1402 - Understanding strain-level differential performances of gut microbiota under a carbohydrate-rich dietary intervention through a metagenomic approach

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

mBio ◽

10.1128/mbio.02348-16 ◽

2017 ◽

Vol 8 (1) ◽

Cited By ~ 19

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.

Abstract 14: An Anti-inflammatory Proton Sensing-receptor Contributes To Cardiovascular Protection Of Gut Microbiota-derived Metabolites

Hypertension ◽

10.1161/hyp.78.suppl_1.14 ◽

2021 ◽

Vol 78 (Suppl_1) ◽

Author(s):

Liang Xie ◽

Rikeish R Muralitharan ◽

Evany Dinakis ◽

Michael E Nakai ◽

Hamdi Jama ◽

...

Keyword(s):

T Cell ◽

Gut Microbiota ◽

Dietary Fibre ◽

Dietary Intervention ◽

Immune Cell ◽

Ang Ii ◽

Direct Role ◽

Cardiovascular Protection ◽

Anti Inflammatory ◽

The Impact

High fibre (HF) diet protects against hypertension via the production of acidic metabolites, e.g. short-chain fatty acids, by the gut microbiota. While these metabolites have a direct role in blood pressure (BP) regulation, their acidic nature may activate proton-sensing receptors, which have anti-inflammatory functions. G-protein coupled receptor 65 (GPR65) is a proton-sensing receptor activated around pH 6.5 and is critical for gut homeostasis. We hypothesized that GPR65 is involved in the cardiovascular protection by dietary fibre. We first measured cecal pH of C57BL/6 (WT) mice after a 7-day dietary intervention with either HF or low fibre (LF) diets (n=6/group). HF diet lowered cecal pH to a level where GPR65 is highly activated, compared to the LF diet (6.5±0.1 vs 7.6±0.1, P<0.001). The impact of pH and GPR65 on T cell production of IFNγ, a pro-inflammatory cytokine, in vitro was measured by flow cytometry. Acidic pH inhibited the production of IFNγ by CD8+ T cells (pH 6.5 vs pH 7.5, P<0.001). Cells lacking GPR65 had higher IFNγ at both pH (P<0.001). To determine if GPR65 is involved in BP regulation by dietary fibre, WT and GPR65 knockout ( Gpr65 -/- ) mice were implanted with minipumps containing angiotensin II (Ang II, 0.5mg/kg/day, 28 days, n=8-9/group) and fed with HF diet. BP, cardiorenal function and immune cell infiltration were measured. Gpr65 -/- mice had higher BP compared to WT mice after 2 weeks (mean arterial pressure ± SEM; WT 79.8±2.4 vs Gpr65 -/- 95.8±1.6mmHg, P<0.001) and 4 weeks of Ang II infusion (WT 92.3±2.4 vs Gpr65 -/- 99.5±1.3, P=0.062). Gpr65 -/- mice developed cardiac (P=0.035) and renal (P=0.025) hypertrophy, and impaired renal natriuretic (P=0.054) and diuretic (P=0.056) function compared to WT mice. This was accompanied by higher macrophage (P=0.009) and γδ T cell (P=0.014) infiltration in the kidneys. In conclusion, our data suggest that pH-sensing by GPR65 contributes to the protection against hypertension by dietary fibre via inflammatory mechanisms. This is a novel mechanism that contributes to BP regulation via the gut microbiota.

