Microbiome research reports最新文献_第6页

Impact of SARS-CoV2 infection on gut microbiota dysbiosis SARS-CoV2 感染对肠道微生物群失调的影响

Microbiome research reports Pub Date : 2023-12-06 DOI: 10.20517/mrr.2023.48

Zhenming Xiao, Miaomiao Pan, Xinyao Li, Chao Zhao

{"title":"Impact of SARS-CoV2 infection on gut microbiota dysbiosis","authors":"Zhenming Xiao, Miaomiao Pan, Xinyao Li, Chao Zhao","doi":"10.20517/mrr.2023.48","DOIUrl":"https://doi.org/10.20517/mrr.2023.48","url":null,"abstract":"The composition and function of the gut microbiota constantly influence health. Disruptions in this delicate balance, termed gut microbiota dysbiosis, have been implicated in various adverse health events. As the largest global epidemic since 1918, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had devastating consequences. While the primary impact of Corona Virus Disease 2019 (COVID-19) has been on the respiratory system, a growing body of research has unveiled the significant involvement of the gastrointestinal tract as well. Emerging evidence underscores notable alterations in the gut microbiome of COVID-19 patients. In addition, the gut microbiome is also characterized by an abundance of opportunistic pathogens, which is related to disease manifestations of COVID-19 patients. The intricate bidirectional interaction between the respiratory mucosa and the gut microbiota, known as the gut-lung axis, emerges as a crucial player in the pathological immune response triggered by SARS-CoV-2. Here, we discuss microbiota-based gut characteristics of COVID-19 patients and the long-term consequences of gut microbiota dysregulation. These insights could potentially transform the development of long-term interventions for COVID-19, offering hope for improved outcomes and enhanced patient recovery.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"61 33","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138594944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Pathways linking microbiota-gut-brain axis with neuroinflammatory mechanisms in Alzheimer’s pathophysiology 阿尔茨海默病病理生理学中微生物群-肠-脑轴与神经炎症机制的联系途径

Microbiome research reports Pub Date : 2023-12-06 DOI: 10.20517/mrr.2023.39

Nathaniel Hochuli, S. Kadyan, Gwoncheol Park, Cole Patoine, R. Nagpal

{"title":"Pathways linking microbiota-gut-brain axis with neuroinflammatory mechanisms in Alzheimer’s pathophysiology","authors":"Nathaniel Hochuli, S. Kadyan, Gwoncheol Park, Cole Patoine, R. Nagpal","doi":"10.20517/mrr.2023.39","DOIUrl":"https://doi.org/10.20517/mrr.2023.39","url":null,"abstract":"Disturbances in the local and peripheral immune systems are closely linked to a wide range of diseases. In the context of neurodegenerative disorders such as Alzheimer’s disease (AD), inflammation plays a crucial role, often appearing as a common manifestation despite the variability in the occurrence of other pathophysiological hallmarks. Thus, combating neuroinflammation holds promise in treating complex pathophysiological diseases like AD. Growing evidence suggests the gut microbiome’s crucial role in shaping the pathogenesis of AD by influencing inflammatory mediators. Gut dysbiosis can potentially activate neuroinflammatory pathways through bidirectional signaling of the gut-brain axis; however, the precise mechanisms of this complex interweaved network remain largely unclear. In these milieus, this review attempts to summarize the contributing role of gut microbiome-mediated neuroinflammatory signals in AD pathophysiology, while also pondering potential mechanisms through which commensal and pathogenic gut microbes affect neuroinflammation. While certain taxa such as Roseburia and Escherichia have been strongly correlated with AD, other clades such as Bacteroides and Faecalibacterium exhibit variations at the species and strain levels. In order to disentangle the inflammatory aspects of neurodegeneration attributed to the gut microbiome, it is imperative that future mechanistic studies investigate the species/strain-level dependency of commensals, opportunistic, and pathogenic gut microbes that consistently show correlations with AD patients across multiple associative studies.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"27 11","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138596422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Saponin treatment for eukaryotic DNA depletion alters the microbial DNA profiles by reducing the abundance of Gram-negative bacteria in metagenomics analyses 真核生物DNA耗竭的皂素处理通过减少宏基因组学分析中革兰氏阴性菌的丰度来改变微生物DNA谱

