MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data

Nucleic Acids Research, Год журнала: 2023, Номер 51(W1), С. W310 - W318

Опубликована: Май 11, 2023

Abstract Microbiome studies have become routine in biomedical, agricultural and environmental sciences with diverse aims, including diversity profiling, functional characterization, translational applications. The resulting complex, often multi-omics datasets demand powerful, yet user-friendly bioinformatics tools to reveal key patterns, important biomarkers, potential activities. Here we introduce MicrobiomeAnalyst 2.0 support comprehensive statistics, visualization, interpretation, integrative analysis of data outputs commonly generated from microbiome studies. Compared the previous version, features three new modules: (i) a Raw Data Processing module for amplicon processing taxonomy annotation that connects directly Marker Profiling downstream statistical analysis; (ii) Metabolomics help dissect associations between community compositions metabolic activities through joint paired metabolomics datasets; (iii) Statistical Meta-Analysis identify consistent signatures by integrating across multiple Other improvements include added multi-factor differential interactive visualizations popular graphical outputs, updated methods prediction correlation analysis, expanded taxon set libraries based on latest literature. These are demonstrated using dataset recent type 1 diabetes study. is freely available at microbiomeanalyst.ca.

Язык: Английский

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Short-chain fatty acids: linking diet, the microbiome and immunity

Nature reviews. Immunology, Год журнала: 2024, Номер 24(8), С. 577 - 595

Опубликована: Апрель 2, 2024

Язык: Английский

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Gut Microbiota Dysbiosis, Oxidative Stress, Inflammation, and Epigenetic Alterations in Metabolic Diseases

Antioxidants, Год журнала: 2024, Номер 13(8), С. 985 - 985

Опубликована: Авг. 14, 2024

Gut dysbiosis, resulting from an imbalance in the gut microbiome, can induce excessive production of reactive oxygen species (ROS), leading to inflammation, DNA damage, activation immune system, and epigenetic alterations critical genes involved metabolic pathways. dysbiosis-induced inflammation also disrupt barrier integrity increase intestinal permeability, which allows gut-derived toxic products enter liver systemic circulation, further triggering oxidative stress, associated with diseases. However, specific metabolites, such as short-chain fatty acids (SCFAs), lactate, vitamins, modulate stress system through mechanisms, thereby improving function. microbiota diet-induced diseases, obesity, insulin resistance, dyslipidemia, hypertension, transfer next generation, involving mechanisms. In this review, we will introduce key that, along dysbiosis ROS, are engaged developing Finally, discuss potential therapeutic interventions dietary modifications, prebiotics, probiotics, postbiotics, fecal transplantation, may reduce syndrome by altering alterations. summary, review highlights crucial role pathogenesis a particular focus on (including histone methylomics, RNA interference) that prevent or improve

Язык: Английский

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The Role of Short Chain Fatty Acids in Inflammation and Body Health

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(13), С. 7379 - 7379

Опубликована: Июль 5, 2024

Short chain fatty acids (SCFAs), mainly including acetate, propionate and butyrate, are produced by intestinal bacteria during the fermentation of partially digested indigestible polysaccharides. SCFAs play an important role in regulating energy metabolism maintaining homeostasis environment also regulatory organs tissues outside gut. In recent years, many studies have shown that can regulate inflammation affect host health, two main signaling mechanisms been identified: activation G-protein coupled receptors (GPCRs) inhibition histone deacetylase (HDAC). addition, a growing body evidence highlights importance every SCFA influencing health maintenance disease development. this review, we summarized advances concerning biological properties their pathways health. Hopefully, it provide systematic theoretical basis for nutritional prevention treatment human diseases.

Язык: Английский

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The maternal gut microbiome during pregnancy and its role in maternal and infant health

Current Opinion in Microbiology, Год журнала: 2023, Номер 74, С. 102309 - 102309

Опубликована: Апрель 15, 2023

There is growing knowledge that the maternal gut microbiome undergoes substantial changes during pregnancy. However, despite recognition influences and infant health, we still have a limited understanding of clinical environmental factors can impact pregnancy consequences these changes. Here, review current body about shaping its role in development complications health.

Язык: Английский

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Gut microbiota and type 1 diabetes: a two-sample bidirectional Mendelian randomization study

