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Palanikumar I, Sinha H, Raman K. Panera: An innovative framework for surmounting uncertainty in microbial community modeling using pan-genera metabolic models. iScience 2024; 27:110358. [PMID: 39092173 PMCID: PMC11292516 DOI: 10.1016/j.isci.2024.110358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/10/2024] [Accepted: 06/20/2024] [Indexed: 08/04/2024] Open
Abstract
Utilization of 16S rRNA data in constraint-based modeling to characterize microbial communities confronts a major hurdle of lack of species-level resolution, impeding the construction of community models. We introduce "Panera," an innovative framework designed to model communities under this uncertainty and yet perform metabolic inferences using pan-genus metabolic models (PGMMs). We demonstrated PGMMs' utility for comprehending the metabolic capabilities of a genus and in characterizing community models using amplicon data. The unique, adaptable nature of PGMMs unlocks their potential in building hybrid communities, combining genome-scale metabolic models (GSMMs) and PGMMs. Notably, these models provide predictions comparable to the standard GSMM-based community models, while achieving a nearly 46% reduction in error compared to the genus model-based communities. In essence, "Panera" presents a potent and effective approach to aid in metabolic modeling by enabling robust predictions of community metabolic potential when dealing with amplicon data, and offers insights into genus-level metabolic landscapes.
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Affiliation(s)
- Indumathi Palanikumar
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Himanshu Sinha
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
- Department of Data Science and AI, Wadhwani School of Data Science and AI, IIT Madras, Chennai 600 036, India
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Dixit Y, Kanojiya K, Bhingardeve N, Ahire JJ, Saroj D. In Vitro Human Gastrointestinal Tract Simulation Systems: A Panoramic Review. Probiotics Antimicrob Proteins 2024; 16:501-518. [PMID: 36988898 DOI: 10.1007/s12602-023-10052-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2023] [Indexed: 03/30/2023]
Abstract
Simulated human gastrointestinal (GI) tract systems are important for their applications in the fields of probiotics, nutrition and health. To date, various in vitro gut systems have been available to study GI tract dynamics and its association with health. In contrast to in vivo investigations, which are constrained by ethical considerations, in vitro models have several benefits despite the challenges involved in mimicking the GI environment. These in vitro models can be used for a range of research, from simple to dynamic, with one compartment to several compartments. In this review, we present a panoramic development of in vitro GI models for the first time through an evolutionary timeline. We tried to provide insight on designing an in vitro gut model, especially for novices. Latest developments and scope for improvement based on the limitations of the existing models were highlighted. In conclusion, designing an in vitro GI model suitable for a particular application is a multifaceted task. The bio-mimicking of the GI tract specific to geometrical, anatomical and mechanical features remains a challenge for the development of effective in vitro GI models. Advances in computer technology, artificial intelligence and nanotechnology are going to be revolutionary for further development. Besides this, in silico high-throughput technologies and miniaturisation are key players in the success of making in vitro modelling cost-effective and reducing the burden of in vivo studies.
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Affiliation(s)
- Yogini Dixit
- Advanced Enzyme Technologies Ltd., 5th Floor, A-Wing, Sun Magnetica, Louiswadi, Maharashtra, Thane West, India
| | - Khushboo Kanojiya
- Advanced Enzyme Technologies Ltd., 5th Floor, A-Wing, Sun Magnetica, Louiswadi, Maharashtra, Thane West, India
| | - Namrata Bhingardeve
- Advanced Enzyme Technologies Ltd., 5th Floor, A-Wing, Sun Magnetica, Louiswadi, Maharashtra, Thane West, India
| | - Jayesh J Ahire
- Advanced Enzyme Technologies Ltd., 5th Floor, A-Wing, Sun Magnetica, Louiswadi, Maharashtra, Thane West, India.
