scholarly journals Introduction to the human gut microbiota

2017 ◽  
Vol 474 (11) ◽  
pp. 1823-1836 ◽  
Author(s):  
Elizabeth Thursby ◽  
Nathalie Juge
Keyword(s):  
Gut Microbiota ◽  
Inflammatory Diseases ◽  
Intestinal Bacteria ◽  
Life Time ◽  
Gi Tract ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Dynamic Population

The human gastrointestinal (GI) tract harbours a complex and dynamic population of microorganisms, the gut microbiota, which exert a marked influence on the host during homeostasis and disease. Multiple factors contribute to the establishment of the human gut microbiota during infancy. Diet is considered as one of the main drivers in shaping the gut microbiota across the life time. Intestinal bacteria play a crucial role in maintaining immune and metabolic homeostasis and protecting against pathogens. Altered gut bacterial composition (dysbiosis) has been associated with the pathogenesis of many inflammatory diseases and infections. The interpretation of these studies relies on a better understanding of inter-individual variations, heterogeneity of bacterial communities along and across the GI tract, functional redundancy and the need to distinguish cause from effect in states of dysbiosis. This review summarises our current understanding of the development and composition of the human GI microbiota, and its impact on gut integrity and host health, underlying the need for mechanistic studies focusing on host–microbe interactions.

scholarly journals The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut

2019 ◽  
Vol 83 (2) ◽  
Author(s):  
Janneke Elzinga ◽  
John van der Oost ◽  
Willem M. de Vos ◽  
Hauke Smidt
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Well Being ◽  
Human Gut ◽  
Human Host ◽  
Advantages And Disadvantages ◽  
Human Gut Microbiota ◽  
Microbe Interactions ◽  
Host Microbe Interactions

SUMMARYThe human intestinal ecosystem is characterized by a complex interplay between different microorganisms and the host. The high variation within the human population further complicates the quest toward an adequate understanding of this complex system that is so relevant to human health and well-being. To study host-microbe interactions, defined synthetic bacterial communities have been introduced in gnotobiotic animals or in sophisticatedin vitrocell models. This review reinforces that our limited understanding has often hampered the appropriate design of defined communities that represent the human gut microbiota. On top of this, some communities have been applied toin vivomodels that differ appreciably from the human host. In this review, the advantages and disadvantages of using defined microbial communities are outlined, and suggestions for future improvement of host-microbe interaction models are provided. With respect to the host, technological advances, such as the development of a gut-on-a-chip system and intestinal organoids, may contribute to more-accuratein vitromodels of the human host. With respect to the microbiota, due to the increasing availability of representative cultured isolates and their genomic sequences, our understanding and controllability of the human gut “core microbiota” are likely to increase. Taken together, these advancements could further unravel the molecular mechanisms underlying the human gut microbiota superorganism. Such a gain of insight would provide a solid basis for the improvement of pre-, pro-, and synbiotics as well as the development of new therapeutic microbes.

scholarly journals From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota

mSystems ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Eugen Bauer ◽  
Ines Thiele
Keyword(s):  
Systems Biology ◽  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Computational Systems Biology ◽  
Human Gut ◽  
Novel Treatments ◽  
Human Gut Microbiota ◽  
Microbe Interactions ◽  
Constraint Based Modeling ◽  
Computational Systems

ABSTRACTAn important hallmark of the human gut microbiota is its species diversity and complexity. Various diseases have been associated with a decreased diversity leading to reduced metabolic functionalities. Common approaches to investigate the human microbiota include high-throughput sequencing with subsequent correlative analyses. However, to understand the ecology of the human gut microbiota and consequently design novel treatments for diseases, it is important to represent the different interactions between microbes with their associated metabolites. Computational systems biology approaches can give further mechanistic insights by constructing data- or knowledge-driven networks that represent microbe interactions. In this minireview, we will discuss current approaches in systems biology to analyze the human gut microbiota, with a particular focus on constraint-based modeling. We will discuss various community modeling techniques with their advantages and differences, as well as their application to predict the metabolic mechanisms of intestinal microbial communities. Finally, we will discuss future perspectives and current challenges of simulating realistic and comprehensive models of the human gut microbiota.

scholarly journals Masked trichothecene and zearalenone mycotoxins withstand digestion and absorption in the upper GI tract but are efficiently hydrolyzed by human gut microbiota in vitro

2017 ◽  
Vol 61 (4) ◽  
pp. 1600680 ◽  
Author(s):  
Silvia W. Gratz ◽  
Reshma Dinesh ◽  
Tomoya Yoshinari ◽  
Grietje Holtrop ◽  
Anthony J. Richardson ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gi Tract ◽  
Human Gut ◽  
Upper Gi ◽  
Human Gut Microbiota ◽  
Upper Gi Tract

scholarly journals Gut Microbiota and Iron: The Crucial Actors in Health and Disease

