scholarly journals Enterotype-like microbiome stratification as emergent structure in complex adaptive systems: A mathematical model

2018 ◽  
Author(s):  
Miguel Ángel Martín
Keyword(s):  
Gut Microbiota ◽  
Complex Adaptive Systems ◽  
Gut Microbiome ◽  
Adaptive Systems ◽  
Underlying Mechanism ◽  
Underlying Structure ◽  
Valuable Insight ◽  
Mathematical Meaning ◽  
Human Gut ◽  
Stability And Resilience

AbstractBackgroundMetagenomics has provided valuable insight into human gut microbiome composition together with its structure and function. Studies suggest that the adult gut microbial community possess a certain amount of stability and resilience. The architecture of host-microbial symbiotic states suggested by microbiome clustering findings and co-occurrence functional networks might be involved in these properties. Models for understanding the underlying structure (including enterotypes) and derived properties are in demand by researchers.Principal findingsWe propose a simple random function system as a model approach of the adaption and self-organization of the microbiome space when fostering the optimal functioning of the system. The construction of this model is based on key facts of microbiota functioning reported in recent studies. We aim to demonstrate the existence of a probability distribution as a microbiome attractor resulting from an intermittent adaption process. Its mathematical structural properties explain the stability of gut microbiota and its ability for restoration after occasional perturbations. The model is consistent with microbiome clustering results and provides precise mathematical meaning to the gradient among enterotypes previously reported. The model also explains how intermittent perturbations, such as long-term dietary patterns, might affect the microbiome structure, and these results are consistent with previously reported experimental results.Conclusions/significanceThese mathematical facts implied by the model unveil an underlying mechanism that may explain gut microbiome structure and related experimental findings. Within this framework, stability and resilience properties of human gut microbiota are explained as a consequence of the model.

scholarly journals Fruits and their impact on the gut microbiota, gut motility and constipation

2021 ◽  
Vol 12 (19) ◽  
pp. 8850-8866
Author(s):  
Zoi Katsirma ◽  
Eirini Dimidi ◽  
Ana Rodriguez-Mateos ◽  
Kevin Whelan
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Nutrient Content ◽  
Mechanisms Of Action ◽  
Human Gut ◽  
Gut Motility ◽  
Gut Function

A summary of the mechanisms of action by which fruit products confer effects on the human gut function, motility and the gut microbiome, as well as an exploration of the effects of processing on the active nutrient content and efficacy of fruits.

scholarly journals Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients

2021 ◽  
Author(s):  
Yueqiong Ni ◽  
Zoltan Lohinai ◽  
Yoshitaro Heshiki ◽  
Balazs Dome ◽  
Judit Moldvay ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Gut Microbiota ◽  
Cancer Patients ◽  
Gut Microbiome ◽  
Human Gut ◽  
Microbial Composition ◽  
Shotgun Metagenomics ◽  
Lung Cancer Patients ◽  
Microbial Species ◽  
Functional Pathways

AbstractCachexia is associated with decreased survival in cancer patients and has a prevalence of up to 80%. The etiology of cachexia is poorly understood, and limited treatment options exist. Here, we investigated the role of the human gut microbiome in cachexia by integrating shotgun metagenomics and plasma metabolomics of 31 lung cancer patients. The cachexia group showed significant differences in the gut microbial composition, functional pathways of the metagenome, and the related plasma metabolites compared to non-cachectic patients. Branched-chain amino acids (BCAAs), methylhistamine, and vitamins were significantly depleted in the plasma of cachexia patients, which was also reflected in the depletion of relevant gut microbiota functional pathways. The enrichment of BCAAs and 3-oxocholic acid in non-cachectic patients were positively correlated with gut microbial species Prevotella copri and Lactobacillus gasseri, respectively. Furthermore, the gut microbiota capacity for lipopolysaccharides biosynthesis was significantly enriched in cachectic patients. The involvement of the gut microbiome in cachexia was further observed in a high-performance machine learning model using solely gut microbial features. Our study demonstrates the links between cachectic host metabolism and specific gut microbial species and functions in a clinical setting, suggesting that the gut microbiota could have an influence on cachexia with possible therapeutic applications.