Individualized Responses of Gut Microbiota to Dietary Intervention Modeled in Humanized Mice

mSystems ◽

10.1128/msystems.00098-16 ◽

2016 ◽

Vol 1 (5) ◽

Cited By ~ 24

Author(s):

Samuel A. Smits ◽

Angela Marcobal ◽

Steven Higginbottom ◽

Justin L. Sonnenburg ◽

Purna C. Kashyap

Keyword(s):

Gut Microbiota ◽

Dietary Intervention ◽

Scientific Evidence ◽

Marker Gene ◽

Gastrointestinal Symptoms ◽

Dietary Interventions ◽

Inflammatory Bowel ◽

Irritable Bowel ◽

And Function ◽

Generation Sequencing

ABSTRACT Dietary modification has long been used empirically to modify symptoms in inflammatory bowel disease, irritable bowel syndrome, and a diverse group of diseases with gastrointestinal symptoms. There is both anecdotal and scientific evidence to suggest that individuals respond quite differently to similar dietary changes, and the highly individualized nature of the gut microbiota makes it a prime candidate for these differences. To overcome the typical confounding factors of human dietary interventions, here we employ ex-germfree mice colonized by microbiotas of three different humans to test how different microbiotas respond to a defined change in carbohydrate content of diet by measuring changes in microbiota composition and function using marker gene-based next-generation sequencing and metabolomics. Our findings suggest that the same diet has very different effects on each microbiota’s membership and function, which may in turn explain interindividual differences in response to a dietary ingredient. Diet plays an important role in shaping the structure and function of the gut microbiota. The microbes and microbial products in turn can influence various aspects of host physiology. One promising route to affect host function and restore health is by altering the gut microbiome using dietary intervention. The individuality of the microbiome may pose a significant challenge, so we sought to determine how different microbiotas respond to the same dietary intervention in a controlled setting. We modeled gut microbiotas from three healthy donors in germfree mice and defined compositional and functional alteration following a change in dietary microbiota-accessible carbohydrates (MACs). The three gut communities exhibited responses that differed markedly in magnitude and in the composition of microbiota-derived metabolites. Adjustments in community membership did not correspond to the magnitude of changes in the microbial metabolites, highlighting potential challenges in predicting functional responses from compositional data and the need to assess multiple microbiota parameters following dietary interventions. IMPORTANCE Dietary modification has long been used empirically to modify symptoms in inflammatory bowel disease, irritable bowel syndrome, and a diverse group of diseases with gastrointestinal symptoms. There is both anecdotal and scientific evidence to suggest that individuals respond quite differently to similar dietary changes, and the highly individualized nature of the gut microbiota makes it a prime candidate for these differences. To overcome the typical confounding factors of human dietary interventions, here we employ ex-germfree mice colonized by microbiotas of three different humans to test how different microbiotas respond to a defined change in carbohydrate content of diet by measuring changes in microbiota composition and function using marker gene-based next-generation sequencing and metabolomics. Our findings suggest that the same diet has very different effects on each microbiota’s membership and function, which may in turn explain interindividual differences in response to a dietary ingredient. Author Video: An author video summary of this article is available.

Species and strain cultivation of skin, oral, and gut microbiota

10.1101/2021.04.01.435439 ◽

2021 ◽

Author(s):

Elizabeth Fleming ◽

Victor Pabst ◽

Amelia Hoyt ◽

Wei Zhou ◽

Rachel Hardy ◽

...

Keyword(s):

Mass Spectrometry ◽

High Resolution ◽

Gut Microbiota ◽

Strain Level ◽

Microbial Consortia ◽

Metagenomic Sequencing ◽

Mechanistic Studies ◽

Microbial Species ◽

Human Microbiota

Genomics-driven discovery of microbial species have provided extraordinary insights into the biodiversity of human microbiota. High resolution genomics to investigate species- and strain-level diversity and mechanistic studies, however, rely on the availability of individual microbes from a complex microbial consortia. Here, we describe and validate a streamlined workflow for cultivating microbes from the skin, oral, and gut microbiota, informed by metagenomic sequencing, mass spectrometry, and strain profiling.

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale

10.1101/125211 ◽

2017 ◽

Cited By ~ 8

Author(s):

Alex Bishara ◽

Eli L. Moss ◽

Ekaterina Tkachenko ◽

Joyce B. Kang ◽

Soumaya Zlitni ◽

...

