Human gut microbiota networks disturbance by parasites in indigenous communities: Effect on bacteria genera related to depression incidence subnetworks

ABSTRACTIf you think you are in control of your behavior, think again. Evidence suggests that behavioral modifications, as development and persistence of depression, may be the consequence of a complex network of communication between macro (i.e. parasites) and micro-organisms capable of modifying the physiological axis of the host. Some parasites cause significant nutritional deficiencies for the host and impair the effectiveness of cognitive processes such as memory, teaching or non-verbal intelligence. Bacterial communities mediate the establishment of parasites and vice versa but this complexity approach remains little explored. We study the gut microbiota-parasite interactions using novel techniques of network analysis using data of individuals from two indigenous communities in the state of Guerrero, Mexico. Our results suggest that A. Lumbricoides, induce a gut microbiota perturbation affecting subnetworks of key species related to depression, consisting in the loss of network features such as path length, heterogeneity, number of nodes and neighbors; and especially by the loss of information emergence. Emergence is related with adaptability that has been linked to the concept of health as a critical balance between (adaptability) and self-organization (robustness). In this way, the loss of emergence means a depart from criticality and ultimately loss of health.

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Understanding Microbiome Data: A Primer for Clinicians

Digestive Diseases ◽

10.1159/000437034 ◽

2015 ◽

Vol 33 (Suppl. 1) ◽

pp. 11-16 ◽

Cited By ~ 13

Author(s):

Philippe Seksik ◽

Cécilia Landman

Keyword(s):

Gut Microbiota ◽

Bacterial Colonization ◽

Data Sets ◽

Human Gut ◽

Microbial Composition ◽

Host Determinants ◽

Host Interaction ◽

Bacterial Genes ◽

Micro Organisms ◽

Microbiome Data

The human gut contains 1014 bacteria and many other micro-organisms such as Archaea, viruses and fungi. This gut microbiota has co-evolved with host determinants through symbiotic and co-dependent relationships. Bacteria, which represent 10 times the number of human cells, form the most depicted part of this black box owing to new tools. Re-evaluating the gut microbiota showed how this entity participates in gut physiology and beyond this in human health. Studying and handling this real ‘hidden organ' remains a challenge for clinicians. In this review, we aimed to bring information about gut microbiota, its structure, its roles and the way to capture and measure it. After bacterial colonization in infant, intestinal microbial composition is unique for each individual although more than 95% can be assigned to 4 major phyla. Besides its biodiversity, the major characteristics of gut microbiota are stability over time and resilience after perturbation. In pathological situations, dysbiosis (i.e. imbalance in gut microbiota composition) is observed with a loss in overall diversity. Dysbiosis associated with inflammatory bowel disease was specified with the reduction in biodiversity, the decreased representation of different taxa in the Firmicutes phylum and an increase in Gammaproteobacteria. Beyond depicting gut microbial composition, metagenomics allows the description of the combined genomes of the microorganisms present in the gut, giving access to their potential functions. In fact, each individual overall microbial metagenome outnumbers the size of human genome by a factor of 150. Besides a functional core in which there is redundancy for mandatory functions assuring the robustness of the ecosystem, human gut contains an important diversity and high number of non-redundant bacterial genes. Clinical data, treatment and all the factors able to influence microbiome should enter integrated big data sets to put in light pathways of interplay within the supra organism composed of gut microbiome and host. A better understanding of dynamics within human gut microbiota and microbes-host interaction will allow new insight into gut pathophysiology especially regarding resilience mechanisms and dysbiosis onset and maintenance. This will lead to description of biomarkers of diseases, development of new probiotics/prebiotics and new therapies.

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Perspectives on the role of the human gut microbiota and its modulation by pro- and prebiotics

Nutrition Research Reviews ◽

10.1079/095442200108729089 ◽

2000 ◽

Vol 13 (2) ◽

pp. 229-254 ◽

Cited By ~ 118

Author(s):

Toni Steer ◽

Hollie Carpenter ◽

Kieran Tuohy ◽

Glenn R. Gibson

Keyword(s):

Gut Microbiota ◽

Dietary Intervention ◽

Gut Microflora ◽

Human Gut ◽

Human Gut Microbiota ◽

Disease States ◽

Health Promoting ◽

Irritable Bowel ◽

Micro Organisms

AbstractOne of the most topical areas of human nutrition is the role of the gut in health and disease. Specifically, this involves interactions between the resident microbiota and dietary ingredients that support their activities. Currently, it is accepted that the gut microflora contains pathogenic, benign and beneficial components. Some microbially induced disease states such as acute gastroenteritis and pseudomembranous colitis have a defined aetiological agent(s). Speculation on the role of microbiota components in disorders such as irritable bowel syndrome, bowel cancer, neonatal necrotising enterocolitis and ulcerative colitis are less well defined, but many studies are convincing. It is evident that the gut microflora composition can be altered through diet. Because of their perceived health-promoting status, bifidobacteria and lactobacilli are the commonest targets. Probiotics involve the use of live micro-organisms in food; prebiotics are carbohydrates selectively metabolized by desirable moieties of the indigenous flora; synbiotics combine the two approaches. Dietary intervention of the human gut microbiota is feasible and has been proven as efficacious in volunteer trials. The health bonuses of such approaches offer the potential to manage many gut disorders prophylactically. However, it is imperative that the best methodologies available are applied to this area of nutritional sciences. This will undoubtedly involve a genomic application to the research and is already under way through molecular tracking of microbiota changes to diet in controlled human trials.

