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Paul B, Siddaramappa S. Comparative analysis of the diversity of trinucleotide repeats in bacterial genomes. Genome 2024; 67:281-291. [PMID: 38593473 DOI: 10.1139/gen-2023-0097] [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] [Indexed: 04/11/2024]
Abstract
The human gut is the most favorable niche for microbial populations, and few studies have explored the possibilities of horizontal gene transfer between host and pathogen. Trinucleotide repeat (TNR) expansion in humans can cause more than 40 neurodegenerative diseases. Further, TNRs are a type of microsatellite that resides on coding regions can contribute to the synthesis of homopolymeric amino acids. Hence, the present study aims to estimate the occurrence and diversity of TNRs in bacterial genomes available in the NCBI Genome database. Genome-wide analyses revealed that several bacterial genomes contain different types of uninterrupted TNRs. It was found that TNRs are abundant in the genomes of Alcaligenes faecalis, Mycoplasma gallisepticum, Mycoplasma genitalium, Sorangium cellulosum, and Thermus thermophilus. Interestingly, the genome of Bacillus thuringiensis strain YBT-1518 contained 169 uninterrupted ATT repeats. The genome of Leclercia adecarboxylata had 46 uninterrupted CAG repeats, which potentially translate into polyglutamine. In some instances, the TNRs were present in genes that potentially encode essential functions. Similar occurrences in human genes are known to cause genetic disorders. Further analysis of the occurrence of TNRs in bacterial genomes is likely to provide a better understanding of mismatch repair, genetic disorders, host-pathogen interaction, and homopolymeric amino acids.
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Affiliation(s)
- Bobby Paul
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Shivakumara Siddaramappa
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru 560100, Karnataka, India
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2
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Tizabi Y, Bennani S, El Kouhen N, Getachew B, Aschner M. Heavy Metal Interactions with Neuroglia and Gut Microbiota: Implications for Huntington's Disease. Cells 2024; 13:1144. [PMID: 38994995 PMCID: PMC11240758 DOI: 10.3390/cells13131144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
Huntington's disease (HD) is a rare but progressive and devastating neurodegenerative disease characterized by involuntary movements, cognitive decline, executive dysfunction, and neuropsychiatric conditions such as anxiety and depression. It follows an autosomal dominant inheritance pattern. Thus, a child who has a parent with the mutated huntingtin (mHTT) gene has a 50% chance of developing the disease. Since the HTT protein is involved in many critical cellular processes, including neurogenesis, brain development, energy metabolism, transcriptional regulation, synaptic activity, vesicle trafficking, cell signaling, and autophagy, its aberrant aggregates lead to the disruption of numerous cellular pathways and neurodegeneration. Essential heavy metals are vital at low concentrations; however, at higher concentrations, they can exacerbate HD by disrupting glial-neuronal communication and/or causing dysbiosis (disturbance in the gut microbiota, GM), both of which can lead to neuroinflammation and further neurodegeneration. Here, we discuss in detail the interactions of iron, manganese, and copper with glial-neuron communication and GM and indicate how this knowledge may pave the way for the development of a new generation of disease-modifying therapies in HD.
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Affiliation(s)
- Yousef Tizabi
- Department of Pharmacology, Howard University College of Medicine, Washington, DC 20059, USA
| | - Samia Bennani
- Faculty of Medicine and Pharmacy of Casablanca, Hassan II University, Casablanca 20670, Morocco
| | - Nacer El Kouhen
- Faculty of Medicine and Pharmacy of Casablanca, Hassan II University, Casablanca 20670, Morocco
| | - Bruk Getachew
- Department of Pharmacology, Howard University College of Medicine, Washington, DC 20059, USA
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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3
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Chmielarz M, Sobieszczańska B, Środa-Pomianek K. Metabolic Endotoxemia: From the Gut to Neurodegeneration. Int J Mol Sci 2024; 25:7006. [PMID: 39000116 PMCID: PMC11241432 DOI: 10.3390/ijms25137006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/22/2024] [Accepted: 06/23/2024] [Indexed: 07/16/2024] Open
Abstract
Metabolic endotoxemia is a severe health problem for residents in developed countries who follow a Western diet, disrupting intestinal microbiota and the whole organism's homeostasis. Although the effect of endotoxin on the human immune system is well known, its long-term impact on the human body, lasting many months or even years, is unknown. This is due to the difficulty of conducting in vitro and in vivo studies on the prolonged effect of endotoxin on the central nervous system. In this article, based on the available literature, we traced the path of endotoxin from the intestines to the blood through the intestinal epithelium and factors promoting the development of metabolic endotoxemia. The presence of endotoxin in the bloodstream and the inflammation it induces may contribute to lowering the blood-brain barrier, potentially allowing its penetration into the central nervous system; although, the theory is still controversial. Microglia, guarding the central nervous system, are the first line of defense and respond to endotoxin with activation, which may contribute to the development of neurodegenerative diseases. We traced the pro-inflammatory role of endotoxin in neurodegenerative diseases and its impact on the epigenetic regulation of microglial phenotypes.