2018 ◽  
Vol 11 (4) ◽  
pp. 98 ◽  
Author(s):  
Bahtiyar Yilmaz ◽  
Hai Li
Keyword(s):  
Gut Microbiota ◽  
Inflammatory Diseases ◽  
Life Forms ◽  
Iron Availability ◽  
Human Beings ◽  
Human Gastrointestinal Tract ◽  
Dynamic Modulation ◽  
Microbe Interactions ◽  
Health And Disease ◽  
Host Microbe Interactions

Iron (Fe) is a highly ample metal on planet earth (~35% of the Earth’s mass) and is particularly essential for most life forms, including from bacteria to mammals. Nonetheless, iron deficiency is highly prevalent in developing countries, and oral administration of this metal is so far the most effective treatment for human beings. Notably, the excessive amount of unabsorbed iron leave unappreciated side effects at the highly interactive host–microbe interface of the human gastrointestinal tract. Recent advances in elucidating the molecular basis of interactions between iron and gut microbiota shed new light(s) on the health and pathogenesis of intestinal inflammatory diseases. We here aim to present the dynamic modulation of intestinal microbiota by iron availability, and conversely, the influence on dietary iron absorption in the gut. The central part of this review is intended to summarize our current understanding about the effects of luminal iron on host–microbe interactions in the context of human health and disease.

scholarly journals Human gut microbiota: does diet matter?

2014 ◽  
Vol 74 (1) ◽  
pp. 23-36 ◽  
Author(s):  
Johanna Maukonen ◽  
Maria Saarela
Keyword(s):  
Gut Microbiota ◽  
Digestive System ◽  
High Protein Diet ◽  
Normal Diet ◽  
Dietary Factors ◽  
The Body ◽  
Gi Tract ◽  
Dietary Interventions ◽  
Human Gut ◽  
Human Gut Microbiota

The human oro-gastrointestinal (GI) tract is a complex system, consisting of oral cavity, pharynx, oesophagus, stomach, small intestine, large intestine, rectum and anus, which all together with the accessory digestive organs constitute the digestive system. The function of the digestive system is to break down dietary constituents into small molecules and then absorb these for subsequent distribution throughout the body. Besides digestion and carbohydrate metabolism, the indigenous microbiota has an important influence on host physiological, nutritional and immunological processes, and commensal bacteria are able to modulate the expression of host genes that regulate diverse and fundamental physiological functions. The main external factors that can affect the composition of the microbial community in generally healthy adults include major dietary changes and antibiotic therapy. Changes in some selected bacterial groups have been observed due to controlled changes to the normal diet e.g. high-protein diet, high-fat diet, prebiotics, probiotics and polyphenols. More specifically, changes in the type and quantity of non-digestible carbohydrates in the human diet influence both the metabolic products formed in the lower regions of the GI tract and the bacterial populations detected in faeces. The interactions between dietary factors, gut microbiota and host metabolism are increasingly demonstrated to be important for maintaining homeostasis and health. Therefore the aim of this review is to summarise the effect of diet, and especially dietary interventions, on the human gut microbiota. Furthermore, the most important confounding factors (methodologies used and intrinsic human factors) in relation to gut microbiota analyses are elucidated.

scholarly journals The role of gut microbiota in health and disease: In vitro modeling of host-microbe interactions at the aerobe-anaerobe interphase of the human gut

Anaerobe ◽  
2017 ◽  
Vol 44 ◽  
pp. 3-12 ◽  
Author(s):  
Julius Z.H. von Martels ◽  
Mehdi Sadaghian Sadabad ◽  
Arno R. Bourgonje ◽  
Tjasso Blokzijl ◽  
Gerard Dijkstra ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Human Gut ◽  
In Vitro Modeling ◽  
Microbe Interactions ◽  
Health And Disease ◽  
Host Microbe Interactions

scholarly journals Changes in human gut microbiota composition are linked to the energy metabolic switch during 10 d of Buchinger fasting

2019 ◽  
Vol 8 ◽  
Author(s):  
Robin Mesnage ◽  
Franziska Grundler ◽  
Andreas Schwiertz ◽  
Yvon Le Maho ◽  
Françoise Wilhelmi de Toledo
Keyword(s):  
Gut Microbiota ◽  
Inflammatory Diseases ◽  
Well Being ◽  
Amplicon Sequencing ◽  
Serum Biochemistry ◽  
Rrna Gene ◽  
Human Gut ◽  
Metabolic Switch ◽  
Human Gut Microbiota ◽  
Inflammatory Status