scholarly journals Adopting seasonal regimen (Ritucharya) to modulate the seasonal variation in gut microbiome

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Deepthi. R ◽  
Vandana Rani M ◽  
Delvin T. Robin ◽  
Anusree Dileep
Keyword(s):  
Public Health ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Health Management ◽  
Disease Process ◽  
The Body ◽  
Leaky Gut ◽  
Human Gut ◽  
Extrinsic Factors ◽  
Application Prospects

AbstractThe science of Ayurveda with its strong and unique fundamentals holds its domain forever amidst all scientific and medical advancements. The concept of Shadkriyakala (the different phases of disease formation) holds relevance in preventive medicine and public health management as it provides ample chance to halt the disease process at each stage by timely intervention. In this review, we would like to bring to the limelight the relevance of Ritucharya (seasonal regimen) in primary prevention by modulating the gut microbiota. The modern gut microbiome researches now help us to better explore the Ayurveda theories of Agni (digestive fire) and Ama (metabolic toxins) preached centuries back. Ayurveda firmly proclaims that no disease ever arises without the derangement of Agni (digestive fire). The whole preventive and treatment methodology in Ayurveda focuses upon the modulation and management of “Agni” (digestive fire). When the functioning of Agni is deranged, Ama (metabolic toxin) is produced and it vitiates the doshas which spread throughout the body and manifest as varied diseases. A biomedical perspective of our reviews suggests that dysbiosis of microbial flora can cause a leaky gut by which the toxins of deranged digestive metabolism enter the bloodstream. Consequently, an inflammatory response occurs within the body which expresses out as diseases opportunistically. We meticulously reviewed the influence of extrinsic factors namely diet and climate on human gut microbiota, and our analysis emphasises the application prospects of Ritucharya (seasonal regimen), in regulating the dynamic host-microbe interaction.

Complex Adaptive Systems in the Behavioral and Social Sciences

1997 ◽  
Vol 1 (1) ◽  
pp. 42-71 ◽  
Author(s):  
Roy J. Eidelson
Keyword(s):  
Social Sciences ◽  
International Relations ◽  
Organizational Development ◽  
Complex Adaptive Systems ◽  
Coalition Formation ◽  
Criminal Behavior ◽  
Adaptive Systems ◽  
Underlying Structure ◽  
Political Transitions ◽  
Complex Adaptive

This article examines applications of complexity theory within the behavioral and social sciences. Specific attention is given to the fundamental characteristics of complex adaptive systems (CAS)—such as individuals, groups, and societies—including the underlying structure of CAS, the internal dynamics of evolving CAS, and how CAS respond to their environment. Examples drawn from psychology, sociology, economics, and political science include attitude formation, majority–minority relations, social networks, family systems, psychotherapy, norm formation, organizational development, coalition formation, economic instabilities, urban development, the electoral process, political transitions, international relations, social movements, drug policy, and criminal behavior. The discussion also addresses the obstacles to implementing the CAS perspective in the behavioral and social sciences and implications for research methodology.

scholarly journals ‘The way to a man's heart is through his gut microbiota’ – dietary pro- and prebiotics for the management of cardiovascular risk

2014 ◽  
Vol 73 (2) ◽  
pp. 172-185 ◽  
Author(s):  
Kieran M. Tuohy ◽  
Francesca Fava ◽  
Roberto Viola
Keyword(s):  
Metabolic Disease ◽  
Risk Factor ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Blood Cholesterol ◽  
Human Gut ◽  
Cvd Risk ◽  
Plant Foods ◽  
Whole Plant ◽  
The Way

