scholarly journals Genomic Microdiversity of Bifidobacterium pseudocatenulatum Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention

mBio ◽  
2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Guojun Wu ◽  
Chenhong Zhang ◽  
Huan Wu ◽  
Ruirui Wang ◽  
Jian Shen ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Dietary Intervention ◽  
Genomic Diversity ◽  
Strain Level ◽  
Transport Systems ◽  
Gene Copy ◽  
Dietary Carbohydrate ◽  
A Genome ◽  
Differential Responses

ABSTRACT The genomic basis of the response to dietary intervention of human gut beneficial bacteria remains elusive, which hinders precise manipulation of the microbiota for human health. After receiving a dietary intervention enriched with nondigestible carbohydrates for 105 days, a genetically obese child with Prader-Willi syndrome lost 18.4% of his body weight and showed significant improvement in his bioclinical parameters. We obtained five isolates (C1, C15, C55, C62, and C95) of one of the most abundantly promoted beneficial species, Bifidobacterium pseudocatenulatum , from a postintervention fecal sample. Intriguingly, these five B. pseudocatenulatum strains showed differential responses during the dietary intervention. Two strains were largely unaffected, while the other three were promoted to different extents by the changes in dietary carbohydrate resources. The differential responses of these strains were consistent with their functional clustering based on the COGs (Clusters of Orthologous Groups), including those involved with the ABC-type sugar transport systems, suggesting that the strain-specific genomic variations may have contributed to the niche adaption. Particularly, B. pseudocatenulatum C15, which had the most diverse types and highest gene copy numbers of carbohydrate-active enzymes targeting plant polysaccharides, had the highest abundance after the dietary intervention. These studies show the importance of understanding genomic diversity of specific members of the gut microbiota if precise nutrition approaches are to be realized. IMPORTANCE The manipulation of the gut microbiota via dietary approaches is a promising option for improving human health. Our findings showed differential responses of multiple B. pseudocatenulatum strains isolated from the same habitat to the dietary intervention, as well as strain-specific correlations with bioclinical parameters of the host. The comparative genomics revealed a genome-level microdiversity of related functional genes, which may have contributed to these differences. These results highlight the necessity of understanding strain-level differences if precise manipulation of gut microbiota through dietary approaches is to be realized.

scholarly journals Honeybee genetics shape the strain-level structure of gut microbiota in social transmission

2020 ◽  
Author(s):  
Jiaqiang Wu ◽  
Haoyu Lang ◽  
Xiaohuan Mu ◽  
Zijing Zhang ◽  
Qinzhi Su ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Receptor Gene ◽  
Level Structure ◽  
Social Transmission ◽  
Strain Level ◽  
Microbial Composition ◽  
Shotgun Metagenomics ◽  
Host Genetics ◽  
A Genome ◽  
Microbiota Structure

AbstractHoneybee gut microbiota transmitted via social interactions are beneficial to the host health. Although the microbial community is relatively stable, individual variations and high strain-level diversity have been detected across honeybees. Although the bee gut microbiota structure is influenced by environmental factors, the heritability of the gut members and the contribution of the host genetics remains elusive. Considering bees within a colony are not readily genetically identical due to the polyandry of queen, we hypothesize that the microbiota structure can be shaped by host genetics. We used shotgun metagenomics to simultaneously profile the microbiota and host genotypes of individuals from hives of four different subspecies. Gut composition is more distant between genetically different bees at both phylotype- and “sequence-discrete population”-level. We then performed a successive passaging experiment within colonies of hybrid bees generated by artificial insemination, which revealed that the microbial composition dramatically shifts across batches of bees during the social transmission. Specifically, different strains from the phylotype of Snodgrassella alvi are preferentially selected by genetically varied hosts, and strains from different hosts show a remarkably biased distribution of single-nucleotide polymorphism in the Type IV pili loci. A genome-wide association analysis identified that the relative abundance of a cluster of Bifidobacterium strains is associated with the host glutamate receptor gene that is specifically expressed in the bee brain. Finally, mono-colonization of Bifidobacterium with a specific polysaccharide utilization locus impacts the expression and alternative splicing of the gluR-B gene, which is associated with an altered circulating metabolomic profile. Our results indicated that host genetics influence the bee gut composition, and suggest a gut-brain connection implicated in the gut bacterial strain preference. Honeybees have been used extensively as a model organism for social behaviors, genetics, and gut microbiome. Further identification of host genetic function as shaping force of microbial structure will advance our understanding of the host-microbe interactions.

scholarly journals Gut Microbial SNPs Induced by High-Fiber Diet Dominate Nutrition Metabolism and Environmental Adaption of Faecalibacterium prausnitzii in Obese Children

2021 ◽  
Vol 12 ◽  
Author(s):  
Hui Li ◽  
Liping Zhao ◽  
Menghui Zhang
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Dietary Intervention ◽  
Nucleotide Metabolism ◽  
Metagenomic Data ◽  
Snp Analysis ◽  
High Fiber ◽  
Faecalibacterium Prausnitzii ◽  
Fiber Diet ◽  
High Fiber Diet