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Bacterial Atlas of Mouse Gut Microbiota

10.21203/rs.3.rs-829178/v1 ◽

2021 ◽

Author(s):

Mengqi Chu ◽

Xiaobo Zhang

Keyword(s):

Complex System ◽

Gut Microbiota ◽

Bacterial Communities ◽

Large Scale ◽

Gut Bacteria ◽

Human Gut ◽

The Core ◽

Human Gut Microbiota ◽

Human Immunity ◽

Mouse Gut Microbiota

Abstract Background: Mouse model is one of of the most widely used animal models for exploring the roles of human gut microbiota, a complex system involving in human immunity and metabolism. However, the structure of mouse gut bacterial community has not been explored at a large scale. To address this concern, the diversity and composition of the gut bacteria of 600 mice was characterized in this study. Results: The results showed that the bacteria belonging to 8 genera were found in the gut microbiota of all mouse individuals, indicating that the 8 bacteria were the core bacteria of mouse gut microbiota. The dominant genera of the mouse gut bacteria contained 15 bacterial genera. It was found that the bacteria in the gut microbiota were mainly involved in host’s metabolisms via the collaborations between the gut bacteria. The further analysis demonstrated that the composition of mouse gut microbiota was similar to that of human gut microbiota. Conclusion: Our study presented a bacterial atlas of mouse gut microbiota, providing a solid basis for investing the bacterial communities of mouse gut microbiota.

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Nutritional Status and the Influence of the Vegan Diet on the Gut Microbiota and Human Health

Medicina ◽

10.3390/medicina56020088 ◽

2020 ◽

Vol 56 (2) ◽

pp. 88 ◽

Cited By ~ 2

Author(s):

Hercules Sakkas ◽

Petros Bozidis ◽

Christos Touzios ◽

Damianos Kolios ◽

Georgia Athanasiou ◽

...

Keyword(s):

Nutritional Status ◽

Gut Microbiota ◽

Human Health ◽

Dietary Habits ◽

Metabolic Diseases ◽

Vegan Diet ◽

Nutritional Deficiencies ◽

Human Gut ◽

Human Gut Microbiota ◽

Medical Disorders

The human gut microbiota is considered a well-known complex ecosystem composed of distinct microbial populations, playing a significant role in most aspects of human health and wellness. Several factors such as infant transitions, dietary habits, age, consumption of probiotics and prebiotics, use of antibiotics, intestinal comorbidities, and even metabolic diseases may continously alter microbiota diversity and function. The study of vegan diet–microbiota interactions is a rapidly evolving field, since plenty of research has been focused on the potential effects of plant-based dietary patterns on the human gut microbiota. It has been reported that well-planned vegan diets and their associated components affect both the bacterial composition and metabolic pathways of gut microbiota. Certain benefits associated with medical disorders but also limitations (including nutritional deficiencies) have been documented. Although the vegan diet may be inadequate in calorific value, it is rich in dietary fiber, polyphenols, and antioxidant vitamins. The aim of the present study was to provide an update of the existing knowledge on nutritional status of vegan diets and the influence of their food components on the human gut microbiota and health.

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Toward Personalized Control of Human Gut Bacterial Communities

mSystems ◽

10.1128/msystems.00165-17 ◽

2018 ◽

Vol 3 (2) ◽

Cited By ~ 2

Author(s):

Lawrence A. David

Keyword(s):

Environmental Management ◽

Big Data ◽

Gut Microbiota ◽

Bacterial Communities ◽

Human Gut ◽

New Challenges ◽

Study Designs ◽

And Control ◽

Research Domains

ABSTRACT A key challenge in microbiology will be developing tools for manipulating human gut bacterial communities. Our ability to predict and control the dynamics of these communities is now in its infancy. To manage human gut microbiota, I am developing methods in three research domains. First, I am refining in vitro tools to experimentally study gut microbes at high throughput and in controlled settings. Second, I am adapting “big data” techniques to overcome statistical challenges confronting microbiota modeling. Third, I am testing study designs that can streamline human testing of microbiota manipulations. Assembling these methods creates new challenges, including training scientists who can work across disciplines such as engineering, ecology, and medicine. Nevertheless, I envision that overcoming these obstacles will enable my group to construct platforms that can personalize microbiota treatments, particularly ones based on diet. More broadly, I anticipate that such platforms will have applications across fields such as agriculture, biotechnology, and environmental management.

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Deciphering microbial interactions in synthetic human gut microbiome communities

10.1101/228395 ◽

2017 ◽

Cited By ~ 2

Author(s):

Ophelia S. Venturelli ◽

Alex C. Carr ◽

Garth Fisher ◽

Ryan H. Hsu ◽

Rebecca Lau ◽

...