Abstract Fasting is increasingly popular to manage metabolic and inflammatory diseases. Despite the role that the human gut microbiota plays in health and diseases, little is known about its composition and functional capacity during prolonged fasting when the external nutrient supply is reduced or suppressed. We analysed the effects of a 10-d periodic fasting on the faecal microbiota of fifteen healthy men. Participants fasted according to the peer-reviewed Buchinger fasting guidelines, which involve a daily energy intake of about 1046 kJ (250 kcal) and an enema every 2 d. Serum biochemistry confirmed the metabolic switch from carbohydrates to fatty acids and ketones. Emotional and physical well-being were enhanced. Faecal 16S rRNA gene amplicon sequencing showed that fasting caused a decrease in the abundance of bacteria known to degrade dietary polysaccharides such as Lachnospiraceae and Ruminococcaceae. There was a concomitant increase in Bacteroidetes and Proteobacteria (Escherichia coli and Bilophila wadsworthia), known to use host-derived energy substrates. Changes in taxa abundance were associated with serum glucose and faecal branched-chain amino acids (BCAA), suggesting that fasting-induced changes in the gut microbiota are associated with host energy metabolism. These effects were reversed after 3 months. SCFA levels were unchanged at the end of the fasting. We also monitored intestinal permeability and inflammatory status. IL-6, IL-10, interferon γ and TNFα levels increased when food was reintroduced, suggesting a reactivation of the postprandial immune response. We suggest that changes in the gut microbiota are part of the physiological adaptations to a 10-d periodic fasting, potentially influencing its beneficial health effects.

scholarly journals Nitric Oxide Impacts Human Gut Microbiota Diversity and Functionalities

mSystems ◽  
2021 ◽  
Author(s):  
Marion Leclerc ◽  
Cassandre Bedu-Ferrari ◽  
Lucie Etienne-Mesmin ◽  
Mahendra Mariadassou ◽  
Lucie Lebreuilly ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Inflammatory Response ◽  
Gut Microbiota ◽  
Inflammatory Diseases ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Microbiota Diversity ◽  
Gut Microbiota Dysbiosis

Gut microbiota dysbiosis has been associated with inflammatory diseases. The human inflammatory response leads to an overproduction of nitric oxide (NO) in the gut.

scholarly journals The Immune System through the Lens of Alcohol Intake and Gut Microbiota

2021 ◽  
Vol 22 (14) ◽  
pp. 7485
Author(s):  
Javier Calleja-Conde ◽  
Victor Echeverry-Alzate ◽  
Kora-Mareen Bühler ◽  
Pedro Durán-González ◽  
Jose Ángel Morales-García ◽  
...  
Keyword(s):  
Immune System ◽  
Gut Microbiota ◽  
Heavy Drinking ◽  
Intestinal Barrier ◽  
Intestinal Bacteria ◽  
Human Gut ◽  
Bacterial Composition ◽  
Intestinal Membrane ◽  
The Many ◽  
Dynamic Population

The human gut is the largest organ with immune function in our body, responsible for regulating the homeostasis of the intestinal barrier. A diverse, complex and dynamic population of microorganisms, called microbiota, which exert a significant impact on the host during homeostasis and disease, supports this role. In fact, intestinal bacteria maintain immune and metabolic homeostasis, protecting our organism against pathogens. The development of numerous inflammatory disorders and infections has been linked to altered gut bacterial composition or dysbiosis. Multiple factors contribute to the establishment of the human gut microbiota. For instance, diet is considered as one of the many drivers in shaping the gut microbiota across the lifetime. By contrast, alcohol is one of the many factors that disrupt the proper functioning of the gut, leading to a disruption of the intestinal barrier integrity that increases the permeability of the mucosa, with the final result of a disrupted mucosal immunity. This damage to the permeability of the intestinal membrane allows bacteria and their components to enter the blood tissue, reaching other organs such as the liver or the brain. Although chronic heavy drinking has harmful effects on the immune system cells at the systemic level, this review focuses on the effect produced on gut, brain and liver, because of their significance in the link between alcohol consumption, gut microbiota and the immune system.

In vitro study of the interaction between human gut microbiota and herbal extracts using willow bark extract as an example

Planta Medica ◽  
2016 ◽  
Vol 81 (S 01) ◽  
pp. S1-S381
Author(s):  
EM Pferschy-Wenzig ◽  
K Koskinen ◽  
C Moissl-Eichinger ◽  
R Bauer
Keyword(s):  
Gut Microbiota ◽  
In Vitro Study ◽  
Vitro Study ◽  
Bark Extract ◽  
Herbal Extracts ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Willow Bark
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