Association of gut microbiota composition and function with an aged rat model of senile osteoporosis using 16S rRNA and metagenomic sequencing analysis

Cardiometabolic disease (CMD), such as type 2 diabetes mellitus and cardiovascular disease, contributes significantly to morbidity and mortality on a global scale. The gut microbiota has emerged as a potential target to beneficially modulate CMD risk, possibly via dietary interventions. Dietary interventions have been shown to considerably alter gut microbiota composition and function. Moreover, several diet-derived microbial metabolites are able to modulate human metabolism and thereby alter CMD risk. Dietary interventions that affect gut microbiota composition and function are therefore a promising, novel, and cost-efficient method to reduce CMD risk. Studies suggest that fermentable carbohydrates can beneficially alter gut microbiota composition and function, whereas high animal protein and high fat intake negatively impact gut microbiota function and composition. This review focuses on the role of macronutrients (i.e., carbohydrate, protein, and fat) and dietary patterns (e.g., vegetarian/vegan and Mediterranean diet) in gut microbiota composition and function in the context of CMD.

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Stress Hormones and the Gut Microbiota Composition and Function

Reference Module in Food Science ◽

10.1016/b978-0-12-819265-8.00070-x ◽

2021 ◽

Author(s):

Hadar Neuman

Keyword(s):

Gut Microbiota ◽

Stress Hormones ◽

Microbiota Composition ◽

And Function ◽

Gut Microbiota Composition

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Diet quality, anthropometrics, and gut microbiota composition in healthy adults

Proceedings of The Nutrition Society ◽

10.1017/s0029665120003171 ◽

2020 ◽

Vol 79 (OCE2) ◽

Author(s):

Anna M. Malinowska ◽

Marcin Schmidt ◽

Agata Chmurzynska

Keyword(s):

Gut Microbiota ◽

Energy Intake ◽

Relative Abundance ◽

Diet Quality ◽

Healthy Eating Index ◽

Metagenomic Sequencing ◽

Microbiota Composition ◽

Anthropometric Parameters ◽

Gut Microbiota Composition ◽

Dietary Indices

AbstractHuman gut microbiota may affect metabolism and health by synthesizing metabolites and processing of food components. Those processes are specific to genus and species (or even strain), and dietary intake and metabolic state (such as obesity) can affect the composition of gut microbiota. The aim of the study was to assess the effect of dietary patterns and intake of several groups of food products and macronutrients, as well as the impact of anthropometric parameters on gut microbiota composition.The study group consisted of 200 men and women between 31 and 50 years of age. The diet was assessed using three-day dietary records and the dietary pattern was determined with the use of the original score method and two dietary indices, namely the Diet Quality Index – International (DQI-I) and the Healthy Eating Index (HEI). Bacterial DNA was isolated from the feces of the participants and microbiota composition was determined using metagenomic sequencing of the V3–V4 region of the 16S rRNA gene.Dietary indices and intake of energy from macronutrients did not correlate with the Firmicutes to Bacteroidetes phylum ratio. However people with greater abundance of the Firmicutes phylum compared to Bacteroidetes consumed higher amounts of fermented milk beverages, hard cheese, and salt (78%, 48%, 14% higher intake respectively; p < 0.05). A higher diet quality as measured by the diet indices was positively correlated with the relative abundance of the Firmicutes phylum, Bacilli, Clostridia class, Lachnospira, Faecalibacterium, Coprococcus, and Prevotella genus and negatively correlated with the relative abundance of the Bacteroidetes phylum, Bacteroidia class, and Bacteroides genus. Higher dietary fiber intake positively correlated with the relative abundance of the Coprococcus, Lachnospira, and Roseburia genera, whereas energy intake from simple carbohydrates was positively correlated with the relative abundance of the Tenericutes phylum and the Mollicutes class. Energy intake from alcohol correlated positively with the relative abundance of Bacteroidetes phylum and Bacteroides class and correlated negatively with Firmicutes phylum and Clostridia class. Lower waist-to-hip-ratio, body mass index, and fat mass led to higher abundance of the Fecalibacterium genus.Both diet and anthropometric parameters are associated with gut microbiota composition. Associations between diet and the relative abundance of microbiota are nutrient-specific.