Keyword(s):

Hematopoietic Cell Transplantation ◽

Susceptibility Testing ◽

Mobile Element ◽

Strain Level ◽

Short Read Sequencing ◽

Bacterial Competition ◽

Structural Differences ◽

Stool Samples ◽

Metagenomic Approach

AbstractAlthough shotgun short-read sequencing has facilitated the study of strain-level architecture within complex microbial communities, existing metagenomic approaches often cannot capture structural differences between closely related co-occurring strains. Recent methods, which employ read cloud sequencing and specialized assembly techniques, provide significantly improved genome drafts and show potential to capture these strain-level differences. Here, we apply this read cloud metagenomic approach to longitudinal stool samples from a patient undergoing hematopoietic cell transplantation. The patient’s microbiome is profoundly disrupted and is eventually dominated by Bacteroides caccae. Comparative analysis of B. caccae genomes obtained using read cloud sequencing together with metagenomic RNA sequencing allows us to predict that particular mobile element integrations result in increased antibiotic resistance, which we further support using in vitro antibiotic susceptibility testing. Thus, we find read cloud sequencing to be useful in identifying strain-level differences that underlie differential fitness.

The Effect of White Rice and White Bread as Staple Foods on Gut Microbiota and Host Metabolism

Nutrients ◽

10.3390/nu10091323 ◽

2018 ◽

Vol 10 (9) ◽

pp. 1323 ◽

Cited By ~ 2

Author(s):

Fumika Mano ◽

Kaori Ikeda ◽

Erina Joo ◽

Yoshihito Fujita ◽

Shunsuke Yamane ◽

...

Keyword(s):

Gut Microbiota ◽

Dietary Intervention ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

White Bread ◽

Fecal Samples ◽

White Rice ◽

Staple Foods ◽

Glucagon Like Peptide 1 ◽

Side Dishes

The purpose of this study was to examine the influence of two kinds of major Japanese staple foods, white rice and white bread, on gut microbiota against the background in which participants eat common side dishes. Seven healthy subjects completed the dietary intervention with two 1-week test periods with a 1-week wash-out period in cross-over design (UMIN registration UMIN000023142). White bread or white rice and 21 frozen prepared side dishes were consumed during the test periods. At baseline and at the end of each period, fasting blood samples, breath samples, and fecal samples were collected. For fecal samples, 16S rRNA gene sequencing was used to analyze the gut microbiota. After the bread period, the abundance of fecal Bifidobacterium genus (19.2 ± 14.5 vs. 6.2 ± 6.6 (%), p = 0.03), fasting glucagon-like peptide 1 (GLP-1) (13.6 ± 2.0 vs. 10.5 ± 2.9 (pg/mL), p = 0.03), and breath hydrogen (23.4 ± 9.9 vs. 8.2 ± 5.5 (ppm), p = 0.02) were significantly higher than those of after the rice period. Plasma SCFAs also tended to be higher after the bread period. White bread contains more dietary fiber than refined short grain rice. These findings suggest that indigestible carbohydrate intake from short grain rice as a staple food may be smaller than that of white bread.

Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries

Gut ◽

10.1136/gutjnl-2019-319654 ◽

2020 ◽

Vol 69 (7) ◽

pp. 1218-1228 ◽

Cited By ~ 58

Author(s):

Tarini Shankar Ghosh ◽

Simone Rampelli ◽

Ian B Jeffery ◽

Aurelia Santoro ◽

Marta Neto ◽

...

