scholarly journals Metanacentome: A genomic methodology proposal for the study of nascent metatranscription of the microbiome

2019 ◽  
Author(s):  
Daniel A. Medina
Keyword(s):  
Gut Microbiota ◽  
Dietary Habits ◽  
Adult Life ◽  
Geographic Location ◽  
Ethnic Origin ◽  
Microbiota Composition ◽  
Health It ◽  
Genome Wide ◽  
Molecular Expression ◽  
Gut Microbiota Composition

The gut microbiota has been shown to have an important influence on host health. It has been reported that microbiota composition of each individual is stable across the adult life, but it may varies between individuals. Moreover, human gut microbiota composition differs across geography, according to host genetics, dietary habits, age, ethnic origin, geographic location and lifestyle. Nevertheless, gene composition or functional capacity is highly conserved across individuals, phenomenon known as functional redundancy. Although metatranscriptomics have the potential of study the mature mRNA from a microbiome sample, it is not easy to identify which bacteria is actively transcribing the genes who drives the molecular expression. The use of genome-wide methodologies to study the active mRNA synthesis seem to be useful to identify the bacterias who drives gene expression in microbiota environment.

scholarly journals Metanacentome: A genomic methodology proposal for the study of nascent metatranscription of the microbiome

2019 ◽  
Author(s):  
Daniel A. Medina
Keyword(s):  
Gut Microbiota ◽  
Dietary Habits ◽  
Adult Life ◽  
Geographic Location ◽  
Ethnic Origin ◽  
Microbiota Composition ◽  
Health It ◽  
Genome Wide ◽  
Molecular Expression ◽  
Gut Microbiota Composition

The gut microbiota has been shown to have an important influence on host health. It has been reported that microbiota composition of each individual is stable across the adult life, but it may varies between individuals. Moreover, human gut microbiota composition differs across geography, according to host genetics, dietary habits, age, ethnic origin, geographic location and lifestyle. Nevertheless, gene composition or functional capacity is highly conserved across individuals, phenomenon known as functional redundancy. Although metatranscriptomics have the potential of study the mature mRNA from a microbiome sample, it is not easy to identify which bacteria is actively transcribing the genes who drives the molecular expression. The use of genome-wide methodologies to study the active mRNA synthesis seem to be useful to identify the bacterias who drives gene expression in microbiota environment.

scholarly journals Metanacentome: A genomic methodology for the study of nascent metatranscription of the microbiome

2018 ◽  
Author(s):  
Daniel A. Medina
Keyword(s):  
Gut Microbiota ◽  
Dietary Habits ◽  
Adult Life ◽  
Geographic Location ◽  
Ethnic Origin ◽  
Microbiota Composition ◽  
Human Gut ◽  
Microbial Composition ◽  
Human Gut Microbiota ◽  
Genome Wide

The gut microbiota has been shown to have an important influence on host health. Microbial composition of the gut microbiota is modulated by diet and human habits. The composition of human gut microbiota changes with age; and alterations in this composition may influence human health. It has been reported that microbiota composition of each individual is stable across the adult life, but it may varies between individuals. Moreover, human gut microbiota composition differs across geography, according to host genetics, dietary habits, age, ethnic origin, geographic location and lifestyle. Nevertheless, gene composition or functional capacity is highly conserved across individuals, phenomenon known as functional redundancy. Although metatranscriptomics can study the mature mRNA from a microbiome sample, it is impossible identify who bacteria is actively transcribing the genes who drives the molecular expression. The use of genome-wide methodologies to study the active mRNA synthesis could be useful to identify the bacterial population who drives gene expression in microbiome environment.

scholarly journals Genome-wide association studies and heritability analysis reveal the involvement of host genetics in the Japanese gut microbiota

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Sachiko Ishida ◽  
Kumiko Kato ◽  
Masami Tanaka ◽  
Toshitaka Odamaki ◽  
Ryuichi Kubo ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Japanese Population ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Microbiota Composition ◽  
Intrinsic Factors ◽  
Genome Wide ◽  
Gut Microbiota Composition

AbstractNumerous host extrinsic and intrinsic factors affect the gut microbiota composition, but their cumulative effects do not sufficiently explain the variation in the microbiota, suggesting contributions of missing factors. The Japanese population possesses homogeneous genetic features suitable for genome-wide association study (GWAS). Here, we performed GWASs for human gut microbiota using 1068 healthy Japanese adults. To precisely evaluate genetic effects, we corrected for the impacts of numerous host extrinsic and demographic factors by introducing them as covariates, enabling us to discover five loci significantly associated with microbiome diversity measures: HS3ST4, C2CD2, 2p16.1, 10p15.1, and 18q12.2. Nevertheless, these five variants explain only a small fraction of the variation in the gut microbiota. We subsequently investigated the heritability of each of the 21 core genera and found that the abundances of six genera are heritable. We propose that the gut microbiota composition is affected by a highly polygenic architecture rather than several strongly associated variants in the Japanese population.