| | - Dina Saroj
- Advanced Enzyme Technologies Ltd., 5th Floor, A-Wing, Sun Magnetica, Louiswadi, Maharashtra, Thane West, India
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Cheng F, Qiao Z, Liang G, Li J, Qiao Y, Yun S, Cao J, Cheng Y, Chang M, Feng C. Polysaccharide from Sparassis latifolia alleviates intestinal barrier dysfunction in mice exposed to lead. Int J Biol Macromol 2023; 253:127615. [PMID: 37879574 DOI: 10.1016/j.ijbiomac.2023.127615] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/27/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023]
Abstract
Exposure to lead can have harmful effects on the intestines and gut microbiota, leading to toxicity. This study aimed to explore the protective role of Sparassis latifolia polysaccharide (SLP) in safeguarding the intestinal barrier of Kunming mice exposed to lead. The findings indicated that SLP effectively alleviates intestinal lesions, increases the density of cupped cells in the intestine, and reduces inflammation in both serum and the small intestine. Furthermore, SLP maintains the expression of key genes such as ZO-1, Occludin, Claudin-1, Lyz, Ang4, and ZO-2, as well as proteins like claudin-1 and Occludin-1. Furthermore, SLP positively impacts the diversity and richness of microorganisms in the mouse gut microbiota at both the genus and gate levels. It also increases the levels of short-chain fatty acids (SCFAs), including acetic acid, butyric acid, and propionic acid, to varying degrees. In summary, SLP plays a role in alleviating the impaired small intestinal barrier in lead-exposed mice by modulating the intestinal flora, which is consistent with reduced lead absorption. This modulation enhances the integrity of the intestinal barrier, suppresses inflammation, and facilitates the excretion of lead.
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Affiliation(s)
- Feier Cheng
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Zening Qiao
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Guodong Liang
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Jiaxin Li
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Yaoyao Qiao
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Shaojun Yun
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, Shanxi 030801, China; Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Taigu, Shanxi 030801, China
| | - Jinling Cao
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Yanfen Cheng
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Mingchang Chang
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Cuiping Feng
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, Shanxi 030801, China.
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Dang K, Zhang N, Gao H, Wang G, Liang H, Xue M. Influence of intestinal microecology in the development of gout or hyperuricemia and the potential therapeutic targets. Int J Rheum Dis 2023; 26:1911-1922. [PMID: 37606177 DOI: 10.1111/1756-185x.14888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/23/2023]
Abstract
Gout and hyperuricemia are common metabolic diseases. Patients with purine metabolism disorder and/or decreased uric acid excretion showed increased uric acid levels in the blood. The increase of uric acid in the blood leads to the deposition of urate crystals in tissues, joints, and kidneys, and causes gout. Recent studies have revealed that imbalance of the intestinal microecology is closely related to the occurrence and development of hyperuricemia and gout. Disorder of the intestinal flora often occurs in patients with gout, and high purine and high fructose may induce the disorder of intestinal flora. Short-chain fatty acids and endotoxins produced by intestinal bacteria are closely related to the inflammatory response of gout. This article summarizes the characteristics of intestinal microecology in patients or animal models with hyperuricemia or gout, and explores the relationship between intestinal microecology and gout or hyperuricemia from the aspect of the intestinal barrier, intestinal microorganisms, intestinal metabolites, and intestinal immune system. We also review the current status of hyperuricemia treatment by targeting intestinal microecology.