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Gut microbiota composition in relation to intake of added sugar, sugar-sweetened beverages and artificially sweetened beverages in the Malmö Offspring Study

European Journal of Nutrition ◽

10.1007/s00394-020-02392-0 ◽

2020 ◽

Author(s):

Stina Ramne ◽

Louise Brunkwall ◽

Ulrika Ericson ◽

Nicola Gray ◽

Gunter G. C. Kuhnle ◽

...

Keyword(s):

Gut Microbiota ◽

Negative Binomial ◽

Metagenomic Sequencing ◽

Microbiota Composition ◽

Multiple Testing Correction ◽

Sugar Sweetened Beverages ◽

Added Sugar ◽

Sweetened Beverages ◽

Gut Microbiota Composition ◽

Artificially Sweetened Beverages

Abstract Purpose It has been suggested that a high intake of sugar or sweeteners may result in an unfavorable microbiota composition; however, evidence is lacking. Hence, in this exploratory epidemiological study, we aim to examine if intake of added sugar, sugar-sweetened beverages (SSBs) or artificially sweetened beverages (ASBs) associate with the gut microbiota composition. Methods Participants (18–70 years) in the Malmö Offspring Study have provided blood, urine, and fecal samples and completed both web-based 4 day food records and short food frequency questionnaires. The gut microbiota was assessed by 16S rRNA sequencing, processed in QIIME and matched to Greengenes (v.13.8), giving 64 included genera after filtering. Intake of added sugar (n = 1371) (also supported by the overnight urinary sugar biomarker in a subgroup n = 577), SSBs (n = 1086) and ASBs (n = 1085) were examined as exposures in negative binomial regressions. Results Various genera nominally associated with intake of added sugar, SSBs, and ASBs. Only the negative association between SSB intake and Lachnobacterium remained significant after multiple testing correction. A positive association between SSB intake and the Firmicutes:Bacteroidetes ratio was also observed. Conclusion In this wide population, the cross-sectional associations between added sugar and sweet beverage intake and the gut microbiota are modest, but the results suggest that SSB intake is associated negatively with the genus Lachnobacterium and positively with the Firmicutes:Bacteroidetes ratio. Larger studies, preferably using metagenomic sequencing, are needed to further evaluate if a link exists between intake of sugars and sweeteners and the human gut microbiota.

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Liver-specific knockdown of ANGPTL8 alters the structure of the gut microbiota in mice

Annals of Microbiology ◽

10.1186/s13213-020-01599-0 ◽

2020 ◽

Vol 70 (1) ◽

Author(s):

Yinlong Cheng ◽

Yining Li ◽

Yonghong Xiong ◽

Yixin Zou ◽

Siyu Chen ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

Shannon Index ◽

Microbiota Composition ◽

Functional Prediction ◽

Adeno Associated Virus ◽

Virus Serotype ◽

Significant Difference ◽

And Function ◽

Gut Microbiota Composition

Abstract Purpose To investigate the effect of liver-specific knockdown of ANGPTL8 on the structure of the gut microbiota. Methods We constructed mice with liver-specific ANGPTL8 knockdown by using an adeno-associated virus serotype 8 (AAV8) system harbouring an ANGPTL8 shRNA. We analysed the structure and function of the gut microbiome through pyrosequencing and KEGG (Kyoto Encyclopedia of Genes and Genomes) functional prediction. Results Compared with controls, ANGPTL8 shRNA reduced the Simpson index and Shannon index (p < 0.01) of the gut microbiota in mice. At the phylum level, the sh-ANGPTL8 group showed a healthier gut microbiota composition than controls (Bacteroidetes: controls 67.52%, sh-ANGPTL8 80.75%; Firmicutes: controls 10.96%, sh-ANGPTL8 8.58%; Proteobacteria: controls 9.29%, sh-ANGPTL8 0.98%; F/B ratio: controls 0.16, sh-ANGPTL8 0.11). PCoA and UPGMA analysis revealed a significant difference in microbiota composition, while KEGG analysis revealed a significant difference in microbiota function between controls and the sh-ANGPTL8 group. Conclusion Our results revealed that inhibition of ANGPTL8 signalling altered the structure of the gut microbiome, which might further affect the metabolism of mice. We have thus identified ANGPTL8 as a novel hepatogenic hormone potentially involving the liver-gut axis and regulating the structure of the gut microbiota.