The human gut microbiota has been identified as a possible novel CVD risk factor. This review aims to summarise recent insights connecting human gut microbiome activities with CVD and how such activities may be modulated by diet. Aberrant gut microbiota profiles have been associated with obesity, type 1 and type 2 diabetes and non-alcoholic fatty liver disease. Transfer of microbiota from obese animals induces metabolic disease and obesity in germ-free animals. Conversely, transfer of pathogen-free microbiota from lean healthy human donors to patients with metabolic disease can increase insulin sensitivity. Not only are aberrant microbiota profiles associated with metabolic disease, but the flux of metabolites derived from gut microbial metabolism of choline, phosphatidylcholine andl-carnitine has been shown to contribute directly to CVD pathology, providing one explanation for increased disease risk of eating too much red meat. Diet, especially high intake of fermentable fibres and plant polyphenols, appears to regulate microbial activities within the gut, supporting regulatory guidelines encouraging increased consumption of whole-plant foods (fruit, vegetables and whole-grain cereals), and providing the scientific rationale for the design of efficacious prebiotics. Similarly, recent human studies with carefully selected probiotic strains show that ingestion of viable microorganisms with the ability to hydrolyse bile salts can lower blood cholesterol, a recognised risk factor in CVD. Taken together such observations raise the intriguing possibility that gut microbiome modulation by whole-plant foods, probiotics and prebiotics may be at the base of healthy eating pyramids advised by regulatory agencies across the globe. In conclusion, dietary strategies which modulate the gut microbiota or their metabolic activities are emerging as efficacious tools for reducing CVD risk and indicate that indeed, the way to a healthy heart may be through a healthy gut microbiota.

scholarly journals Alterations in human gut microbiome composition and metabolism after exposure to glyphosate and Roundup and/or a spore-based formulation using the SHIME® technology

2021 ◽  
Author(s):  
Robin Mesnage ◽  
Marta Calatayud ◽  
Cindy Duysburgh ◽  
Massimo Marzorati ◽  
Michael Antoniou
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Large Scale ◽  
Epidemiological Studies ◽  
Human Gut ◽  
Microbiome Composition ◽  
Human Gut Microbiome ◽  
Ammonium Production ◽  
Profiling Techniques ◽  
Microbial Environment

Despite extensive research into the toxicology of the herbicide glyphosate, there are still major unknowns regarding its effects on the human gut microbiome. As a step in addressing this knowledge gap, we describe for the first time the effects of glyphosate and a Roundup glyphosate-based herbicide on infant gut microbiota using SHIME technology, which mimics the entire gastrointestinal tract. SHIME microbiota culture was undertaken in the presence of a concentration of 100 mg/L (corresponding to a dose of 1.6 mg/kg/day) glyphosate and the same glyphosate equivalent concentration of Roundup, which is in the range of the US chronic reference dose, and subjected to molecular profiling techniques to assess outcomes. Roundup and to a lesser extent glyphosate caused an increase in fermentation activity, resulting in acidification of the microbial environment. This was also reflected by an increase in lactate and acetate production concomitant to a decrease in the levels of propionate, valerate, caproate and butyrate. Ammonium production reflecting proteolytic activities was increased by Roundup exposure. Global metabolomics revealed large scale disturbances in metabolite profiles, including an increased abundance of long chain polyunsaturated fatty acids (n3 and n6). Although changes in bacterial composition measured by qPCR and 16S rRNA sequencing were less clear, our results suggested that lactobacilli had their growth stimulated as a result of microenvironment acidification. Co-treatment with the spore-based probiotic formulation MegaSporeBiotic reverted some of the changes in short-chain fatty acid levels. Altogether, our results suggest that glyphosate can exert effects on human gut microbiota at permitted regulatory levels of exposure, highlighting the need for epidemiological studies aimed at evaluating the effects of glyphosate herbicides on human gut microbiome function.

scholarly journals Adjunctive Probiotics Alleviates Asthmatic Symptoms via Modulating the Gut Microbiome and Serum Metabolome