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Affiliation(s)
- Kai Dang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Nan Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Haiqi Gao
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Guifa Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Hui Liang
- Department of Human Nutrition, College of Public Health, Qingdao University, Qingdao, China
| | - Meilan Xue
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Qingdao University, Qingdao, China
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Shirvani-Rad S, Khatibzade-Nasari N, Ejtahed HS, Larijani B. Exploring the role of gut microbiota dysbiosis in gout pathogenesis: a systematic review. Front Med (Lausanne) 2023; 10:1163778. [PMID: 37265486 PMCID: PMC10230090 DOI: 10.3389/fmed.2023.1163778] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Objectives Gut dysbiosis is believed to be one of the several mechanisms that are involved in the pathogenesis of gout. This systematic review aimed to summarize the role of gut dysbiosis in gout disease and uncover the underlying mechanisms. Methods A comprehensive search was conducted on PubMed, Web of Science, and Scopus databases up to October 2021. Animal studies and human observational studies, including case-control, cross-sectional, and cohort studies assessing the association between gut microbiota composition and gout were included. The quality of included studies has been evaluated using the Newcastle-Ottawa Quality Assessment scale (NOS) and the SYRCLE's risk of bias tool. Results Initially, we found 274 studies among which 15 studies were included in this systematic review. Of them, 10 studies were conducted on humans and 5 studies were conducted on animals. Increased abundance of Alistipes and decreased abundance of Enterobacteriaceae alters purine metabolism, thereby aggravating gout condition. Moreover, a higher abundance of Phascolarctobacterium and Bacteroides in gout modulates enzymatic activity in purine metabolism. Butyrate-producing bacteria such as Faecalibacterium, prausnitzii, Oscillibacter, Butyricicoccus, and Bifidobacterium have higher abundance in healthy controls compared to gout patients, suggesting the anti-inflammatory and anti-microbial role of short-chain fatty acids (SCFAs). Lipopolysaccharides (LPS)-releasing bacteria, such as Enterobacteriaceae, Prevotella, and Bacteroides, are also involved in the pathogenesis of gout disease by stimulating the innate immune system. Conclusion Exploring the role of gut dysbiosis in gout and the underlying mechanisms can help develop microbiota-modulating therapies for gout.
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Affiliation(s)
- Salman Shirvani-Rad
- Microbiota Research Group, Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Faculty of Medicine, Qeshm International Medical Sciences Branch, Islamic Azad University, Qeshm, Iran
| | - Niloufar Khatibzade-Nasari
- Faculty of Medicine, Qeshm International Medical Sciences Branch, Islamic Azad University, Qeshm, Iran
- Young Researchers and Elite Club, Qeshm International Medical Sciences Branch, Islamic Azad University, Qeshm, Iran
| | - Hanieh-Sadat Ejtahed
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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Forwood DL, Innes DJ, Parra MC, Stark T, de Souza DP, Chaves AV, Meale SJ. Feeding an unsalable carrot total-mixed ration altered bacterial amino acid degradation in the rumen of lambs. Sci Rep 2023; 13:6942. [PMID: 37117259 PMCID: PMC10147942 DOI: 10.1038/s41598-023-34181-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 04/25/2023] [Indexed: 04/30/2023] Open
Abstract
The objective of this study was to determine the influence of a total-mixed ration including unsalable carrots at 45% DM on the rumen microbiome; and the plasma, rumen and liver metabolomes. Carrots discarded at processing were investigated as an energy-dense substitute for barley grain in a conventional feedlot diet, and improved feed conversion efficiency by 25%. Here, rumen fluid was collected from 34 Merino lambs at slaughter (n = 16 control; n = 18 carrot) after a feeding period of 11-weeks. The V4 region of the 16S rRNA gene was sequenced to profile archaeal and bacterial microbe communities. Further, a comprehensive, targeted profile of known metabolites was constructed for blood plasma, rumen fluid and biopsied liver metabolites using a gas chromatography mass spectrometry (GC-MS) metabolomics approach. An in vitro batch culture was used to characterise ruminal fermentation including gas and methane (CH4) production. In vivo rumen microbial community structure of carrot fed lambs was dissimilar (P < 0.01; PERMANOVA), and all measures of alpha diversity were greater (P < 0.01), compared to those fed the control diet. Unclassified genera in Bacteroidales (15.9 ± 6.74% relative abundance; RA) were more abundant (P < 0.01) in the rumen fluid of carrot-fed lambs, while unclassified taxa in the Succinivibrionaceae family (11.1 ± 3.85% RA) were greater (P < 0.01) in the control. The carrot diet improved in vitro ruminal fermentation evidenced as an 8% increase (P < 0.01) in DM digestibility and a 13.8% reduction (P = 0.01) in CH4 on a mg/ g DM basis, while the control diet increased (P = 0.04) percentage of propionate within total VFA by 20%. Fourteen rumen fluid metabolites and 27 liver metabolites were influenced (P ≤ 0.05) by diet, while no effect (P ≥ 0.05) was observed in plasma metabolites. The carrot diet enriched (impact value = 0.13; P = 0.01) the tyrosine metabolism pathway (acetoacetic acid, dopamine and pyruvate), while the control diet enriched (impact value = 0.42; P ≤ 0.02) starch and sucrose metabolism (trehalose and glucose) in rumen fluid. This study demonstrated that feeding 45% DM unsalable carrots diversified bacterial communities in the rumen. These dietary changes influenced pathways of tyrosine degradation, such that previous improvements in feed conversion efficiency in lambs could be explained.
