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Systems Biology of Human Microbiome for the Prediction of Personal Glycaemic Response
Nikhil Kirtipal, Youngchang Seo, Jangwon Son, Sunjae Lee
Diabetes Metab J. 2024;48(5):821-836.   Published online September 12, 2024
DOI: https://doi.org/10.4093/dmj.2024.0382
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  • 267 Download
AbstractAbstract PDFPubReader   ePub   
The human gut microbiota is increasingly recognized as a pivotal factor in diabetes management, playing a significant role in the body’s response to treatment. However, it is important to understand that long-term usage of medicines like metformin and other diabetic treatments can result in problems, gastrointestinal discomfort, and dysbiosis of the gut flora. Advanced sequencing technologies have improved our understanding of the gut microbiome’s role in diabetes, uncovering complex interactions between microbial composition and metabolic health. We explore how the gut microbiota affects glucose metabolism and insulin sensitivity by examining a variety of -omics data, including genomics, transcriptomics, epigenomics, proteomics, metabolomics, and metagenomics. Machine learning algorithms and genome-scale modeling are now being applied to find microbiological biomarkers associated with diabetes risk, predicted disease progression, and guide customized therapy. This study holds promise for specialized diabetic therapy. Despite significant advances, some concerns remain unanswered, including understanding the complex relationship between diabetes etiology and gut microbiota, as well as developing user-friendly technological innovations. This mini-review explores the relationship between multiomics, precision medicine, and machine learning to improve our understanding of the gut microbiome’s function in diabetes. In the era of precision medicine, the ultimate goal is to improve patient outcomes through personalized treatments.
Original Articles
Genetics
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Metagenomic Analysis of the Gut Microbiome Reveals Enrichment of Menaquinones (Vitamin K2) Pathway in Diabetes Mellitus
Nihar Ranjan Dash, Mohammad Tahseen Al Bataineh
Diabetes Metab J. 2021;45(1):77-85.   Published online May 11, 2020
DOI: https://doi.org/10.4093/dmj.2019.0202
  • 65,535 View
  • 224 Download
  • 23 Web of Science
  • 24 Crossref
AbstractAbstract PDFSupplementary MaterialPubReader   ePub   
Background

Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease with a high prevalence worldwide, especially among overweight and obese populations. T2DM is multifactorial with several genetic and acquired risk factors that lead to insulin resistance. Mounting evidence indicates that alteration of gut microbiome composition contribute to insulin resistance and inflammation. However, the precise link between T2DM and gut microbiome role and composition remains unknown.

Methods

We evaluated the metabolic capabilities of the gut microbiome of twelve T2DM and six healthy individuals through shotgun metagenomics using MiSeq platform.

Results

We identified no significant differences in the overall taxonomic composition between healthy and T2DM subjects when controlling for differences in diet. However, results showed that T2DM enriched in metabolic pathways involved in menaquinone (vitamin K2) superpathway biosynthesis (PWY-5838) as compared to healthy individuals. Covariance analysis between the bacterial genera and metabolic pathways displaying difference in abundance (analysis of variance P<0.05) in T2DM as compared to healthy subjects revealed that genera belonging Firmicutes, Actinobacteria, and Bacteroidetes phyla contribute significantly to vitamin K2 biosynthesis. Further, the microbiome corresponding to T2DM with high glycosylated hemoglobin (HbA1c) (>6.5%) exhibit high abundance of genes involved in lysine biosynthesis and low abundance of genes involved in creatinine degradation as compared to T2DM with lower HbA1c (<6.5%).

Conclusion

The identified differences in metabolic capabilities provide important information that may eventually lead to the development of novel biomarkers and more effective management strategies to treat T2DM.

Citations

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Clinical Diabetes & Therapeutics
Additional Effect of Dietary Fiber in Patients with Type 2 Diabetes Mellitus Using Metformin and Sulfonylurea: An Open-Label, Pilot Trial
Seung-Eun Lee, Yongbin Choi, Ji Eun Jun, You-Bin Lee, Sang-Man Jin, Kyu Yeon Hur, Gwang Pyo Ko, Moon-Kyu Lee
Diabetes Metab J. 2019;43(4):422-431.   Published online April 23, 2019
DOI: https://doi.org/10.4093/dmj.2018.0090
  • 6,843 View
  • 93 Download
  • 10 Web of Science
  • 9 Crossref
AbstractAbstract PDFPubReader   
Background

Metformin, sulfonylurea, and dietary fiber are known to affect gut microbiota in patients with type 2 diabetes mellitus (T2DM). This open and single-arm pilot trial investigated the effects of the additional use of fiber on glycemic parameters, insulin, incretins, and microbiota in patients with T2DM who had been treated with metformin and sulfonylurea.

Methods

Participants took fiber for 4 weeks and stopped for the next 4 weeks. Glycemic parameters, insulin, incretins during mixed-meal tolerance test (MMTT), lipopolysaccharide (LPS) level, and fecal microbiota were analyzed at weeks 0, 4, and 8. The first tertile of difference in glucose area under the curve during MMTT between weeks 0 and 4 was defined as ‘responders’ and the third as ‘nonresponders,’ respectively.

Results

In all 10 participants, the peak incretin levels during MMTT were higher and LPS were lower at week 4 as compared with at baseline. While the insulin sensitivity of the ‘responders’ increased at week 4, that of the ‘nonresponders’ showed opposite results. However, the results were not statistically significant. In all participants, metabolically unfavorable microbiota decreased at week 4 and were restored at week 8. At baseline, metabolically hostile bacteria were more abundant in the ‘nonresponders.’ In ‘responders,’ Roseburia intestinalis increased at week 4.

