreasing the Bacteroidetes:Firmicutes ratios. At the genera level, the relative abundance of Prevotella, NK4A214_group, norank_f_UCG-011, Prevotellaceae_UCG-003, Christensenellaceae_R-7_treatment, Prevotellaceae_UCG-001, norank_f_Bacteroidales_UCG-001, Pseudobutyrivibrio, and Butyrivibrio significantly differed due to GA addition (p < 0.05). Carbohydrate and amino acid transport and metabolism, as well as energy production and conversion, were significantly enriched in the GA treatment (p < 0.05). In summary, the findings indicated that adding glycyrrhetinic acid to the diet could improve growth performance and modify the rumen microbial composition and diversity of beef cattle.},
}