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Affiliation(s)
- Daniel L Forwood
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, Gatton, Australia
| | - David J Innes
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, Gatton, Australia
| | - Mariano C Parra
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, Gatton, Australia
| | - Terra Stark
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - David P de Souza
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Parkville, Australia
| | - Alex V Chaves
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, Australia
| | - Sarah J Meale
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, Gatton, Australia.
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Wang X, Long H, Chen M, Zhou Z, Wu Q, Xu S, Li G, Lu Z. Modified Baihu decoction therapeutically remodels gut microbiota to inhibit acute gouty arthritis. Front Physiol 2022; 13:1023453. [PMID: 36589463 PMCID: PMC9798006 DOI: 10.3389/fphys.2022.1023453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Background: Acute gouty arthritis (AGA) is the most common first symptom of gout, and the development of gout as a metabolic and immune inflammatory disease is also correlated with the gut microbiota. However, the mechanism of the effect of changes in the gut microbiota on AGA remains unclear. The intestinal flora can not only affect purine metabolism or regulate inflammation, but also influence the therapeutic effect of drugs on AGA. The aim of this study was to investigate the exact mechanism of modified Baihu decoction (MBD) in the treatment of AGA and whether it is related to the regulation of the structure of the intestinal flora. Methods: On the 21st day of MBD administration by continuous gavage, a rat acute gouty arthritis model was constructed using sodium urate (0.1 mL/rat, 50 mg/mL), and the ankle joint swelling was measured before and 4 h, 8 h, 24 h, and 48 h after the injection of sodium urate. After 48 h of sodium urate injection, serum, liver, kidney, ankle synovial tissue and feces were collected from rats. The collected samples were examined and analyzed using H&E, Elisa, Immunohistochemistry, Histopathology, 16S rDNA, and Biochemical analysis. To investigate the mechanism of MBD to alleviate AGA using pro-inflammatory factors and intestinal flora. Results: MBD (5.84, 35 g/kg) was administered orally to AGA rats and diclofenac sodium tablets (DS-tablets) were used as standard treatment control. Serum biochemical assessment confirmed that MBD is a safe drug for the treatment of AGA. In addition, our findings confirmed that MBD relieved AGA-related symptoms, such as toe swelling. Lowering serum levels of uric acid, IL-1β, and TGF-β1 immunohistochemical results also confirmed that MBD reduced the expression of inflammatory elements such as IL-1β, NLRP3, ASC, and Caspase-1 in synovial tissue.Furthermore, compared with control group, the 16s rDNA sequencing of AGA rat faeces revealed an increase in the relative abundance of Lachnospiraceae, Muribaculaceae, and Bifidobacteriaceae species. While the relative abundance of Lactobacillaceae, Erysipelotrichaceae, Ruminococcaceae, Prevotellaceae and Enterobacteriaceae showed a relative decrease in species abundance. Of these, the reduction in species abundance of Enterobacteriaceae was associated with a reduction in amino acid metabolism and environmental perception. After MBD therapeutic intervention, the disturbance of the intestinal flora caused by AGA was restored. Conclusion: In summary, MBD is an effective agent for the treatment of AGA, with the potential mechanism being the regulation of intestinal flora to control inflammation. This would help to promote the therapeutic effect of MBD on AGA.