Conclusion

While dietary fiber did not induce additional changes in glycemic parameters, it showed a trend of improvement in insulin sensitivity in ‘responders.’ Even if patients are already receiving diabetes treatment, the additional administration of fiber can lead to additional benefits in the treatment of diabetes.

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Sulwon Lecture 2014
Gut Microbiota and Metabolic Disorders
Kyu Yeon Hur, Myung-Shik Lee
Diabetes Metab J. 2015;39(3):198-203.   Published online June 15, 2015
DOI: https://doi.org/10.4093/dmj.2015.39.3.198
  • 11,874 View
  • 264 Download
  • 167 Web of Science
  • 170 Crossref
AbstractAbstract PDFPubReader   

Gut microbiota plays critical physiological roles in the energy extraction and in the control of local or systemic immunity. Gut microbiota and its disturbance also appear to be involved in the pathogenesis of diverse diseases including metabolic disorders, gastrointestinal diseases, cancer, etc. In the metabolic point of view, gut microbiota can modulate lipid accumulation, lipopolysaccharide content and the production of short-chain fatty acids that affect food intake, inflammatory tone, or insulin signaling. Several strategies have been developed to change gut microbiota such as prebiotics, probiotics, certain antidiabetic drugs or fecal microbiota transplantation, which have diverse effects on body metabolism and on the development of metabolic disorders.

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    Asia Pacific Journal of Clinical Trials: Nervous System Diseases.2018; 3(3): 120.     CrossRef
  • Ketogenic diet enhances neurovascular function with altered gut microbiome in young healthy mice
    David Ma, Amy C. Wang, Ishita Parikh, Stefan J. Green, Jared D. Hoffman, George Chlipala, M. Paul Murphy, Brent S. Sokola, Björn Bauer, Anika M. S. Hartz, Ai-Ling Lin
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  • Oral hydroxysafflor yellow A reduces obesity in mice by modulating the gut microbiota and serum metabolism
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  • Probiotics Ingestion Does Not Directly Affect Thyroid Hormonal Parameters in Hypothyroid Patients on Levothyroxine Treatment
    Giorgia Spaggiari, Giulia Brigante, Sara De Vincentis, Umberto Cattini, Laura Roli, Maria Cristina De Santis, Enrica Baraldi, Simonetta Tagliavini, Manuela Varani, Tommaso Trenti, Vincenzo Rochira, Manuela Simoni, Daniele Santi
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  • Effects of mutation of Asn694 in Aspergillus niger α-glucosidase on hydrolysis and transglucosylation
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  • A Fermented Whole Grain Prevents Lipopolysaccharides‐Induced Dysfunction in Human Endothelial Progenitor Cells
    Laura Giusti, Morena Gabriele, Giuseppe Penno, Monia Garofolo, Vincenzo Longo, Stefano Del Prato, Daniela Lucchesi, Laura Pucci, Grant N. Pierce
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  • An Extracellular Cell-Attached Pullulanase Confers Branched α-Glucan Utilization in Human Gut Lactobacillus acidophilus
    Marie S. Møller, Yong Jun Goh, Kasper Bøwig Rasmussen, Wojciech Cypryk, Hasan Ufuk Celebioglu, Todd R. Klaenhammer, Birte Svensson, Maher Abou Hachem, Patrick D. Schloss
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  • Flos Lonicera Combined with Metformin Ameliorates Hepatosteatosis and Glucose Intolerance in Association with Gut Microbiota Modulation
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  • Understanding the Impact of Omega-3 Rich Diet on the Gut Microbiota
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  • Human Microbiome and its Association With Health and Diseases
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  • Redefining Healthy Urine: A Cross-Sectional Exploratory Metagenomic Study of People With and Without Bladder Dysfunction
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  • Sasa quelpaertensis leaf extract regulates microbial dysbiosis by modulating the composition and diversity of the microbiota in dextran sulfate sodium-induced colitis mice
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  • Integrative analysis of metabolome and gut microbiota in diet-induced hyperlipidemic rats treated with berberine compounds
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  • Improved glucose metabolism following bariatric surgery is associated with increased circulating bile acid concentrations and remodeling of the gut microbiome
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  • Inulin Supplementation Lowered the Metabolic Defects of Prolonged Exposure to Chlorpyrifos from Gestation to Young Adult Stage in Offspring Rats
    Julie Reygner, Lydia Lichtenberger, Ghada Elmhiri, Samir Dou, Narges Bahi-Jaber, Larbi Rhazi, Flore Depeint, Veronique Bach, Hafida Khorsi-Cauet, Latifa Abdennebi-Najar, Hauke Smidt
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  • The human gut microbiome in health: establishment and resilience of microbiota over a lifetime
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  • Surgical Management of Metabolic Syndrome Related to Morbid Obesity
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  • Dietary silver nanoparticles can disturb the gut microbiota in mice
    Sybille van den Brule, Jérôme Ambroise, Hélène Lecloux, Clément Levard, Romain Soulas, Pieter-Jan De Temmerman, Mihaly Palmai-Pallag, Etienne Marbaix, Dominique Lison
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  • Probiotics as Complementary Treatment for Metabolic Disorders
    Mélanie Le Barz, Fernando F. Anhê, Thibaut V. Varin, Yves Desjardins, Emile Levy, Denis Roy, Maria C. Urdaci, André Marette
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  • Impact of Gut Microbiota on Obesity, Diabetes, and Cardiovascular Disease Risk
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  • Prebiotic consumption and the incidence of overweight in a Mediterranean cohort: the Seguimiento Universidad de Navarra Project
    Aurora Perez-Cornago, Miguel A Martinez-Gonzalez, Miguel Ruiz-Canela, Ignacio Jaurrieta, Silvia Carlos, Carmen Sayon-Orea, Maira Bes-Rastrollo
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