scholarly journals Prediction Correction Topic Evolution Research for Metabolic Pathways of the Gut Microbiota

2020 ◽  
Vol 7 ◽  
Author(s):  
Li Ning ◽  
Peng Lifang ◽  
He Huixin
Keyword(s):  
Cardiovascular Disease ◽  
Gut Microbiota ◽  
Human Health ◽  
Metabolic Pathways ◽  
Latent Dirichlet Allocation ◽  
Rapid Development ◽  
Hepatic Metabolism ◽  
Future Trend ◽  
Analysis Tool ◽  
Brain Reaction

The gut microbiota is composed of a large number of different bacteria, that play a key role in the construction of a metabolic signaling network. Deepening the link between metabolic pathways of the gut microbiota and human health, it seems increasingly essential to evolutionarily define the principal technologies applied in the field and their future trends. We use a topic analysis tool, Latent Dirichlet Allocation, to extract themes as a probabilistic distribution of latent topics from literature dataset. We also use the Prophet neural network prediction tool to predict future trend of this area of study. A total of 1,271 abstracts (from 2006 to 2020) were retrieved from MEDLINE with the query on “gut microbiota” and “metabolic pathway.” Our study found 10 topics covering current research types: dietary health, inflammation and liver cancer, fatty and diabetes, microbiota community, hepatic metabolism, metabolomics-based approach and SFCAs, allergic and immune disorders, gut dysbiosis, obesity, brain reaction, and cardiovascular disease. The analysis indicates that, with the rapid development of gut microbiota research, the metabolomics-based approach and SCFAs (topic 6) and dietary health (topic 1) have more studies being reported in the last 15 years. We also conclude from the data that, three other topics could be heavily focused in the future: metabolomics-based approach and SCFAs (topic 6), obesity (topic 8) and brain reaction and cardiovascular disease (topic 10), to unravel microbial affecting human health.

scholarly journals Associations between habitual diet, metabolic disease, and the gut microbiota using latent Dirichlet allocation

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Taylor A. Breuninger ◽  
Nina Wawro ◽  
Jakob Breuninger ◽  
Sandra Reitmeier ◽  
Thomas Clavel ◽  
...  
Keyword(s):  
Risk Factors ◽  
Gut Microbiota ◽  
Dietary Intake ◽  
Human Health ◽  
Latent Dirichlet Allocation ◽  
Metabolic Diseases ◽  
Healthy Eating Index ◽  
Lower Probability ◽  
Habitual Diet ◽  
Dirichlet Allocation

Abstract Background The gut microbiome impacts human health through various mechanisms and is involved in the development of a range of non-communicable diseases. Diet is a well-known factor influencing microbe-host interaction in health and disease. However, very few findings are based on large-scale analysis using population-based studies. Our aim was to investigate the cross-sectional relationship between habitual dietary intake and gut microbiota structure in the Cooperative Health Research in the Region of Augsburg (KORA) FF4 study. Results Fecal microbiota was analyzed using 16S rRNA gene amplicon sequencing. Latent Dirichlet allocation (LDA) was applied to samples from 1992 participants to identify 20 microbial subgroups within the study population. Each participant’s gut microbiota was subsequently described by a unique composition of these 20 subgroups. Associations between habitual dietary intake, assessed via repeated 24-h food lists and a Food Frequency Questionnaire, and the 20 subgroups, as well as between prevalence of metabolic diseases/risk factors and the subgroups, were assessed with multivariate-adjusted Dirichlet regression models. After adjustment for multiple testing, eight of 20 microbial subgroups were significantly associated with habitual diet, while nine of 20 microbial subgroups were associated with the prevalence of one or more metabolic diseases/risk factors. Subgroups 5 (Faecalibacterium, Lachnospiracea incertae sedis, Gemmiger, Roseburia) and 14 (Coprococcus, Bacteroides, Faecalibacterium, Ruminococcus) were particularly strongly associated with diet. For example, participants with a high probability for subgroup 5 were characterized by a higher Alternate Healthy Eating Index and Mediterranean Diet Score and a higher intake of food items such as fruits, vegetables, legumes, and whole grains, while participants with prevalent type 2 diabetes mellitus were characterized by a lower probability for subgroup 5. Conclusions The associations between habitual diet, metabolic diseases, and microbial subgroups identified in this analysis not only expand upon current knowledge of diet-microbiota-disease relationships, but also indicate the possibility of certain microbial groups to be modulated by dietary intervention, with the potential of impacting human health. Additionally, LDA appears to be a powerful tool for interpreting latent structures of the human gut microbiota. However, the subgroups and associations observed in this analysis need to be replicated in further studies.