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Affiliation(s)
- Xianyang Wang
- Animal Experiment Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haishan Long
- Animal Experiment Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ming Chen
- Haikou Hospital of Traditional Chinese Medicine, Haikou, Hainan, China
| | - Zongbo Zhou
- Haikou Hospital of Traditional Chinese Medicine, Haikou, Hainan, China
| | - Qinlin Wu
- Haikou Hospital of Traditional Chinese Medicine, Haikou, Hainan, China
| | - Shijie Xu
- Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Shijie Xu, ; Geng Li, ; Zhifu Lu,
| | - Geng Li
- Animal Experiment Center, Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Shijie Xu, ; Geng Li, ; Zhifu Lu,
| | - Zhifu Lu
- Haikou Hospital of Traditional Chinese Medicine, Haikou, Hainan, China,*Correspondence: Shijie Xu, ; Geng Li, ; Zhifu Lu,
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Beura S, Kundu P, Das AK, Ghosh A. Metagenome-scale community metabolic modelling for understanding the role of gut microbiota in human health. Comput Biol Med 2022; 149:105997. [DOI: 10.1016/j.compbiomed.2022.105997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/03/2022] [Accepted: 08/14/2022] [Indexed: 11/03/2022]
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Wang Z, Li Y, Liao W, Huang J, Liu Y, Li Z, Tang J. Gut microbiota remodeling: A promising therapeutic strategy to confront hyperuricemia and gout. Front Cell Infect Microbiol 2022; 12:935723. [PMID: 36034697 PMCID: PMC9399429 DOI: 10.3389/fcimb.2022.935723] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
The incidence of hyperuricemia (HUA) and gout continuously increases and has become a major public health problem. The gut microbiota, which colonizes the human intestine, has a mutually beneficial and symbiotic relationship with the host and plays a vital role in the host’s metabolism and immune regulation. Structural changes or imbalance in the gut microbiota could cause metabolic disorders and participate in the synthesis of purine-metabolizing enzymes and the release of inflammatory cytokines, which is closely related to the occurrence and development of the metabolic immune disease HUA and gout. The gut microbiota as an entry point to explore the pathogenesis of HUA and gout has become a new research hotspot. This review summarizes the characteristics of the gut microbiota in patients with HUA and gout. Meanwhile, the influence of different dietary structures on the gut microbiota, the effect of the gut microbiota on purine and uric acid metabolism, and the internal relationship between the gut microbiota and metabolic endotoxemia/inflammatory factors are explored. Moreover, the intervention effects of probiotics, prebiotics, and fecal microbial transplantation on HUA and gout are also systematically reviewed to provide a gut flora solution for the prevention and treatment of related diseases.
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Affiliation(s)
- Zhilei Wang
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Zhilei Wang, ; Jianyuan Tang,
| | - Yuchen Li
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wenhao Liao
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ju Huang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yanping Liu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhiyong Li
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Jianyuan Tang
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Zhilei Wang, ; Jianyuan Tang,
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Zhang W, Wang T, Guo R, Cui W, Yu W, Wang Z, Jiang Y, Jiang M, Wang X, Liu C, Xiao J, Shang J, Wen X, Zhao Z. Variation of Serum Uric Acid Is Associated With Gut Microbiota in Patients With Diabetes Mellitus. Front Cell Infect Microbiol 2022; 11:761757. [PMID: 35118005 PMCID: PMC8803748 DOI: 10.3389/fcimb.2021.761757] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/15/2021] [Indexed: 02/04/2023] Open
Abstract
Diabetes mellitus is a metabolic disease closely related to a disordered gut microbiome. Diabetic patients usually suffer from various metabolic disorders, such as increased serum uric acid levels. Although serum uric acid levels depend partially on intestine excretion, the relationship between uric acid and gut microbiome in diabetic patients remains unknown. We collected a total of 126 fecal samples from diabetic patients for 16S ribosomal RNA gene amplicon sequencing and recorded clinical data. We analyzed the correlation between clinical indicators and gut microbiota of diabetic patients using Spearman analysis. Since uric acid was the most prominent one, we classified diabetic patients based on their uric acid levels to find the microbiome associated with uric acid