Dietary intervention is effective in human health promotion through modulation of gut microbiota. Diet can cause single-nucleotide polymorphisms (SNPs) to occur in the gut microbiota, and some of these variations may lead to functional changes in human health. In this study, we performed a systematic SNP analysis based on metagenomic data collected from children with Prader–Willi syndrome (PWS, n = 17) and simple obese (SO) children (n = 19), who had better healthy conditions after receiving high-fiber diet intervention. We found that the intervention increased the SNP proportions of Faecalibacterium, Bifidobacterium, and Clostridium and decreased those of Bacteroides in all children. Besides, the PWS children had Collinsella increased and Ruminococcus decreased, whereas the SO had Blautia and Escherichia decreased. There were much more BiasSNPs in PWS than in SO (4,465 vs 303), and only 81 of them appeared in both groups, of which 78 were from Faecalibacterium prausnitzii, and 51 were nonsynonymous mutations. These nonsynonymous variations were mainly related to pathways of environmental adaptation and nutrition metabolism, particularly to carbohydrate and nucleotide metabolism. In addition, dominant strains carrying BiasSNPs in all children shifted from F. prausnitzii AF32-8AC and F. prausnitzii 942/30-2 to F. prausnitzii SSTS Bg7063 and F. prausnitzii JG BgPS064 after the dietary intervention. Furthermore, although the abundance of Bifidobacterium increased significantly by the intervention and became dominant strains responsible for nutrition metabolism, they had less BiasSNPs between the pre- and post-intervention group in comparison with Faecalibacterium. The finding of F. prausnitzii as important functional strains influenced by the intervention highlights the superiority of applying SNP analysis in studies of gut microbiota. This study provided evidence and support for the effect of dietary intervention on gut microbial SNPs, and gave some enlightenments for disease treatment.

scholarly journals Honeybee Genetics Shape the Strain-Level Structure of Gut Microbiota in Social Transmission

2020 ◽  
Author(s):  
Jiaqiang Wu ◽  
Haoyu Lang ◽  
Xiaohuan Mu ◽  
Zijing Zhang ◽  
Qinzhi Su ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Receptor Gene ◽  
Level Structure ◽  
Social Transmission ◽  
Strain Level ◽  
Microbial Composition ◽  
Shotgun Metagenomics ◽  
Host Genetics ◽  
A Genome ◽  
Microbiota Structure

Abstract Background : Honeybee gut microbiota transmitted via social interactions are beneficial to the host health. Although the microbial community is relatively stable, individual variations and high strain-level diversity have been detected across honeybees. Although the bee gut microbiota structure is influenced by environmental factors, the heritability of the gut members and the contribution of the host genetics remains elusive. Considering bees within a colony are not readily genetically identical due to the polyandry of queen, we hypothesize that the microbiota structure can be shaped by host genetics. Results : We used shotgun metagenomics to simultaneously profile the microbiota and host genotypes of individuals from hives of four different subspecies. Gut composition is more distant between genetically different bees at both phylotype- and “sequence-discrete population”-level. We then performed a successive passaging experiment within colonies of hybrid bees generated by artificial insemination, which revealed that the microbial composition dramatically shifts across batches of bees during the social transmission. Specifically, different strains from the phylotype of Snodgrassella alvi are preferentially selected by genetically varied hosts, and strains from different hosts show a remarkably biased distribution of single-nucleotide polymorphism in the Type IV pili loci. A genome-wide association analysis identified that the relative abundance of a cluster of Bifidobacterium strains is associated with the host glutamate receptor gene that is specifically expressed in the bee brain. Finally, mono-colonization of Bifidobacterium with a specific polysaccharide utilization locus impacts the expression and alternative splicing of the gluR-B gene, which is associated with an altered circulating metabolomic profile. Conclusions : Our results indicated that host genetics influence the bee gut composition, and suggest a gut-brain connection implicated in the gut bacterial strain preference. Honeybees have been used extensively as a model organism for social behaviors, genetics, and gut microbiome. Further identification of host genetic function as shaping force of microbial structure will advance our understanding of the host-microbe interactions.

scholarly journals Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species

2020 ◽  
Author(s):  
Kirsten M Ellegaard ◽  
Shota Suenami ◽  
Ryo Miyazaki ◽  
Philipp Engel
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Microbial Communities ◽  
Honey Bee ◽  
Genomic Diversity ◽  
Strain Level ◽  
Gene Content ◽  
Rrna Gene ◽  
Gene Repertoire ◽  
Shotgun Metagenomics

AbstractMost bacterial species encompass strains with vastly different gene content. Strain diversity in microbial communities is therefore considered to be of functional importance. Yet, little is known about the extent to which related microbial communities differ in diversity at this level and which underlying mechanisms may constrain and maintain strain-level diversity. Here, we used shotgun metagenomics to characterize and compare the gut microbiota of two honey bee species, Apis mellifera and Apis cerana, which have diverged about 6 mio years ago. While both host species are colonized by largely overlapping bacterial 16S rRNA phylotypes, we find that their communities are highly host-specific when analyzed with genomic resolution. Despite their similar ecology, A. mellifera displayed a much higher extent of strain-level diversity and functional gene content in the microbiota than A. cerana, per colony and per individual bee. In particular, the gene repertoire for polysaccharide degradation was massively expanded in the microbiota of A. mellifera relative to A. cerana. Bee management practices, divergent ecological adaptation, or habitat size may have contributed to the observed differences in microbiota composition of these two key pollinator species. Our results illustrate that the gut microbiota of closely related animal hosts can differ vastly in genomic diversity despite sharing similar levels of diversity at the 16S rRNA gene. This is likely to have consequences for gut microbiota functioning and host-symbiont interactions, highlighting the need for metagenomic studies to understand the ecology and evolution of microbial communities.

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 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...

Sign in / Sign up

Export Citation Format

Share Document