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Affiliation(s)
- Mateusz Chmielarz
- Department of Microbiology, Wroclaw University of Medicine, Chalubinskiego 4 Street, 50-368 Wroclaw, Poland
| | - Beata Sobieszczańska
- Department of Microbiology, Wroclaw University of Medicine, Chalubinskiego 4 Street, 50-368 Wroclaw, Poland
| | - Kamila Środa-Pomianek
- Department of Biophysics and Neuroscience, Wroclaw University of Medicine, Chalubinskiego 3a, 50-368 Wroclaw, Poland
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Qian SX, Bao YF, Li XY, Dong Y, Zhang XL, Wu ZY. Multi-omics Analysis Reveals Key Gut Microbiota and Metabolites Closely Associated with Huntington's Disease. Mol Neurobiol 2024:10.1007/s12035-024-04271-9. [PMID: 38850348 DOI: 10.1007/s12035-024-04271-9] [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: 02/09/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024]
Abstract
Dysbiosis of the gut microbiota is closely associated with neurodegenerative diseases, including Huntington's disease (HD). Gut microbiome-derived metabolites are key factors in host-microbiome interactions. This study aimed to investigate the crucial gut microbiome and metabolites in HD and their correlations. Fecal and serum samples from 11 to 26 patients with HD, respectively, and 16 and 23 healthy controls, respectively, were collected. The fecal samples were used for shotgun metagenomics while the serum samples for metabolomics analysis. Integrated analysis of the metagenomics and metabolomics data was also conducted. Firmicutes, Bacteroidota, Proteobacteria, Uroviricota, Actinobacteria, and Verrucomicrobia were the dominant phyla. At the genus level, the presence of Bacteroides, Faecalibacterium, Parabacteroides, Alistipes, Dialister, and Christensenella was higher in HD patients, while the abundance of Lachnospira, Roseburia, Clostridium, Ruminococcus, Blautia, Butyricicoccus, Agathobaculum, Phocaeicola, Coprococcus, and Fusicatenibacter decreased. A total of 244 differential metabolites were identified and found to be enriched in the glycerophospholipid, nucleotide, biotin, galactose, and alpha-linolenic acid metabolic pathways. The AUC value from the integrated analysis (1) was higher than that from the analysis of the gut microbiota (0.8632). No significant differences were found in the ACE, Simpson, Shannon, Sobs, and Chao indexes between HD patients and controls. Our study determined crucial functional gut microbiota and potential biomarkers associated with HD pathogenesis, providing new insights into the role of the gut microbiota-brain axis in HD occurrence and development.
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Affiliation(s)
- Shu-Xia Qian
- Department of Medical Genetics and Center for Rare Diseases, Department of Neurology in the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, China
- Nanhu Brain-Computer Interface Institute, Hangzhou, China
- Department of Neurology, the Second Affiliated Hospital of Jiaxing University, 1518 Huancheng North Road, Jiaxing, Zhejiang, China
| | - Yu-Feng Bao
- Department of Medical Genetics and Center for Rare Diseases, Department of Neurology in the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, China
| | - Xiao-Yan Li
- Department of Medical Genetics and Center for Rare Diseases, Department of Neurology in the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, China
| | - Yi Dong
- Department of Medical Genetics and Center for Rare Diseases, Department of Neurology in the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, China
| | - Xiao-Ling Zhang
- Department of Neurology, the Second Affiliated Hospital of Jiaxing University, 1518 Huancheng North Road, Jiaxing, Zhejiang, China.
| | - Zhi-Ying Wu
- Department of Medical Genetics and Center for Rare Diseases, Department of Neurology in the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, China.
- Nanhu Brain-Computer Interface Institute, Hangzhou, China.