disturbance. We constructed Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway profiles using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to identify variations between the different groups. Among all the clinical indicators, uric acid had the strongest correlation with gut microbiota. First, we divided the patients into three groups according to their uric acid levels. The two low uric acid groups were similar, while the elevated uric acid group had significant differences in gut microbiota and metabolic pathways. The elevated uric acid group had a significantly lower gut microbiota diversity. At the genus level, this group had remarkably higher Escherichia–Shigella amounts and notably lower Faecalibacterium, Oscillospiraceae_UCG−002, and Oscillospiraceae_UCG−005 amounts. The gut microbiota of the high uric acid group was predicted to be enriched in metabolism, human diseases, and lipopolysaccharide biosynthesis. Since the two low uric acid groups were similar, we regrouped and matched the abnormal uric acid patients with normal uric acid patients. The differences in gut microbiota and metabolic pathways related to nucleotide metabolism became more significant. The serum uric acid levels were associated with gut microbiome changes. This might be related to uric acid metabolism by gut microbes. Our study indicates that targeting the gut microbiome could help manage elevated uric acid levels.
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Affiliation(s)
- Weifeng Zhang
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ting Wang
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ruixue Guo
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wen Cui
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Yu
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhihui Wang
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yumin Jiang
- Department of Emergency, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Minghan Jiang
- Department of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiaojie Wang
- Department of Pharmacology, Shandong University School of Basic Medical Sciences, Jinan, China
| | - Chao Liu
- Shanghai Mobio Biomedical Technology Co., Ltd., Shanghai, China
| | - Jing Xiao
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jin Shang
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Zhanzheng Zhao, ; Xuejun Wen, ; Jin Shang,
| | - Xuejun Wen
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, United States
- *Correspondence: Zhanzheng Zhao, ; Xuejun Wen, ; Jin Shang,
| | - Zhanzheng Zhao
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Zhanzheng Zhao, ; Xuejun Wen, ; Jin Shang,
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Yuan X, Chen R, Zhang Y, Lin X, Yang X. Altered Gut Microbiota in Children With Hyperuricemia. Front Endocrinol (Lausanne) 2022; 13:848715. [PMID: 35574004 PMCID: PMC9091909 DOI: 10.3389/fendo.2022.848715] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND In adults, gut dysbiosis may contribute to the pathogenesis of gout. However, the characteristics of gut microbiota in children with hyperuricemia (HUA) in the absence of clinical gout have not been explored. OBJECTIVE This present study analyzed the gut microbiota in children with HUA as compared to controls (Con) and explored bacterial associations that may account for differences. METHODS A total of 80 children were enrolled in this study; they were divided into HUA and Con according to the level of serum uric acid (UA). The composition of gut microbiota was investigated by 16S rRNA high-throughput sequencing. RESULTS Principal coordinate analysis revealed that gut microbiota of the HUA group was clustered together and separated partly from the Con group. There was no difference in alpha-diversity between the two groups. However, Spearman's correlation analysis revealed that serum UA level positively correlated with genera Actinomyces, Morganella, and Streptococcus, and negatively associated with the producers of short-chain fatty acids (SCFAs), such as Alistipes, Faecalibacterium, and Oscillospira, and the sulfidogenic bacteria Bilophila. The members of the genera Alistipes and Bilophila in the Con group were significantly more prevalent than the HUA subjects. Compared to the Con cohort, metabolic pathway predictions found that the superpathways of purine nucleotide de novo biosynthesis were decreased in HUA subjects, whereas the superpathway of purine deoxyribonucleoside de gradation was increased. CONCLUSION The composition of the gut microbiota in children with HUA differs from Con. Although causality cannot be established, modification in the microbiota that produces SCFA and sulfide may promote HUA.
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