Microbiome research reports Pub Date : 2023-11-15 DOI: 10.20517/mrr.2023.02

Giulia Longhi, Chiara Argentini, Federico Fontana, Chiara Tarracchini, Leonardo Mancabelli, Gabriele Andrea Lugli, Giulia Alessandri, Edith Lahner, Giulia Pivetta, Francesca Turroni, Marco Ventura, Christian Milani

{"title":"Saponin treatment for eukaryotic DNA depletion alters the microbial DNA profiles by reducing the abundance of Gram-negative bacteria in metagenomics analyses","authors":"Giulia Longhi, Chiara Argentini, Federico Fontana, Chiara Tarracchini, Leonardo Mancabelli, Gabriele Andrea Lugli, Giulia Alessandri, Edith Lahner, Giulia Pivetta, Francesca Turroni, Marco Ventura, Christian Milani","doi":"10.20517/mrr.2023.02","DOIUrl":"https://doi.org/10.20517/mrr.2023.02","url":null,"abstract":"Background: Recent advances in microbiome sequencing techniques have provided new insights into the role of the microbiome on human health with potential diagnostic implications. However, these developments are often hampered by the presence of a large amount of human DNA interfering with the analysis of the bacterial content. Nowadays, extensive scientific literature focuses on eukaryotic DNA depletion methods, which successfully remove host DNA in microbiome studies, even if a precise assessment of the impact on bacterial DNA is often missing. Methods: Here, we have investigated a saponin-based DNA isolation protocol commonly applied to different biological matrices to deplete the released host DNA. Results: The bacterial DNA obtained was used to assess the relative abundance of bacterial and human DNA, revealing that the inclusion of 2.5% wt/vol saponin allowed the depletion of most of the host’s DNA in favor of bacterial DNA enrichment. However, shotgun metagenomic sequencing showed inaccurate microbial profiles of the DNA samples, highlighting an erroneous increase in Gram-positive DNA. Even the application of 0.0125% wt/vol saponin altered the bacterial profile by depleting Gram-negative bacteria, resulting in an overall increase of Gram-positive bacterial DNA. Conclusion: The application of the saponin-based protocol drastically changes the detection of the microbial composition of human-related biological specimens. In this context, we revealed that saponin targets not only host cells but also specific bacterial cells, thus inducing a drastic reduction in the profiling of Gram-negative bacterial DNA.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"2 5","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136229211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Understanding the role of gut microfloral bifidobacterium in cancer and its potential therapeutic applications 了解肠道菌群双歧杆菌在癌症中的作用及其潜在的治疗应用

Microbiome research reports Pub Date : 2023-10-31 DOI: 10.20517/mrr.2023.51

Devanshi Sharma, Devanshi Gajjar, Sriram Seshadri

引用次数: 0

Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome 酵母宏基因组学:真核微生物组分析中的分析挑战

Microbiome research reports Pub Date : 2023-10-23 DOI: 10.20517/mrr.2023.27

Sonia Renzi, Stefano Nenciarini, Giovanni Bacci, Duccio Cavalieri

引用次数: 0

Bifidobacterium and the intestinal mucus layer 双歧杆菌和肠道黏液层

Microbiome research reports Pub Date : 2023-09-27 DOI: 10.20517/mrr.2023.37

Alyssa Gutierrez, Brenton Pucket, Melinda A. Engevik

引用次数: 0

Interplay between inflammatory bowel disease therapeutics and the gut microbiome reveals opportunities for novel treatment approaches. 炎症性肠病疗法和肠道微生物组之间的相互作用揭示了新的治疗方法的机会。

Microbiome research reports Pub Date : 2023-09-26 DOI: 10.20517/mrr.2023.41

Catherine O'Reilly, Susan Mills, Mary C Rea, Aonghus Lavelle, Subrata Ghosh, Colin Hill, R Paul Ross