Keyword(s):

Gut Microbiota ◽

Mediterranean Diet ◽

Dietary Intervention ◽

European Countries ◽

Elderly Subjects ◽

Interleukin 17 ◽

Fatty Acid Production ◽

Short Branch ◽

Reactive Protein ◽

Before And After

ObjectiveAgeing is accompanied by deterioration of multiple bodily functions and inflammation, which collectively contribute to frailty. We and others have shown that frailty co-varies with alterations in the gut microbiota in a manner accelerated by consumption of a restricted diversity diet. The Mediterranean diet (MedDiet) is associated with health. In the NU-AGE project, we investigated if a 1-year MedDiet intervention could alter the gut microbiota and reduce frailty.DesignWe profiled the gut microbiota in 612 non-frail or pre-frail subjects across five European countries (UK, France, Netherlands, Italy and Poland) before and after the administration of a 12-month long MedDiet intervention tailored to elderly subjects (NU-AGE diet).ResultsAdherence to the diet was associated with specific microbiome alterations. Taxa enriched by adherence to the diet were positively associated with several markers of lower frailty and improved cognitive function, and negatively associated with inflammatory markers including C-reactive protein and interleukin-17. Analysis of the inferred microbial metabolite profiles indicated that the diet-modulated microbiome change was associated with an increase in short/branch chained fatty acid production and lower production of secondary bile acids, p-cresols, ethanol and carbon dioxide. Microbiome ecosystem network analysis showed that the bacterial taxa that responded positively to the MedDiet intervention occupy keystone interaction positions, whereas frailty-associated taxa are peripheral in the networks.ConclusionCollectively, our findings support the feasibility of improving the habitual diet to modulate the gut microbiota which in turn has the potential to promote healthier ageing.

Targeting the perinatal diet to modulate the gut microbiota increases dietary variety and prebiotic and probiotic food intakes: results from a randomised controlled trial

Public Health Nutrition ◽

10.1017/s1368980020003511 ◽

2020 ◽

pp. 1-13

Author(s):

Samantha L Dawson ◽

Mohammadreza Mohebbi ◽

Jeffrey M Craig ◽

Phillip Dawson ◽

Gerard Clarke ◽

...

Keyword(s):

Randomised Controlled Trial ◽

Gut Microbiota ◽

Pregnant Women ◽

Diet Quality ◽

Dietary Intervention ◽

Controlled Trial ◽

Control Group ◽

Dietary Variety ◽

Probiotic Food ◽

Randomised Controlled

Abstract Objective: To evaluate the hypothesis that a perinatal educational dietary intervention focused on ‘eating for the gut microbiota’ improves diet quality of pregnant women pre- and postnatally. Design: The Healthy Parents, Healthy Kids study is a prospectively registered randomised controlled trial designed to evaluate the efficacy of a dietary intervention in altering the maternal and infant gut microbiota and improving perinatal diet quality. Eligible pregnant women were randomised to receive dietary advice from their healthcare provider or to additionally receive a three session dietary intervention. Dietary data were collected at gestation weeks 26, 31, 36 and postnatal week 4. Outcome measures were diet quality, dietary variety, prebiotic and probiotic food intakes, energy, fibre, saturated fat and discretionary food intakes. Between-group differential changes from baseline before and after birth in these dietary measures were assessed using generalised estimating equations. Setting: Melbourne, Australia. Participants: Healthy pregnant women from gestation week 26. Results: Forty-five women were randomised (twenty-two control, twenty-three intervention). Compared with the control group, the intervention group improved diet quality prior to birth (5·66 (95 % CI 1·65, 9·67), Cohen’s d: 0·82 (se 0·33)). The intervention improved dietary variety (1·05 (95 % CI 0·17, 1·94), d: 0·66 (se 0·32)) and increased intakes of prebiotic (0·8 (95 % CI 0·27, 1·33), d: 0·91 (se 0·33)) and probiotic foods (1·05 (95 % CI 0·57, 1·53), d: 1·3(se 0·35)) over the whole study period compared with the control group. Conclusion: A dietary intervention focused on ‘eating for the gut microbiota’ can improve aspects of perinatal diet quality during and after pregnancy.

Characterization of the Gut Microbiota of Individuals at Different T2D Stages Reveals a Complex Relationship with the Host

Microorganisms ◽

10.3390/microorganisms8010094 ◽

2020 ◽

Vol 8 (1) ◽

pp. 94 ◽

Cited By ~ 4

Author(s):

Alejandra Chávez-Carbajal ◽

María Luisa Pizano-Zárate ◽

Fernando Hernández-Quiroz ◽

Guillermo Federico Ortiz-Luna ◽

Rosa María Morales-Hernández ◽

...