Keyword(s):

Gut Microbiota ◽

Community Assembly ◽

Gut Microbiome ◽

Community Dynamics ◽

Microbial Interactions ◽

Model Parameters ◽

Human Gut ◽

Human Gut Microbiome ◽

Pairwise Interactions ◽

Key Species

ABSTRACTThe human gut microbiota comprises a dynamic ecological system that contributes significantly to human health and disease. The ecological forces that govern community assembly and stability in the gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-order consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse 12-member human gut microbiome synthetic community. We show that microbial growth parameters and pairwise interactions are the major drivers of multi-species community dynamics, as opposed to context-dependent (conditional) interactions. The inferred microbial interaction network as well as a top-down approach to community assembly pinpointed both ecological driver and responsive species that were significantly modulated by microbial inter-relationships. Our model demonstrated that negative pairwise interactions could generate history-dependent responses of initial species proportions on physiological timescales that frequently does not originate from bistability. The model elucidated a topology for robust coexistence in pairwise assemblages consisting of a negative feedback loop that balances disparities in monospecies fitness levels. Bayesian statistical methods were used to evaluate the constraint of model parameters by the experimental data. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis for competitive and cooperative interactions in the community. However, these data failed to predict influential organisms shaping community assembly. In sum, these methods defined the ecological roles of key species shaping community assembly and illuminated network design principles of microbial communities.

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Prevalence of Antibiotic Resistance Genes among Human Gut-Derived Bifidobacteria

Applied and Environmental Microbiology ◽

10.1128/aem.02894-16 ◽

2016 ◽

Vol 83 (3) ◽

Cited By ~ 37

Author(s):

Sabrina Duranti ◽

Gabriele Andrea Lugli ◽

Leonardo Mancabelli ◽

Francesca Turroni ◽

Christian Milani ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gut Microbiota ◽

Resistance Genes ◽

Bacterial Communities ◽

Life Stage ◽

Antibiotic Resistance Genes ◽

Later Life ◽

Limited Information ◽

Human Gut ◽

Content Type

ABSTRACT The microbiota of the human gastrointestinal tract (GIT) may regularly be exposed to antibiotics, which are used to prevent and treat infectious diseases caused by bacteria and fungi. Bacterial communities of the gut retain a reservoir of antibiotic resistance (AR) genes, and antibiotic therapy thus positively selects for those microorganisms that harbor such genetic features, causing microbiota modulation. During the first months following birth, bifidobacteria represent some of the most dominant components of the human gut microbiota, although little is known about their AR gene complement (or resistome). In the current study, we assessed the resistome of the Bifidobacterium genus based on phenotypic and genotypic data of members that represent all currently recognized bifidobacterial (sub)species. Moreover, a comparison between the bifidobacterial resistome and gut metagenome data sets from adults and infants shows that the bifidobacterial community present at the first week following birth possesses a reduced AR arsenal compared to that present in the infant bifidobacterial population in subsequent weeks of the first year of life. Our findings reinforce the concept that the early infant gut microbiota is more susceptible to disturbances by antibiotic treatment than the gut microbiota developed at a later life stage. IMPORTANCE The spread of resistance to antibiotics among bacterial communities has represented a major concern since their discovery in the last century. The risk of genetic transfer of resistance genes between microorganisms has been extensively investigated due to its relevance to human health. In contrast, there is only limited information available on antibiotic resistance among human gut commensal microorganisms such as bifidobacteria, which are widely exploited by the food industry as health-promoting microorganisms or probiotic ingredients. In the current study, we explored the occurrence of antibiotic resistance genes in the genomes of bifidobacteria and evaluated their genetic mobility to other human gut commensal microorganisms.

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Gut health: predictive biomarkers for preventive medicine and development of functional foods

British Journal Of Nutrition ◽

10.1017/s0007114509993400 ◽

2010 ◽

Vol 103 (10) ◽

pp. 1539-1544 ◽

Cited By ~ 17

Author(s):

Raish Oozeer ◽

Maria Rescigno ◽

R. Paul Ross ◽

Jan Knol ◽

Michael Blaut ◽

...

Keyword(s):

Gut Microbiota ◽

Predictive Biomarkers ◽

Gut Health ◽

Human Gut ◽

Observation Study ◽

Industry Collaboration ◽

Health And Disease ◽

Micro Organisms ◽

First Time

There is an urgent need to develop and validate a series of biomarkers, which accurately measure and inform on how the human gut microbiota can affect human health. The human gut hosts a complex community of micro-organisms, with unique features in each individual. The functional role of this gut microbiota in health and disease is increasingly evident, but poorly understood. Comprehension of this ecosystem implies a significant challenge in the elucidation of interactions between all of its components, but promises a paradigm shift in preventive nutrition and medicine. ‘Omics’ technologies for the first time offer tools of sufficient subtlety to tackle this challenge. However, these techniques must be allied with traditional skills of the microbial physiologist, which are in danger of being lost. Targeting these efforts at the identification of biomarkers associated with gut health will require access to a ‘biobank’ from a pan-European or worldwide observation study, which would include samples taken with appropriate frequency from healthy individuals of different ages. This offers a pragmatic opportunity for a unique food and pharmaceutical industry collaboration.

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