{"title":"Interplay between inflammatory bowel disease therapeutics and the gut microbiome reveals opportunities for novel treatment approaches.","authors":"Catherine O'Reilly, Susan Mills, Mary C Rea, Aonghus Lavelle, Subrata Ghosh, Colin Hill, R Paul Ross","doi":"10.20517/mrr.2023.41","DOIUrl":"10.20517/mrr.2023.41","url":null,"abstract":"Inflammatory bowel disease (IBD) is a complex heterogeneous disorder defined by recurring chronic inflammation of the gastrointestinal tract, attributed to a combination of factors including genetic susceptibility, altered immune response, a shift in microbial composition/microbial insults (infection/exposure), and environmental influences. Therapeutics generally used to treat IBD mainly focus on the immune response and include non-specific anti-inflammatory and immunosuppressive therapeutics and targeted therapeutics aimed at specific components of the immune system. Other therapies include exclusive enteral nutrition and emerging stem cell therapies. However, in recent years, scientists have begun to examine the interplay between these therapeutics and the gut microbiome, and we present this information here. Many of these therapeutics are associated with alterations to gut microbiome composition and functionality, often driving it toward a \"healthier profile\" and preclinical studies have revealed that such alterations can play an important role in therapeutic efficacy. The gut microbiome can also improve or hinder IBD therapeutic efficacy or generate undesirable metabolites. For certain IBD therapeutics, the microbiome composition, particularly before treatment, may serve as a biomarker of therapeutic efficacy. Utilising this information and manipulating the interactions between the gut microbiome and IBD therapeutics may enhance treatment outcomes in the future and bring about new opportunities for personalised, precision medicine.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"2 ","pages":"35"},"PeriodicalIF":0.0,"publicationDate":"2023-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7615213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41242966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microbiota-gut-brain axis and ketogenic diet: how close are we to tackling epilepsy? 微生物-肠-脑轴和生酮饮食:我们离治疗癫痫还有多远?

Microbiome research reports Pub Date : 2023-08-29 eCollection Date: 2023-01-01 DOI: 10.20517/mrr.2023.24

Mariachiara Mengoli, Gabriele Conti, Marco Fabbrini, Marco Candela, Patrizia Brigidi, Silvia Turroni, Monica Barone

{"title":"Microbiota-gut-brain axis and ketogenic diet: how close are we to tackling epilepsy?","authors":"Mariachiara Mengoli, Gabriele Conti, Marco Fabbrini, Marco Candela, Patrizia Brigidi, Silvia Turroni, Monica Barone","doi":"10.20517/mrr.2023.24","DOIUrl":"10.20517/mrr.2023.24","url":null,"abstract":"The microbiota-gut-brain axis refers to the intricate bidirectional communication between commensal microorganisms residing in the digestive tract and the central nervous system, along neuroendocrine, metabolic, immune, and inflammatory pathways. This axis has been suggested to play a role in several neurological disorders, such as Parkinson's disease, Alzheimer's disease, multiple sclerosis, and epilepsy, paving the way for microbiome-based intervention strategies for the mitigation and treatment of symptoms. Epilepsy is a multifaceted neurological condition affecting more than 50 million individuals worldwide, 30% of whom do not respond to conventional pharmacological therapies. Among the first-hand microbiota modulation strategies, nutritional interventions represent an easily applicable option in both clinical and home settings. In this narrative review, we summarize the mechanisms underlying the microbiota-gut-brain axis involvement in epilepsy, discuss the impact of antiepileptic drugs on the gut microbiome, and then the impact of a particular dietary pattern, the ketogenic diet, on the microbiota-gut-brain axis in epileptic patients. The investigation of the microbiota response to non-pharmacological therapies is an ever-expanding field with the potential to allow the design of increasingly accessible and successful intervention strategies.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"1 1","pages":"32"},"PeriodicalIF":0.0,"publicationDate":"2023-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688818/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81337422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Connect the dots: sketching out microbiome interactions through networking approaches. 连接点:通过网络方法勾勒出微生物组的相互作用。

Microbiome research reports Pub Date : 2023-07-18 eCollection Date: 2023-01-01 DOI: 10.20517/mrr.2023.25