scholarly journals Vegan Diet and the Gut Microbiota Composition in Healthy Adults

Nutrients ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 2402
Author(s):  
Emily A. Losno ◽  
Katharina Sieferle ◽  
Federico J. Armando Perez-Cueto ◽  
Christian Ritz
Keyword(s):  
Gut Microbiota ◽  
Dietary Habits ◽  
The Body ◽  
Vegan Diet ◽  
Microbiota Composition ◽  
Cross Sectional ◽  
Health Maintenance ◽  
Faecal Analysis ◽  
Randomised Controlled ◽  
Gut Microbiota Composition

The human gut microbiota are the microorganisms (generally bacteria and archaea) that live in the digestive tracts of humans. Due to their numerous functions, the gut microbiota can be considered a virtual organ of the body, playing a pivotal role in health maintenance. Dietary habits contribute to gut microbiota composition, and evidence from observational and intervention studies suggest that vegan diets may promote health, potentially through affecting the diverse ecosystem of beneficial bacteria in the gut. A systematic literature search was conducted on PubMed and Scopus to identify studies investigating the microbiota composition in vegans. Vegans are defined as people excluding food products that are derived from animals from their diet. Nine observational studies were identified. The main outcome of the systematic review was an increase in Bacteroidetes on the phylum level and a higher abundance of Prevotella on the genus level. In conclusion, the present systematic literature review highlighted some benefits of a vegan diet but also demonstrated the complexity of evaluating results from gut microbiota research. The available evidence only consisted of cross-sectional studies, therefore suggesting the need for well-designed randomised controlled trials. Furthermore, the quality assessment of the studies included in the review suggested a lack of standardised and validated methods for participant selection as well as for faecal sampling and faecal analysis.

scholarly journals The influence of dietary compounds on gut microbiota

2021 ◽  
pp. 1-15
Author(s):  
Maja Šikić Pogačar ◽  
Dušanka Mičetić-Turk
Keyword(s):  
Gut Microbiota ◽  
Energy Homeostasis ◽  
High Throughput Sequencing ◽  
Dietary Habits ◽  
Lifestyle Changes ◽  
Bioactive Metabolites ◽  
Microbiota Composition ◽  
Interindividual Variations ◽  
Mass Spectrometry Identification ◽  
Gut Microbiota Composition

The gut microbiota is a complex community composed of trillions of microbes that adapts to its host over the lifetime. Recently, the advances of the methods of high-throughput sequencing have allowed the identification of microbial species in a stool sample, and mass spectrometry identification of their metabolites, both of which together have enabled much of the relevant research in the field. It has became evident that gut microbiota plays an important role in human health and influences the risk of developing many chronic diseases, including obesity, inflammatory bowel disease, type 2 diabetes, cardiovascular disease, and cancer. The diverse ecosystem of the gut includes bacteria, viruses, phages, yeasts, archaea, fungi and protozoa. They are responsible for the production of bioactive metabolites, regulation of immune function, energy homeostasis and protection against pathogens. The mentioned functions are dependent on the diversity and abundance of the microbiota which is the reflection of the dietary habits and genetics of the host among other factors. As such, gut microbiota has significant interindividual variations. Diet and lifestyle changes present important determinants in microbiota shaping. The use of antibiotics, different sanitation measures, consumption of processed food and different diets are also reflected in the shifts of gut microbiota composition. Some of the dramatic dietary alterations can cause changes in gut microbiota composition already within 24 h and some of these changes may be difficult to reverse. Through modulation of gut microbiota composition, diet could offer a potential to manage the risk of developing disease and at the same time improving the quality of life and longevity. In this review we look at the role of diet, and specific dietary components, namely carbohydrates, proteins, fats and polyphenols on gut microbiota composition.

scholarly journals What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases

2019 ◽  
Vol 7 (1) ◽  
pp. 14 ◽  
Author(s):  
Emanuele Rinninella ◽  
Pauline Raoul ◽  
Marco Cintoni ◽  
Francesco Franceschi ◽  
Giacinto Miggiano ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Structural Integrity ◽  
Dietary Habits ◽  
Therapeutic Interventions ◽  
Mucosal Barrier ◽  
Microbiota Composition ◽  
Immune Functions ◽  
Nutrient Metabolism ◽  
Exercise Frequency ◽  
Gut Microbiota Composition