The Food-gut Human Axis: The Effects of Diet on Gut Microbiota and Metabolome

2019 ◽  
Vol 26 (19) ◽  
pp. 3567-3583 ◽  
Author(s):  
Maria De Angelis ◽  
Gabriella Garruti ◽  
Fabio Minervini ◽  
Leonilde Bonfrate ◽  
Piero Portincasa ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Dietary Habits ◽  
Short Chain Fatty Acids ◽  
Human Organism ◽  
Immune Functions ◽  
Intestinal Microbes ◽  
Dietary Components ◽  
Dietary Treatments ◽  
The Relationship

Gut microbiota, the largest symbiont community hosted in human organism, is emerging as a pivotal player in the relationship between dietary habits and health. Oral and, especially, intestinal microbes metabolize dietary components, affecting human health by producing harmful or beneficial metabolites, which are involved in the incidence and progression of several intestinal related and non-related diseases. Habitual diet (Western, Agrarian and Mediterranean omnivore diets, vegetarian, vegan and gluten-free diets) drives the composition of the gut microbiota and metabolome. Within the dietary components, polymers (mainly fibers, proteins, fat and polyphenols) that are not hydrolyzed by human enzymes seem to be the main leads of the metabolic pathways of gut microbiota, which in turn directly influence the human metabolome. Specific relationships between diet and microbes, microbes and metabolites, microbes and immune functions and microbes and/or their metabolites and some human diseases are being established. Dietary treatments with fibers are the most effective to benefit the metabolome profile, by improving the synthesis of short chain fatty acids and decreasing the level of molecules, such as p-cresyl sulfate, indoxyl sulfate and trimethylamine N-oxide, involved in disease state. Based on the axis diet-microbiota-health, this review aims at describing the most recent knowledge oriented towards a profitable use of diet to provide benefits to human health, both directly and indirectly, through the activity of gut microbiota.

scholarly journals Modulation of Gut Microbiota for the Prevention and Treatment of COVID-19

2021 ◽  
Vol 10 (13) ◽  
pp. 2903
Author(s):  
Jiezhong Chen ◽  
Luis Vitetta
Keyword(s):  
Clinical Trials ◽  
Trace Elements ◽  
Gut Microbiota ◽  
Human Health ◽  
Intestinal Microbiota ◽  
Narrative Review ◽  
Bacterial Metabolites ◽  
Gut Dysbiosis ◽  
Prevention And Treatment

The gut microbiota is well known to exert multiple benefits on human health including protection from disease causing pathobiont microbes. It has been recognized that healthy intestinal microbiota is of great importance in the pathogenesis of COVID-19. Gut dysbiosis caused by various reasons is associated with severe COVID-19. Therefore, the modulation of gut microbiota and supplementation of commensal bacterial metabolites could reduce the severity of COVID-19. Many approaches have been studied to improve gut microbiota in COVID-19 including probiotics, bacterial metabolites, and prebiotics, as well as nutraceuticals and trace elements. So far, 19 clinical trials for testing the efficacy of probiotics and synbiotics in COVID-19 prevention and treatment are ongoing. In this narrative review, we summarize the effects of various approaches on the prevention and treatment of COVID-19 and discuss associated mechanisms.