2021 ◽  
Author(s):  
Ailing Liu ◽  
Teng Ma ◽  
Ning Xu ◽  
Hao Jin ◽  
Feiyan Zhao ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Conventional Therapy ◽  
Potential Effect ◽  
Therapeutic Strategies ◽  
Disease Phenotype ◽  
Human Gut ◽  
Asthma Symptoms ◽  
Novel Therapeutic Strategies ◽  
Novel Therapeutic

The human gut microbiota has a potential effect on the pathogenesis of asthma and is closely related to the disease phenotype. Our trial has demonstrated that co-administering Probio-M8 synergized with conventional therapy to alleviate asthma symptoms. The findings of the present study provide new insights into the pathogenesis and treatment of asthma, mechanisms of novel therapeutic strategies, and application of probiotics-based therapy.

scholarly journals Natural and after colon washing fecal samples: the two sides of the coin for investigating the human gut microbiome

2021 ◽  
Author(s):  
Elisabetta Piancone ◽  
Bruno Fosso ◽  
Mariangela De Robertis ◽  
Elisabetta Notario ◽  
Annarita Oranger ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Digital Pcr ◽  
Shannon Index ◽  
Individual Variability ◽  
Rrna Gene ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Taxonomic Analysis ◽  
Paired Samples

To date there are several studies focusing on the importance of gut microbiome for human health, however the selection of a universal sampling matrix representative of the microbial biodiversity associated to the gastrointestinal (GI) tract, still represents a challenge. Here we present a study in which, through a deep metabarcoding analysis of the 16S rRNA gene, we compared two sampling matrices, feces (F) and colonic lavage liquid (LL), in order to evaluate their accuracy to represent the complexity of the human gut microbiome. A training set of 37 volunteers was attained and paired F and LL samples were collected from each subject. A preliminary absolute quantification of total 16S rDNA, performed by droplet digital PCR (ddPCR), confirmed that sequencing and taxonomic analysis were performed on same total bacterial abundance obtained from the two sampling methods. The taxonomic analysis of paired samples revealed that, although specific taxa were predominantly or exclusively observed in LL samples, as well as other taxa were detectable only or were predominant in stool, the microbiomes of the paired samples F and LL in the same subject hold overlapping taxonomic composition. Moreover, LL samples revealed a higher biodiversity than stool at all taxonomic ranks, as demonstrated by the Shannon Index and the Inverse Simpson's Index. We also found greater inter-individual variability than intra-individual variability in both sample matrices. Finally, functional differences were unveiled in the gut microbiome detected in the F and LL samples. A significant overrepresentation of 22 and 13 metabolic pathways, mainly occurring in Firmicutes and Proteobacteria, was observed in gut microbiota detected in feces and LL samples, respectively. This suggests that LL samples may allow for the detection of microbes adhering to the intestinal mucosal surface as members of the resident flora that are not easily detectable in stool, most likely representative of a diet-influenced transient microbiota. This first comparative study on feces and LL samples for the study of the human gut microbiome demonstrates that the use of both types of sample matrices may represent a possible choice to obtain a more complete view of the human gut microbiota in response to different biological and clinical questions.

Antrodin A from Antrodia camphorata modulates the gut microbiome and liver metabolome in mice exposed to acute alcohol intake

2021 ◽  
Vol 12 (7) ◽  
pp. 2925-2937
Author(s):  
Zhenwei Yi ◽  
Xiaofeng Liu ◽  
Lihong Liang ◽  
Guangqiang Wang ◽  
Zhiqiang Xiong ◽  
...  
Keyword(s):  
Liver Injury ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Alcohol Intake ◽  
Underlying Mechanism ◽  
Antrodia Camphorata ◽  
Hepatoprotective Effects

In this study, we investigated the hepatoprotective effects of AdA and the underlying mechanism at the liver metabolomics and gut microbiota levels under alcohol-induced liver injury conditions.

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