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Dietary Protein and Gut Microbiota Composition and Function

Current Protein and Peptide Science ◽

10.2174/1389203719666180514145437 ◽

2018 ◽

Vol 20 (2) ◽

pp. 145-154 ◽

Cited By ~ 25

Author(s):

Jianfei Zhao ◽

Xiaoya Zhang ◽

Hongbin Liu ◽

Michael A. Brown ◽

Shiyan Qiao

Keyword(s):

Gut Microbiota ◽

Dietary Protein ◽

Microbiota Composition ◽

And Function ◽

Gut Microbiota Composition

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Systems biology analysis of omeprazole therapy in cirrhosis demonstrates significant shifts in gut microbiota composition and function

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.00268.2014 ◽

2014 ◽

Vol 307 (10) ◽

pp. G951-G957 ◽

Cited By ~ 95

Author(s):

Jasmohan S. Bajaj ◽

I. Jane Cox ◽

Naga S. Betrapally ◽

Douglas M. Heuman ◽

Mitchell L. Schubert ◽

...

Keyword(s):

Systems Biology ◽

Gut Microbiota ◽

Serum Gastrin ◽

Bacterial Overgrowth ◽

Infectious Complications ◽

Functional Change ◽

Microbiota Composition ◽

And Function ◽

Stool Microbiota ◽

Gut Microbiota Composition

Proton pump inhibitors (PPI) have been associated with infectious complications in cirrhosis, but their impact on distal gut microbiota composition and function is unclear. We aimed to evaluate changes in stool microbiota composition and function in patients with cirrhosis and healthy controls after omeprazole therapy. Both 15 compensated cirrhotic patients and 15 age-matched controls underwent serum gastrin measurement, stool microbiota profiling with multitagged pyrosequencing, and urinary metabolic profiling with NMR spectroscopy to assess microbial cometabolites before/after a 14-day course of 40 mg/day omeprazole under constant diet conditions. Results before (pre) and after PPI were compared in both groups, compared with baseline by systems biology techniques. Adherence was >95% without changes in diet or MELD (model for end-stage liver disease) score during the study. Serum gastrin concentrations significantly increased after PPI in cirrhosis (pre 38.3 ± 35.8 vs. 115.6 ± 79.3 pg/ml P < 0.0001) and controls (pre 29.9 ± 14.5 vs. 116.0 ± 74.0 pg/ml, P = 0.001). A significant microbiota change was seen in both controls and cirrhosis after omeprazole (QIIME P < 0.0001). Relative Streptococcaceae abundance, normally abundant in saliva, significantly increased postomeprazole in controls (1 vs. 5%) and cirrhosis (0 vs. 9%) and was correlated with serum gastrin levels ( r = 0.4, P = 0.005). We found significantly reduced hippurate in cirrhosis vs. controls both pre- and postomeprazole and increased lactate in both groups post vs. preomeprazole, whereas dimethylamine (DMA) decreased in cirrhosis only. On correlation network analysis, significant changes in linkages of bacteria with metabolites (hippurate/DMA/lactate) were found postomeprazole, compared with pre-PPI in cirrhosis patients. In conclusion, omeprazole is associated with a microbiota shift and functional change in the distal gut in patients with compensated cirrhosis that could set the stage for bacterial overgrowth.

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Metformin Affects Gut Microbiome Composition and Function and Circulating Short-Chain Fatty Acids: A Randomized Trial

10.2337/figshare.14340419 ◽

2021 ◽

Author(s):

Noel T. Mueller ◽

Moira K. Differding ◽

Mingyu Zhang ◽

Nisa Maruthar ◽

Stephen P Juraschek ◽

...