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Burtscher J, Strasser B, Pepe G, Burtscher M, Kopp M, Di Pardo A, Maglione V, Khamoui AV. Brain-Periphery Interactions in Huntington's Disease: Mediators and Lifestyle Interventions. Int J Mol Sci 2024; 25:4696. [PMID: 38731912 PMCID: PMC11083237 DOI: 10.3390/ijms25094696] [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] [Received: 03/28/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Prominent pathological features of Huntington's disease (HD) are aggregations of mutated Huntingtin protein (mHtt) in the brain and neurodegeneration, which causes characteristic motor (such as chorea and dystonia) and non-motor symptoms. However, the numerous systemic and peripheral deficits in HD have gained increasing attention recently, since those factors likely modulate disease progression, including brain pathology. While whole-body metabolic abnormalities and organ-specific pathologies in HD have been relatively well described, the potential mediators of compromised inter-organ communication in HD have been insufficiently characterized. Therefore, we applied an exploratory literature search to identify such mediators. Unsurprisingly, dysregulation of inflammatory factors, circulating mHtt, and many other messenger molecules (hormones, lipids, RNAs) were found that suggest impaired inter-organ communication, including of the gut-brain and muscle-brain axis. Based on these findings, we aimed to assess the risks and potentials of lifestyle interventions that are thought to improve communication across these axes: dietary strategies and exercise. We conclude that appropriate lifestyle interventions have great potential to reduce symptoms and potentially modify disease progression (possibly via improving inter-organ signaling) in HD. However, impaired systemic metabolism and peripheral symptoms warrant particular care in the design of dietary and exercise programs for people with HD.
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Affiliation(s)
- Johannes Burtscher
- Institute of Sport Sciences, University of Lausanne, 1015 Lausanne, Switzerland
| | - Barbara Strasser
- Ludwig Boltzmann Institute for Rehabilitation Research, 1100 Vienna, Austria;
- Faculty of Medicine, Sigmund Freud Private University, 1020 Vienna, Austria
| | - Giuseppe Pepe
- IRCCS Neuromed, 86077 Pozzilli, Italy; (G.P.); (A.D.P.); (V.M.)
| | - Martin Burtscher
- Department of Sport Science, University of Innsbruck, 6020 Innsbruck, Austria; (M.B.); (M.K.)
| | - Martin Kopp
- Department of Sport Science, University of Innsbruck, 6020 Innsbruck, Austria; (M.B.); (M.K.)
| | - Alba Di Pardo
- IRCCS Neuromed, 86077 Pozzilli, Italy; (G.P.); (A.D.P.); (V.M.)
| | | | - Andy V. Khamoui
- Department of Exercise Science and Health Promotion, Florida Atlantic University, Boca Raton, FL 33458, USA;
- Institute for Human Health and Disease Intervention, Florida Atlantic University, Jupiter, FL 33458, USA
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Xu R, Cao JW, Lv HL, Geng Y, Guo MY. Polyethylene microplastics induced gut microbiota dysbiosis leading to liver injury via the TLR2/NF-κB/NLRP3 pathway in mice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170518. [PMID: 38286276 DOI: 10.1016/j.scitotenv.2024.170518] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 01/31/2024]
Abstract
Microplastics (MPs) are ubiquitous environmental contaminants that have negative impacts on health and safety. The gut microbiota plays multiple roles as a newly discovered virtual metabolic organ. The objective of this study was to investigate the potential of MPs to cause liver injury by disrupting the balance of gut microbiota. The results indicated that exposure to MPs resulted in liver damage and disrupted the homeostasis of gut microbiota. MPs significantly reduced the liver organ coefficient, leading to liver cell injury and impaired function. Additionally, there was an increase in the expression of fibril-related proteins, which positively correlated with MPs concentration. Furthermore, MPs increased the relative abundances of Desulfovibrio, Clostridia, Enterorhabdus, Bacteroides, and Gemella while decreasing the abundance of Dubosoella. Different concentrations of MPs exhibited varying effects on specific bacterial groups, however, both concentrations resulted in an increase in pathogenic bacteria and a decrease in beneficial bacteria, as well as alterations in microbial structure. Moreover, MPs induced oxidative stress, inflammation, apoptosis and necrosis in liver cells. The study found that MPs disrupted gut microbiota homeostasis and activated TLR2/NF-κB/NLRP3 pathway in the liver, providing a new insight into the mechanism underlying MPs-induced liver injury. These findings serve as a warning regarding environmental pollution caused by MPs.
