scholarly journals Human Gut Mycobiome in IBD

2020 ◽  
Author(s):  
Mario Matijasic ◽  
Tomislav Meštrović ◽  
Hana Čipčić Paljetak ◽  
Mihaela Perić ◽  
Anja Barešić ◽  
...  
Keyword(s):  
Fungal Communities ◽  
Host Immune System ◽  
Gastrointestinal Microbiota ◽  
Human Gut ◽  
Microbial Ecosystem ◽  
Functional Roles ◽  
The Past ◽  
Bacterial Microbiota ◽  
Health And Disease ◽  
Inflammatory Bowel

The human microbiota is a diverse microbial ecosystem associated with many beneficial physiological functions, as well as numerous disease etiologies. Dominated by bacteria, the microbiota also includes commensal populations of fungi, viruses, archaea, and protists. Unlike bacterial microbiota, which was extensively studied in the past two decades, these non-bacterial microorganisms, their functional roles, and their interaction with one another or with host immune system have not been as widely explored. This review covers the recent findings on the fungal communities of the human gastrointestinal microbiota, termed the “mycobiome”, and their involvement in health and disease, with particular focus on the pathophysiology of inflammatory bowel disease.

scholarly journals Gut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD

2020 ◽  
Vol 21 (8) ◽  
pp. 2668 ◽  
Author(s):  
Mario Matijašić ◽  
Tomislav Meštrović ◽  
Hana Čipčić Paljetak ◽  
Mihaela Perić ◽  
Anja Barešić ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Bacterial Communities ◽  
Host Immune System ◽  
Gastrointestinal Microbiota ◽  
Microbial Ecosystem ◽  
Functional Roles ◽  
The Past ◽  
Bacterial Microbiota ◽  
Health And Disease ◽  
Inflammatory Bowel

The human microbiota is a diverse microbial ecosystem associated with many beneficial physiological functions as well as numerous disease etiologies. Dominated by bacteria, the microbiota also includes commensal populations of fungi, viruses, archaea, and protists. Unlike bacterial microbiota, which was extensively studied in the past two decades, these non-bacterial microorganisms, their functional roles, and their interaction with one another or with host immune system have not been as widely explored. This review covers the recent findings on the non-bacterial communities of the human gastrointestinal microbiota and their involvement in health and disease, with particular focus on the pathophysiology of inflammatory bowel disease.

Gut Mycobiota and Fungal Metabolites in Human Homeostasis

2018 ◽  
Vol 20 (2) ◽  
pp. 232-240 ◽  
Author(s):  
Izabella Mogilnicka ◽  
Marcin Ufnal
Keyword(s):  
Wide Spectrum ◽  
Biological Effects ◽  
Fungal Species ◽  
Fungal Metabolites ◽  
Human Gut ◽  
Fecal Transplantation ◽  
Bacterial Microbiota ◽  
Bowel Diseases ◽  
Inflammatory Bowel

Background:Accumulating evidence suggests that microbiota play an important role in host’s homeostasis. Thus far, researchers have mostly focused on the role of bacterial microbiota. However, human gut is a habitat for several fungal species, which produce numerous metabolites. Furthermore, various types of food and beverages are rich in a wide spectrum of fungi and their metabolites.Methods:We searched PUBMED and Google Scholar databases to identify clinical and pre-clinical studies on fungal metabolites, composition of human mycobiota and fungal dysbiosis.Results:Fungal metabolites may serve as signaling molecules and exert significant biological effects including trophic, anti-inflammatory or antibacterial actions. Finally, research suggests an association between shifts in gut fungi composition and human health. Changes in mycobiota composition have been found in obesity, hepatitis and inflammatory bowel diseases.Conclusion:The influence of mycobiota and dietary fungi on homeostasis in mammals suggests a pharmacotherapeutic potential of modulating the mycobiota which may include treatment with probiotics and fecal transplantation. Furthermore, antibacterial action of fungi-derived molecules may be considered as a substitution for currently used antibacterial agents and preservatives in food industry.

scholarly journals Understanding human gut diseases at single-cell resolution

2020 ◽  
Vol 29 (R1) ◽  
pp. R51-R58 ◽  
Author(s):  
Emilia Bigaeva ◽  
Werna T C Uniken Venema ◽  
Rinse K Weersma ◽  
Eleonora A M Festen
Keyword(s):  
Single Cell ◽  
Digestive System ◽  
Cell Types ◽  
Specific Cell ◽  
Human Gut ◽  
The Past ◽  
Distinct Cell ◽  
Transcriptional Variation ◽  
Single Cell Rna Sequencing ◽  
Inflammatory Bowel

Abstract Our understanding of gut functioning and pathophysiology has grown considerably in the past decades, and advancing technologies enable us to deepen this understanding. Single-cell RNA sequencing (scRNA-seq) has opened a new realm of cellular diversity and transcriptional variation in the human gut at a high, single-cell resolution. ScRNA-seq has pushed the science of the digestive system forward by characterizing the function of distinct cell types within complex intestinal cellular environments, by illuminating the heterogeneity within specific cell populations and by identifying novel cell types in the human gut that could contribute to a variety of intestinal diseases. In this review, we highlight recent discoveries made with scRNA-seq that significantly advance our understanding of the human gut both in health and across the spectrum of gut diseases, including inflammatory bowel disease, colorectal carcinoma and celiac disease.

scholarly journals Gut Inflammation and Immunity: What Is the Role of the Human Gut Virome?