Keyword(s):

Weight Loss ◽

Gut Microbiota ◽

Randomized Trial ◽

Short Chain Fatty Acids ◽

Metagenomic Sequencing ◽

Microbiota Composition ◽

Behavioral Weight Loss ◽

Microbiome Composition ◽

Weight Loss Group ◽

And Function

Objective: To determine the longer-term effects of metformin and behavioral weight loss on gut microbiota and SCFAs. Methods: We conducted a parallel-arm, randomized trial. We enrolled overweight/obese adults who had been treated for solid tumors but had no ongoing cancer treatment and randomized them (n=121) to: 1) metformin (up to 2000mg), 2) coach-directed behavioral weight loss, or 3) self-directed care (control) for 12 months. We collected stool and serum at baseline (n=114), 6 months (n=109) and 12 months (n=105). From stool, we extracted microbial DNA and conducted amplicon and metagenomic sequencing. We measured SCFAs and other biochemical parameters from fasting serum. Results: Of the 121 participants, 79% were female, 46% were black, and the mean age was 60y. Only metformin intervention significantly altered microbiota composition. Compared to control, metformin increased E. Coli and Ruminococcus torques and decreased Intestinibacter Bartletti at both 6 and 12 months, and decreased the genus Roseburia (genus), including R. faecis and R. intestinalis, at 12 months. Effects were similar when comparing metformin to the behavioral weight loss group. Metformin also altered 62 metagenomic functional pathways and increased butyrate, acetate, and valerate at 6 months. Behavioral weight loss vs. control did not significantly alter microbiota composition, but did increase acetate at 6 months. Increases in acetate were associated with decreases in fasting insulin. Conclusions: Metformin, but not behavioral weight loss, impacted gut microbiota composition and function at 6 months and 12 months. Both metformin and behavioral weight loss altered 6-month SCFAs, including increasing acetate which correlated with improved insulin sensitivity.

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Effects of cat ownership on the gut microbiota of owners

PLoS ONE ◽

10.1371/journal.pone.0253133 ◽

2021 ◽

Vol 16 (6) ◽

pp. e0253133

Author(s):

Guankui Du ◽

Hairong Huang ◽

Qiwei Zhu ◽

Li Ying

Keyword(s):

Gut Microbiota ◽

Microbial Diversity ◽

Metabolic Pathways ◽

Normal Weight ◽

Female Group ◽

Microbiota Composition ◽

Pet Ownership ◽

Weight Group ◽

And Function ◽

Gut Microbiota Composition

Pet ownership is an essential environmental exposure that might influence the health of the owner. This study’s primary objectives were to explore the effects of cat ownership on the gut microbial diversity and composition of owners. Raw data from the American Gut Project were obtained from the SRA database. A total of 214 Caucasian individuals (111 female) with cats and 214 individuals (111 female) without cats were used in the following analysis. OTU number showed significant alteration in the Cat group and Female_cat group, compared with that of the no cat (NC) group and Female_ NC group, respectively. Compared with the NC group, the microbial phylum Proteobacteria was significantly decreased in the Cat group. The microbial families Alcaligenaceae and Pasteurellaceae were significantly reduced, while Enterobacteriaceae and Pseudomonadaceae were significantly increased in the Cat group. Fifty metabolic pathways were predicted to be significantly changed in the Cat group. Twenty-one and 13 metabolic pathways were predicted to be significantly changed in the female_cat and male_cat groups, respectively. Moreover, the microbial phylum Cyanobacteria was significantly decreased, while the families Alcaligenaceae, Pseudomonadaceae and Enterobacteriaceae were significantly changed in the normal weight cat group. In addition, 41 and 7 metabolic pathways were predicted to be significantly changed in the normal-weight cat and overweight cat groups, respectively. Therefore, this study demonstrated that cat ownership could influence owners’ gut microbiota composition and function, especially in the female group and normal-weight group.

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