High animal protein diet and gut microbiota in human health

2021 ◽  
pp. 1-13
Author(s):  
Jie Cai ◽  
Zhongxu Chen ◽  
Wei Wu ◽  
Qinlu Lin ◽  
Ying Liang
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Animal Protein ◽  
Protein Diet ◽  
High Animal

scholarly journals Guild-based analysis for understanding gut microbiome in human health and diseases

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Guojun Wu ◽  
Naisi Zhao ◽  
Chenhong Zhang ◽  
Yan Y. Lam ◽  
Liping Zhao
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Gut Microbiome ◽  
Association Studies ◽  
Causative Role ◽  
Disease Phenotypes ◽  
Genetic Complexity ◽  
Causative Agents ◽  
Specific Health

AbstractTo demonstrate the causative role of gut microbiome in human health and diseases, we first need to identify, via next-generation sequencing, potentially important functional members associated with specific health outcomes and disease phenotypes. However, due to the strain-level genetic complexity of the gut microbiota, microbiome datasets are highly dimensional and highly sparse in nature, making it challenging to identify putative causative agents of a particular disease phenotype. Members of an ecosystem seldomly live independently from each other. Instead, they develop local interactions and form inter-member organizations to influence the ecosystem’s higher-level patterns and functions. In the ecological study of macro-organisms, members are defined as belonging to the same “guild” if they exploit the same class of resources in a similar way or work together as a coherent functional group. Translating the concept of “guild” to the study of gut microbiota, we redefine guild as a group of bacteria that show consistent co-abundant behavior and likely to work together to contribute to the same ecological function. In this opinion article, we discuss how to use guilds as the aggregation unit to reduce dimensionality and sparsity in microbiome-wide association studies for identifying candidate gut bacteria that may causatively contribute to human health and diseases.

scholarly journals Associations between stool micro-transcriptome, gut microbiota, and infant growth

2021 ◽  
pp. 1-7
Author(s):  
Molly C. Carney ◽  
Xiang Zhan ◽  
Akanksha Rangnekar ◽  
Maria Z. Chroneos ◽  
Sarah J.C. Craig ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Activity ◽  
Metabolic Pathways ◽  
Weight Status ◽  
Transcriptional Activity ◽  
High Throughput Sequencing ◽  
Infant Growth ◽  
Adult Obesity ◽  
Term Infants ◽  
Ribonucleic Acids

Abstract Rapid infant growth increases the risk for adult obesity. The gut microbiome is associated with early weight status; however, no study has examined how interactions between microbial and host ribonucleic acid (RNA) expression influence infant growth. We hypothesized that dynamics in infant stool micro-ribonucleic acids (miRNAs) would be associated with both microbial activity and infant growth via putative metabolic targets. Stool was collected twice from 30 full-term infants, at 1 month and again between 6 and 12 months. Stool RNA were measured with high-throughput sequencing and aligned to human and microbial databases. Infant growth was measured by weight-for-length z-score at birth and 12 months. Increased RNA transcriptional activity of Clostridia (R = 0.55; Adj p = 3.7E-2) and Burkholderia (R = −0.820, Adj p = 2.62E-3) were associated with infant growth. Of the 25 human RNAs associated with growth, 16 were miRNAs. The miRNAs demonstrated significant target enrichment (Adj p < 0.05) for four metabolic pathways. There were four associations between growth-related miRNAs and growth-related phyla. We have shown that longitudinal trends in gut microbiota activity and human miRNA levels are associated with infant growth and the metabolic targets of miRNAs suggest these molecules may regulate the biosynthetic landscape of the gut and influence microbial activity.

Identification of novel cardiovascular disease associated metabolites using untargeted metabolomics

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Shams Tabrez ◽  
Mohammed Razeeth Shait Mohammed ◽  
Nasimudeen R. Jabir ◽  
Mohammad Imran Khan
Keyword(s):  
Cardiovascular Disease ◽  
Metabolic Pathways ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Healthy Individuals ◽  
Great Opportunity ◽  
Pathway Enrichment ◽  
Pathophysiological Role ◽  
The World ◽  
Metabolomic Approach