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Affiliation(s)
- Ran Xu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Jing-Wen Cao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Hong-Li Lv
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Yuan Geng
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Meng-Yao Guo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China.
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Zou X, Zou G, Zou X, Wang K, Chen Z. Gut microbiota and its metabolites in Alzheimer's disease: from pathogenesis to treatment. PeerJ 2024; 12:e17061. [PMID: 38495755 PMCID: PMC10944166 DOI: 10.7717/peerj.17061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/15/2024] [Indexed: 03/19/2024] Open
Abstract
Introduction An increasing number of studies have demonstrated that altered microbial diversity and function (such as metabolites), or ecological disorders, regulate bowel-brain axis involvement in the pathophysiologic processes in Alzheimer's disease (AD). The dysregulation of microbes and their metabolites can be a double-edged sword in AD, presenting the possibility of microbiome-based treatment options. This review describes the link between ecological imbalances and AD, the interactions between AD treatment modalities and the microbiota, and the potential of interventions such as prebiotics, probiotics, synbiotics, fecal microbiota transplantation, and dietary interventions as complementary therapeutic strategies targeting AD pathogenesis and progression. Survey methodology Articles from PubMed and china.com on intestinal flora and AD were summarized to analyze the data and conclusions carefully to ensure the comprehensiveness, completeness, and accuracy of this review. Conclusions Regulating the gut flora ecological balance upregulates neurotrophic factor expression, regulates the microbiota-gut-brain (MGB) axis, and suppresses the inflammatory responses. Based on emerging research, this review explored novel directions for future AD research and clinical interventions, injecting new vitality into microbiota research development.
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Affiliation(s)
- Xinfu Zou
- Subject of Integrated Chinese and Western Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Guoqiang Zou
- Subject of Traditional Chinese Medicine, Shandong University Of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Xinyan Zou
- College of Traditional Chinese Medicine, Hebei University, Baoding, Hebei, China
| | - Kangfeng Wang
- Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Zetao Chen
- Subject of Integrated Chinese and Western Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
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Ma YY, Li X, Yu JT, Wang YJ. Therapeutics for neurodegenerative diseases by targeting the gut microbiome: from bench to bedside. Transl Neurodegener 2024; 13:12. [PMID: 38414054 PMCID: PMC10898075 DOI: 10.1186/s40035-024-00404-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
The aetiologies and origins of neurodegenerative diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) and Huntington's disease (HD), are complex and multifaceted. A growing body of evidence suggests that the gut microbiome plays crucial roles in the development and progression of neurodegenerative diseases. Clinicians have come to realize that therapeutics targeting the gut microbiome have the potential to halt the progression of neurodegenerative diseases. This narrative review examines the alterations in the gut microbiome in AD, PD, ALS and HD, highlighting the close relationship between the gut microbiome and the brain in neurodegenerative diseases. Processes that mediate the gut microbiome-brain communication in neurodegenerative diseases, including the immunological, vagus nerve and circulatory pathways, are evaluated. Furthermore, we summarize potential therapeutics for neurodegenerative diseases that modify the gut microbiome and its metabolites, including diets, probiotics and prebiotics, microbial metabolites, antibacterials and faecal microbiome transplantation. Finally, current challenges and future directions are discussed.
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Affiliation(s)
- Yuan-Yuan Ma
- Department of Neurology and Centre for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
- Institute of Brain and Intelligence, Third Military Medical University, Chongqing, 400042, China
- Chongqing Key Laboratory of Ageing and Brain Diseases, Chongqing, 400042, China
| | - Xin Li
- Army 953 Hospital, Shigatse Branch of Xinqiao Hospital, Third Military Medical University, Shigatse, 857000, China
| | - Jin-Tai Yu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China.
| | - Yan-Jiang Wang
- Department of Neurology and Centre for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China.
- Institute of Brain and Intelligence, Third Military Medical University, Chongqing, 400042, China.
- Chongqing Key Laboratory of Ageing and Brain Diseases, Chongqing, 400042, China.
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Mascellino MT. Molecular Research in Human Microbiome. Int J Mol Sci 2023; 24:14975. [PMID: 37834423 PMCID: PMC10573423 DOI: 10.3390/ijms241914975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Recent evidence has shown that the human microbiome is associated with a wide range of diseases, from non-neoplastic to tumourigenesis, including cancer, inflammation, intestinal damage, etc [...].
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Affiliation(s)
- Maria Teresa Mascellino
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
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