Frontiers in Cellular and Infection Microbiology, Год журнала: 2023, Номер 13

Опубликована: Май 29, 2023

Objective The real causal relationship between human gut microbiota and T1D remains unclear difficult to establish. Herein, we adopted a two-sample bidirectional mendelian randomization (MR) study evaluate the causality T1D. Methods We leveraged publicly available genome-wide association (GWAS) summary data perform MR analysis. microbiota-related GWAS from 18,340 individuals international consortium MiBioGen were used. statistic for (n = 264,137) obtained latest release FinnGen as outcome of interest. selection instrumental variables conformed strictly series preset inclusion exclusion criteria. MR-Egger, weighted median, inverse variance (IVW), mode methods used assess association. Cochran’s Q test, MR-Egger intercept leave-one-out analysis conducted identify heterogeneity pleiotropy. Results At phylum level, only Bacteroidetes was indicated have on (OR 1.24, 95% CI 1.01-1.53, P 0.044) in IVW When it comes their subcategories, Bacteroidia class 1.28, 1.06-1.53, 0.009, FDR 0.085), Bacteroidales order Eubacterium eligens group genus 0.64, 0.50-0.81, 2.84×10 -4 , 0.031) observed with No pleiotropy detected. Conclusions present reports that phylum, class, causally increase risk, whereas genus, which belongs Firmicutes decreases risk. Nevertheless, future studies are warranted dissect underlying mechanisms specific bacterial taxa’s role pathophysiology

Язык: Английский

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Advancing lifelong precision medicine for cardiovascular diseases through gut microbiota modulation

Gut Microbes, Год журнала: 2024, Номер 16(1)

Опубликована: Фев. 27, 2024

The gut microbiome is known as the tenth system of human body that plays a vital role in intersection between health and disease. considerable inter-individual variability microbiota poses both challenges great prospects promoting precision medicine cardiovascular diseases (CVDs). In this review, based on development, evolution, influencing factors full life circle, we summarized recent advances characteristic alteration CVDs throughout different stages, depicted their pathological links mechanism, well highlight achievements targeting prevention, diagnosis treatment. Personalized strategies could be tailored according to characteristics including microbiota-blood metabolites combined prediction diagnosis, dietary interventions, lifestyle improvements, probiotic or prebiotic supplements. However, fulfill promise lifelong health, more mechanism studies should progress from correlation causality decipher novel mechanisms linking specific microbes CVDs. It also promising use burgeoning artificial intelligence machine learning target for developing screening new therapeutic interventions.

Язык: Английский

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Pre-Type 1 Diabetes in Adolescents and Teens: Screening, Nutritional Interventions, Beta-Cell Preservation, and Psychosocial Impacts

Journal of Clinical Medicine, Год журнала: 2025, Номер 14(2), С. 383 - 383

Опубликована: Янв. 9, 2025

Type 1 Diabetes (T1D) is a progressive autoimmune disease often identified in childhood or adolescence, with early stages detectable through pre-diabetic markers such as autoantibodies and subclinical beta-cell dysfunction. The identification of the pre-T1D stage critical for preventing complications, diabetic ketoacidosis, enabling timely interventions that may alter progression. This review examines multifaceted approach to managing T1D risk adolescents teens, emphasizing detection, nutritional interventions, preservation strategies, psychosocial support. Screening T1D-associated offers predictive insight into risk, particularly when combined education family resources promote lifestyle adjustments. Although alone are not capable T1D, certain weight management specific choices, have shown potential preserve insulin sensitivity, reduce inflammation, mitigate metabolic strain. Pharmacological including immune-modulating drugs like teplizumab, alongside emerging regenerative cell-based therapies, offer delay onset by protecting function. social psychological impacts diagnosis also significant, affecting adolescents' quality life, dynamics, mental health. Supportive counseling, cognitive-behavioral therapy (CBT), group support, recommended emotional burden pre-diabetes. Future directions call integrating universal targeted screening programs within schools primary care, advancing research nutrition promoting policies enhance access preventive resources. Advocacy insurance coverage screening, health services crucial support families risk. By addressing these areas, healthcare systems can intervention, improve preservation, overall well-being at T1D.

Язык: Английский

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Discovery of robust and highly specific microbiome signatures of non-alcoholic fatty liver disease

Microbiome, Год журнала: 2025, Номер 13(1)

Опубликована: Янв. 14, 2025

The pathogenesis of non-alcoholic fatty liver disease (NAFLD) with a global prevalence 30% is multifactorial and the involvement gut bacteria has been recently proposed. However, finding robust bacterial signatures NAFLD great challenge, mainly due to its co-occurrence other metabolic diseases. Here, we collected public metagenomic data integrated taxonomy profiles in silico generated community outputs, detailed clinical data, 1206 Chinese subjects w/wo diseases, including (obese lean), obesity, T2D, hypertension, atherosclerosis. We identified highly specific microbiome through building accurate machine learning models (accuracy = 0.845–0.917) for high portability (generalizable) low prediction rate (specific) when applied as well approach involving differential co-abundance ecological networks. Moreover, using these coupled further mediation analysis dependency modeling, propose synergistic defined microbial consortia associated phenotype overweight lean individuals, respectively. Our study reveals offers more realistic microbiome-therapeutics over individual species this complex disease.

Язык: Английский

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Targeting gut S. aureofaciens Tü117 serves as a new potential therapeutic intervention for the prevention and treatment of hypertension

Cell Metabolism, Год журнала: 2025, Номер 37(2), С. 496 - 513.e11

Опубликована: Фев. 1, 2025

Язык: Английский

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