Abstract Cardiovascular disease (CVD) remains the leading cause of morbidity and mortality around the world. Early diagnosis of CVD could provide the opportunity for sensible management and better clinical outcome along with the prevention of further progression of the disease. In the current study, we used an untargeted metabolomic approach to identify possible metabolite(s) that associate well with the CVD and could serve either as therapeutic target or disease-associated metabolite. We identified 26 rationally adjusted unique metabolites that were differentially present in the serum of CVD patients compared with healthy individuals, among them 15 were found to be statistically significant. Out of these metabolites, we identified some novel metabolites like UDP-l-rhamnose and N1-acetylspermidine that have not been reported to be linked with CVD directly. Further, we also found that some metabolites like ethanolamide, solanidine, dimethylarginine, N-acetyl-l-tyrosine, can act as a discriminator of CVD. Metabolites integrating pathway enrichment analysis showed enrichment of various important metabolic pathways like histidine metabolism, methyl histidine metabolism, carnitine synthesis, along with arginine and proline metabolism in CVD patients. Our study provides a great opportunity to understand the pathophysiological role and impact of the identified unique metabolites and can be extrapolated as specific CVD specific metabolites.

scholarly journals Main drivers of (poly)phenols effects on human health: metabolites production and(or) gut microbiota-associated metabotypes?

2021 ◽  
Author(s):  
Carlos E. Iglesias-Aguirre ◽  
Adrián Cortés-Martín ◽  
María Á. Ávila-Gálvez ◽  
Juan Antonio Gimenez Bastida ◽  
Maria Victoria Selma ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Endothelial Function ◽  
Olive Oil ◽  
Human Health ◽  
Health Effects ◽  
Interindividual Variability ◽  
Effect Relationship ◽  
Metabolites Production

Despite the high human interindividual variability in response to (poly)phenols consumption, the cause-effect relationship between some dietary (poly)phenols (flavanols and olive oil phenolics) and health effects (endothelial function and prevention...

scholarly journals Relationship between Nutrient Intake and Human Gut Microbiota in Monozygotic Twins

Medicina ◽  
2021 ◽  
Vol 57 (3) ◽  
pp. 275
Author(s):  
Natsuko Matsumoto ◽  
Jonguk Park ◽  
Rie Tomizawa ◽  
Hitoshi Kawashima ◽  
Koji Hosomi ◽  
...  
Keyword(s):  
Individual Differences ◽  
Environmental Factors ◽  
Gut Microbiota ◽  
Human Health ◽  
Negative Correlation ◽  
Nutrient Intake ◽  
Monozygotic Twins ◽  
Human Gut ◽  
Positive Correlation ◽  
Human Gut Microbiota

Background and Objectives: The gut microbiota is associated with human health and dietary nutrition. Various studies have been reported in this regard, but it is difficult to clearly analyze human gut microbiota as individual differences are significant. The causes of these individual differences in intestinal microflora are genetic and/or environmental. In this study, we focused on differences between identical twins in Japan to clarify the effects of nutrients consumed on the entire gut microbiome, while excluding genetic differences. Materials and Methods: We selected healthy Japanese monozygotic twins for the study and confirmed their zygosity by matching 15 short tandem repeat loci. Their fecal samples were subjected to 16S rRNA sequencing and bioinformatics analyses to identify and compare the fluctuations in intestinal bacteria. Results: We identified 12 genera sensitive to environmental factors, and found that Lactobacillus was relatively unaffected by environmental factors. Moreover, we identified protein, fat, and some nutrient intake that can affect 12 genera, which have been identified to be more sensitive to environmental factors. Among the 12 genera, Bacteroides had a positive correlation with retinol equivalent intake (rs = 0.38), Lachnospira had a significantly negative correlation with protein, sodium, iron, vitamin D, vitamin B6, and vitamin B12 intake (rs = −0.38, −0.41, −0.39, −0.63, −0.42, −0.49, respectively), Lachnospiraceae ND3007 group had a positive correlation with fat intake (rs = 0.39), and Lachnospiraceae UCG-008 group had a negative correlation with the saturated fatty acid intake (rs = −0.45). Conclusions: Our study is the first to focus on the relationship between human gut microbiota and nutrient intake using samples from Japanese twins to exclude the effects of genetic factors. These findings will broaden our understanding of the more intuitive relationship between nutrient intake and the gut microbiota and can be a useful basis for finding useful biomarkers that contribute to human health.

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