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Alfredo Focà ◽  
Maria Carla Liberto ◽  
Angela Quirino ◽  
Nadia Marascio ◽  
Emilia Zicca ◽  
...  
Keyword(s):  
Immune System ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Dynamic Equilibrium ◽  
Plant Viruses ◽  
Host Cells ◽  
Host Immune System ◽  
Intestinal Immunity ◽  
Human Gut ◽  
Bacterial Microbiota

The human virome comprises viruses that infect host cells, virus-derived elements in our chromosomes, and viruses that infect other organisms, including bacteriophages and plant viruses. The development of high-throughput sequencing techniques has shown that the human gut microbiome is a complex community in which the virome plays a crucial role into regulation of intestinal immunity and homeostasis. Nevertheless, the size of the human virome is still poorly understood. Indeed the enteric virome is in a continuous and dynamic equilibrium with other components of the gut microbiome and the gut immune system, an interaction that may influence the health and disease of the host. We review recent evidence on the viruses found in the gastrointestinal tract, discussing their interactions with the resident bacterial microbiota and the host immune system, in order to explore the potential impact of the virome on human health.

scholarly journals The gut virome: the ‘missing link’ between gut bacteria and host immunity?

2019 ◽  
Vol 12 ◽  
pp. 175628481983662 ◽  
Author(s):  
Indrani Mukhopadhya ◽  
Jonathan P. Segal ◽  
Simon R. Carding ◽  
Ailsa L. Hart ◽  
Georgina L. Hold
Keyword(s):  
Inflammatory Bowel Disease ◽  
Gut Microbiota ◽  
Well Being ◽  
Living Cells ◽  
Host Immunity ◽  
Current Understanding ◽  
Human Gut ◽  
Bacterial Microbiome ◽  
Health And Disease ◽  
Inflammatory Bowel

The human gut virome includes a diverse collection of viruses that infect our own cells as well as other commensal organisms, directly impacting on our well-being. Despite its predominance, the virome remains one of the least understood components of the gut microbiota, with appropriate analysis toolkits still in development. Based on its interconnectivity with all living cells, it is clear that the virome cannot be studied in isolation. Here we review the current understanding of the human gut virome, specifically in relation to other constituents of the microbiome, its evolution and life-long association with its host, and our current understanding in the context of inflammatory bowel disease and associated therapies. We propose that the gut virome and the gut bacterial microbiome share similar trajectories and interact in both health and disease and that future microbiota studies should in parallel characterize the gut virome to uncover its role in health and disease.

scholarly journals GutCyc: a Multi-Study Collection of Human Gut Microbiome Metabolic Models

2016 ◽  
Author(s):  
Aria S. Hahn ◽  
Tomer Altman ◽  
Kishori M. Konwar ◽  
Niels W. Hanson ◽  
Dongjae Kim ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Human Microbiome ◽  
Therapeutic Interventions ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Disease States ◽  
Health And Disease ◽  
Inflammatory Bowel

AbstractAdvances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GUTCYC, a compendium of environmental pathway genome databases constructed from 418 assembled human microbiome datasets using METAPATHWAYS, enabling reproducible functional metagenomic annotation. We also generated metabolic network reconstructions for each metagenome using the PATHWAY TOOLS software, empowering researchers and clinicians interested in visualizing and interpreting metabolic pathways encoded by the human gut microbiome. For the first time, GUTCYC provides consistent annotations and metabolic pathway predictions, making possible comparative community analyses between health and disease states in inflammatory bowel disease, Crohn’s disease, and type 2 diabetes. GUTCYC data products are searchable online, or may be downloaded and explored locally using METAPATHWAYS and PATHWAY TOOLS.

scholarly journals Digestive Dysbiosis in Systemic Scleroderma: a Review

2021 ◽  
Vol 6 (2) ◽  
pp. 53-59
Author(s):  
Ioana Bratoiu ◽  
Alexandra Burlui ◽  
Patricia Richter ◽  
Anca Cardoneanu ◽  
Ciprian Rezus ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Clinical Manifestations ◽  
Scientific Data ◽  
Host Immune System ◽  
Gastrointestinal Microbiota ◽  
Internal Organs ◽  
Health And Disease ◽  
Gastrointestinal Dysbiosis ◽  
The Relationship