Each individual is provided with a unique gut microbiota profile that plays many specific functions in host nutrient metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation, and protection against pathogens. Gut microbiota are composed of different bacteria species taxonomically classified by genus, family, order, and phyla. Each human’s gut microbiota are shaped in early life as their composition depends on infant transitions (birth gestational date, type of delivery, methods of milk feeding, weaning period) and external factors such as antibiotic use. These personal and healthy core native microbiota remain relatively stable in adulthood but differ between individuals due to enterotypes, body mass index (BMI) level, exercise frequency, lifestyle, and cultural and dietary habits. Accordingly, there is not a unique optimal gut microbiota composition since it is different for each individual. However, a healthy host–microorganism balance must be respected in order to optimally perform metabolic and immune functions and prevent disease development. This review will provide an overview of the studies that focus on gut microbiota balances in the same individual and between individuals and highlight the close mutualistic relationship between gut microbiota variations and diseases. Indeed, dysbiosis of gut microbiota is associated not only with intestinal disorders but also with numerous extra-intestinal diseases such as metabolic and neurological disorders. Understanding the cause or consequence of these gut microbiota balances in health and disease and how to maintain or restore a healthy gut microbiota composition should be useful in developing promising therapeutic interventions.

scholarly journals Food Components and Dietary Habits: Keys for a Healthy Gut Microbiota Composition

Nutrients ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 2393 ◽  
Author(s):  
Rinninella ◽  
Cintoni ◽  
Raoul ◽  
Lopetuso ◽  
Scaldaferri ◽  
...  
Keyword(s):  
Immune System ◽  
Gut Microbiota ◽  
Dietary Habits ◽  
Food Additives ◽  
Intestinal Barrier ◽  
Health Concern ◽  
Microbiota Composition ◽  
Food Components ◽  
The Impact ◽  
Gut Microbiota Composition

The gut microbiota is a changing ecosystem, containing trillions of bacteria, continuously shaped by many factors, such as dietary habits, seasonality, lifestyle, stress, antibiotics use, or diseases. A healthy host–microorganisms balance must be respected in order to optimally maintain the intestinal barrier and immune system functions and, consequently, prevent disease development. In the past several decades, the adoption of modern dietary habits has become a growing health concern, as it is strongly associated with obesity and related metabolic diseases, promoting inflammation and both structural and behavioral changes in gut microbiota. In this context, novel dietary strategies are emerging to prevent diseases and maintain health. However, the consequences of these different diets on gut microbiota modulation are still largely unknown, and could potentially lead to alterations of gut microbiota, intestinal barrier, and the immune system. The present review aimed to focus on the impact of single food components (macronutrients and micronutrients), salt, food additives, and different dietary habits (i.e., vegan and vegetarian, gluten-free, ketogenic, high sugar, low FODMAP, Western-type, and Mediterranean diets) on gut microbiota composition in order to define the optimal diet for a healthy modulation of gut microbiota.

Understanding the gut–kidney axis in nephrolithiasis: an analysis of the gut microbiota composition and functionality of stone formers

Gut ◽  
2018 ◽  
Vol 67 (12) ◽  
pp. 2097-2106 ◽  
Author(s):  
Andrea Ticinesi ◽  
Christian Milani ◽  
Angela Guerra ◽  
Franca Allegri ◽  
Fulvio Lauretani ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Dietary Habits ◽  
Bacterial Species ◽  
Inverse Correlation ◽  
Microbiota Composition ◽  
Shotgun Metagenomics ◽  
Microbial Profiling ◽  
Stone Formers ◽  
Faecal Samples ◽  
Gut Microbiota Composition

ObjectivesThe involvement of the gut microbiota in the pathogenesis of calcium nephrolithiasis has been hypothesised since the discovery of the oxalate-degrading activity of Oxalobacter formigenes, but never comprehensively studied with metagenomics. The aim of this case–control study was to compare the faecal microbiota composition and functionality between recurrent idiopathic calcium stone formers (SFs) and controls.DesignFaecal samples were collected from 52 SFs and 48 controls (mean age 48±11). The microbiota composition was analysed through 16S rRNA microbial profiling approach. Ten samples (five SFs, five controls) were also analysed with deep shotgun metagenomics sequencing, with focus on oxalate-degrading microbial metabolic pathways. Dietary habits, assessed through a food-frequency questionnaire, and 24-hour urinary excretion of prolithogenic and antilithogenic factors, including calcium and oxalate, were compared between SFs and controls, and considered as covariates in the comparison of microbiota profiles.ResultsSFs exhibited lower faecal microbial diversity than controls (Chao1 index 1460±363vs 1658±297, fully adjusted p=0.02 with stepwise backward regression analysis). At multivariate analyses, three taxa (Faecalibacterium, Enterobacter, Dorea) were significantly less represented in faecal samples of SFs. The Oxalobacter abundance was not different between groups. Faecal samples from SFs exhibited a significantly lower bacterial representation of genes involved in oxalate degradation, with inverse correlation with 24-hour oxalate excretion (r=−0.87, p=0.002). The oxalate-degrading genes were represented in several bacterial species, whose cumulative abundance was inversely correlated with oxaluria (r=−0.85, p=0.02).ConclusionsIdiopathic calcium SFs exhibited altered gut microbiota composition and functionality that could contribute to nephrolithiasis physiopathology.

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