Marco Fabbrini, Daniel Scicchitano, Marco Candela, Silvia Turroni, Simone Rampelli

{"title":"Connect the dots: sketching out microbiome interactions through networking approaches.","authors":"Marco Fabbrini, Daniel Scicchitano, Marco Candela, Silvia Turroni, Simone Rampelli","doi":"10.20517/mrr.2023.25","DOIUrl":"10.20517/mrr.2023.25","url":null,"abstract":"Microbiome networking analysis has emerged as a powerful tool for studying the complex interactions among microorganisms in various ecological niches, including the human body and several environments. This analysis has been used extensively in both human and environmental studies, revealing key taxa and functional units peculiar to the ecosystem considered. In particular, it has been mainly used to investigate the effects of environmental stressors, such as pollution, climate change or therapies, on host-associated microbial communities and ecosystem function. In this review, we discuss the latest advances in microbiome networking analysis, including methods for constructing and analyzing microbiome networks, and provide a case study on how to use these tools. These analyses typically involve constructing a network that represents interactions among microbial taxa or functional units, such as genes or metabolic pathways. Such networks can be based on a variety of data sources, including 16S rRNA sequencing, metagenomic sequencing, and metabolomics data. Once constructed, these networks can be analyzed to identify key nodes or modules important for the stability and function of the microbiome. By providing insights into essential ecological features of microbial communities, microbiome networking analysis has the potential to transform our understanding of the microbial world and its impact on human health and the environment.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"2 4","pages":"25"},"PeriodicalIF":0.0,"publicationDate":"2023-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10696587/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138500662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cross-feeding interactions between human gut commensals belonging to the Bacteroides and Bifidobacterium genera when grown on dietary glycans. 属拟杆菌属和双歧杆菌属的人类肠道共生菌在饮食聚糖上生长时的交叉摄食相互作用。

Microbiome research reports Pub Date : 2022-03-18 eCollection Date: 2022-01-01 DOI: 10.20517/mrr.2021.05

Pedro Fernandez-Julia, Daniel M Commane, Douwe van Sinderen, Jose Munoz-Munoz

{"title":"Cross-feeding interactions between human gut commensals belonging to the Bacteroides and Bifidobacterium genera when grown on dietary glycans.","authors":"Pedro Fernandez-Julia, Daniel M Commane, Douwe van Sinderen, Jose Munoz-Munoz","doi":"10.20517/mrr.2021.05","DOIUrl":"10.20517/mrr.2021.05","url":null,"abstract":"Elements of the human gut microbiota metabolise many host- and diet-derived, non-digestible carbohydrates (NDCs). Intestinal fermentation of NDCs salvages energy and resources for the host and generates beneficial metabolites, such as short chain fatty acids, which contribute to host health. The development of functional NDCs that support the growth and/or metabolic activity of specific beneficial gut bacteria, is desirable, but dependent on an in-depth understanding of the pathways of carbohydrate fermentation. The purpose of this review is to provide an appraisal of what is known about the roles of, and interactions between, Bacteroides and Bifidobacterium as key members involved in NDC utilisation. Bacteroides is considered an important primary degrader of complex NDCs, thereby generating oligosaccharides, which in turn can be fermented by secondary degraders. In this review, we will therefore focus on Bacteroides as an NDC-degrading specialist and Bifidobacterium as an important and purported probiotic representative of secondary degraders. We will describe cross-feeding interactions between members of these two genera. We note that there are limited studies exploring the interactions between Bacteroides and Bifidobacterium, specifically concerning β-glucan and arabinoxylan metabolism. This review therefore summarises the roles of these organisms in the breakdown of dietary fibre and the molecular mechanisms and interactions involved. Finally, it also highlights the need for further research into the phenomenon of cross-feeding between these organisms for an improved understanding of these cross-feeding mechanisms to guide the rational development of prebiotics to support host health or to prevent or combat disease associated with microbial dysbiosis.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"1 2","pages":"12"},"PeriodicalIF":0.0,"publicationDate":"2022-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688802/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138479961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12