Abstract Systemic sclerosis (SSc) is a rare autoimmune disease characterized by widespread microvasculopathy, inflammation, and fibrosis of the skin and internal organs. The involvement of the gastrointestinal tract is associated with a wide variety of symptoms and affects circa 90% of patients during the course of the disease. The gastrointestinal microbiota contains trillions of microbial cells and has been found to contribute to both local and systemic homeostasis. In both health and disease, a dynamic interrelationship between gut microbiome activity and the host immune system has been identified. Gastrointestinal dysbiosis has been described as having an important role in obesity, diabetes mellitus, liver disease, cardiovascular and neuropsychiatric disorders, neoplasia, as well as autoimmunity. Recent scientific data indicates a notable role of dysbiosis in the pathogenesis of SSc-related digestive involvement together with various other clinical manifestations. The present review aims to summarize the recent findings regarding digestive dysbiosis as well as the relationship between gastrointestinal microbiota and certain features of SSc.

scholarly journals Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth–gut axis

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Vishnu Prasoodanan P. K. ◽  
Ashok K. Sharma ◽  
Shruti Mahajan ◽  
Darshan B. Dhakan ◽  
Abhijit Maji ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Antibiotic Resistance Genes ◽  
Human Gut ◽  
Metabolizing Enzymes ◽  
Plant Polysaccharides ◽  
Profound Impact ◽  
Functional Roles ◽  
Inflammatory Bowel ◽  
Abundance And Diversity ◽  
Polysaccharide Utilization Loci

AbstractThe abundance and diversity of host-associated Prevotella species have a profound impact on human health. To investigate the composition, diversity, and functional roles of Prevotella in the human gut, a population-wide analysis was carried out on 586 healthy samples from western and non-western populations including the largest Indian cohort comprising of 200 samples, and 189 Inflammatory Bowel Disease samples from western populations. A higher abundance and diversity of Prevotella copri species enriched in complex plant polysaccharides metabolizing enzymes, particularly pullulanase containing polysaccharide-utilization-loci (PUL), were found in Indian and non-western populations. A higher diversity of oral inflammations-associated Prevotella species and an enrichment of virulence factors and antibiotic resistance genes in the gut microbiome of western populations speculates an existence of a mouth-gut axis. The study revealed the landscape of Prevotella composition in the human gut microbiome and its impact on health in western and non-western populations.

scholarly journals Phages and Human Health: More Than Idle Hitchhikers

Viruses ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 587 ◽  
Author(s):  
Lawrence ◽  
Baldridge ◽  
Handley
Keyword(s):  
Human Health ◽  
Current Knowledge ◽  
Metagenomic Sequencing ◽  
Human Gut ◽  
Viral Origin ◽  
Complex Samples ◽  
Disease States ◽  
Healthy Infants ◽  
Health And Disease ◽  
Inflammatory Bowel

Bacteriophages, or phages, are viruses that infect bacteria and archaea. Phages have diverse morphologies and can be coded in DNA or RNA and as single or double strands with a large range of genome sizes. With the increasing use of metagenomic sequencing approaches to analyze complex samples, many studies generate massive amounts of “viral dark matter”, or sequences of viral origin unable to be classified either functionally or taxonomically. Metagenomic analysis of phages is still in its infancy, and uncovering novel phages continues to be a challenge. Work over the past two decades has begun to uncover key roles for phages in different environments, including the human gut. Recent studies in humans have identified expanded phage populations in both healthy infants and in inflammatory bowel disease patients, suggesting distinct phage activity during development and in specific disease states. In this review, we examine our current knowledge of phage biology and discuss recent efforts to improve the analysis and discovery of novel phages. We explore the roles phages may play in human health and disease and discuss the future of phage research.

scholarly journals Molecular Pathogenesis of Hodgkin Lymphoma: Past, Present, Future

2020 ◽  
Vol 21 (18) ◽  
pp. 6623 ◽  
Author(s):  
Marc Bienz ◽  
Salima Ramdani ◽  
Hans Knecht
Keyword(s):  
Immune System ◽  
Targeted Therapy ◽  
Signaling Pathways ◽  
Hodgkin Lymphoma ◽  
Genetic Instability ◽  
Host Immune System ◽  
Cellular Interactions ◽  
Classical Hodgkin Lymphoma ◽  
The Past

Our understanding of the tumorigenesis of classical Hodgkin lymphoma (cHL) and the formation of Reed–Sternberg cells (RS-cells) has evolved drastically in the last decades. More recently, a better characterization of the signaling pathways and the cellular interactions at play have paved the way for new targeted therapy in the hopes of improving outcomes. However, important gaps in knowledge remain that may hold the key for significant changes of paradigm in this lymphoma. Here, we discuss the past, present, and future of cHL, and review in detail the more recent discoveries pertaining to genetic instability, anti-apoptotic signaling pathways, the tumoral microenvironment, and host-immune system evasion in cHL.

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