Keyword(s):

Gut Microbiota ◽

Metabolic Pathways ◽

Dietary Intervention ◽

Metabolic Characteristics ◽

Significant Difference ◽

Bacterial Richness ◽

Microbiota Diversity ◽

Improve Glucose Tolerance ◽

M 14

In this work, we studied 217 Mexican subjects divided into six groups with different stages of glucose intolerance: 76 Controls (CO), 54 prediabetes (PRE), 14 T2D no medication (T2D−No−M), 14 T2D with Metformin (T2D−M), 22 T2D with polypharmacy (T2D−P), and 37 T2D with polypharmacy and insulin (T2D−P+I). We aimed to determine differences in the gut microbiota diversity for each condition. At the phylum level, we found that Firmicutes and Bacteroidetes outline major changes in the gut microbiota. The gut bacterial richness and diversity of individuals in the T2D−No−M group were lesser than other groups. Interestingly, we found a significant difference in the beta diversity of the gut microbiota among all groups. Higher abundance was found for Comamonadaceae in PRE, and Sutterella spp. in T2D−No−M. In addition, we found associations of specific microbial taxa with clinical parameters. Finally, we report predicted metabolic pathways of gut microbiota linked to T2D−M and PRE conditions. Collectively, these results indicate that each group has specific predicted metabolic characteristics and gut bacteria populations for each phenotype. The results of this study could be used to define strategies to modulate gut microbiota through noninvasive treatments, such as dietary intervention, probiotics or prebiotics, and to improve glucose tolerance of individuals with prediabetes or T2D.

Lactobacillus probiotics improved the gut microbiota profile of a Drosophila melanogaster Alzheimer’s disease model and alleviated neurodegeneration in the eye

Beneficial Microbes ◽

10.3920/bm2019.0086 ◽

2020 ◽

Vol 11 (1) ◽

pp. 79-89 ◽

Cited By ~ 2

Author(s):

F.H.P. Tan ◽

G. Liu ◽

S.-Y.A. Lau ◽

M.H. Jaafar ◽

Y.-H. Park ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Drosophila Melanogaster ◽

Gut Microbiota ◽

Neurodegenerative Disorders ◽

Dietary Intervention ◽

Disease Model ◽

Brain Health ◽

Potential Biomarker ◽

Microbiota Diversity

Alzheimer’s disease (AD) is a progressive disease and one of the most common forms of neurodegenerative disorders. Emerging evidence is supporting the use of various strategies that modulate gut microbiota to exert neurological and psychological changes. This includes the utilisation of probiotics as a natural and dietary intervention for brain health. Here, we showed the potential AD-reversal effects of Lactobacillus probiotics through feeding to our Drosophila melanogaster AD model. The administration of Lactobacillus strains was able to rescue the rough eye phenotype (REP) seen in AD-induced Drosophila, with a more prominent effect observed upon the administration of Lactobacillus plantarum DR7 (DR7). Furthermore, we analysed the gut microbiota of the AD-induced Drosophila and found elevated levels of Wolbachia. The administration of DR7 restored the gut microbiota diversity of AD-induced Drosophila with a significant reduction in Wolbachia’s relative abundance, accompanied by an increase of Stenotrophomonas and Acetobacter. Through functional predictive analyses, Wolbachia was predicted to be positively correlated with neurodegenerative disorders, such as Parkinson’s, Huntington’s and Alzheimer’s diseases, while Stenotrophomonas was negatively correlated with these neurodegenerative disorders. Altogether, our data exhibited DR7’s ability to ameliorate the AD effects in our AD-induced Drosophila. Thus, we propose that Wolbachia be used as a potential biomarker for AD.