scholarly journals High-throughput sequencing analysis of intestinal flora changes in ESRD and CKD patients

2019 ◽  
Author(s):  
Jianguang Hu ◽  
Xiaoshi Zhong ◽  
Jing Yan ◽  
Daoyuan Zhou ◽  
Danping Qin ◽  
...  
Keyword(s):  
Peritoneal Dialysis ◽  
High Throughput Sequencing ◽  
Intestinal Flora ◽  
Albumin Level ◽  
Control Group ◽  
Sequencing Analysis ◽  
Dominant Type ◽  
Inflammatory Conditions ◽  
Rdna Sequencing ◽  
Family Level

Abstract Background Chronic kidney disease (CKD) disease affects gut flora by causing dysbiosis and lead to systemic inflammatory conditions. Here, we provide intestinal flora changes of CKD patients undertook different hemodialysis therapy.Methods Patients were recruited during 2017-2019 and divided into healthy control group (CT), CKD non-dialysis group (CKD), hemodialysis group (HD) and peritoneal dialysis group (PD). Intestinal flora genome 16S rDNA sequencing and further bio-informatic analysis were performed.Results Decreased diversity and altered communities of intestinal flora in PD patients, in which microbial diversity was positive correlated with the albumin level were observed. A total of 20 intestinal flora phyla were detected in 166 fecal samples, divided into 3 dominant intestinal types including Bacteroides-dominant gut type, Firmicutes-dominant type and Proteobacteria-dominant gut type. Further analyses found 198 genera, the abundance of 86 genera were significantly different. Butyrate-producing taxa as Faecalibacterium in genera level and Bifidobacteriaceae and Prevotellaceae in family level were dominant genus in CT, CKD, and HD groups, while urease containing-, indole- and p-cresol-forming taxa as Escherichia in genera and Enterobacteriaceae , Enterococcaceae in family level was dominated genus in PD group. Number of differential expressed genes in KEGG enrichment pathways were significantly different in PD group in carbohydrate metabolism, amino acid metabolism, energy metabolism, translation, and membrane transport.Conclusion Our results suggest peritoneal dialysis therapy could result in reduced diversity and altered microbial communities, with reduced probiotic butyrate-producing taxa and increased urease containing-, indole- and p-cresol-forming taxa. The disordered intestinal flora can seriously affect the nutrition level in CKD patients with PD therapy.

scholarly journals High-throughput sequencing analysis of intestinal flora changes in ESRD and CKD patients

2019 ◽  
Author(s):  
yan liu ◽  
Jianguang Hu ◽  
Xiaoshi Zhong ◽  
Jing Yan ◽  
Daoyuan Zhou ◽  
...  
Keyword(s):  
Peritoneal Dialysis ◽  
High Throughput Sequencing ◽  
Intestinal Flora ◽  
Albumin Level ◽  
Control Group ◽  
Sequencing Analysis ◽  
Dominant Type ◽  
Inflammatory Conditions ◽  
Rdna Sequencing ◽  
Family Level

Abstract Background Chronic kidney disease (CKD) disease affects gut flora by causing dysbiosis and lead to systemic inflammatory conditions. Here, we provide intestinal flora changes of CKD patients undertook different hemodialysis therapy.Methods Patients were recruited during 2017-2019 and divided into healthy control group (CT), CKD non-dialysis group (CKD), hemodialysis group (HD) and peritoneal dialysis group (PD). Intestinal flora genome 16S rDNA sequencing and further bio-informatic analysis were performed.Results Decreased diversity and altered communities of intestinal flora in PD patients, in which microbial diversity was positive correlated with the albumin level were observed. A total of 20 intestinal flora phyla were detected in 166 fecal samples, divided into 3 dominant intestinal types including Bacteroides-dominant gut type, Firmicutes-dominant type and Proteobacteria-dominant gut type. Further analyses found 198 genera, the abundance of 86 genera were significantly different. Butyrate-producing taxa as Faecalibacterium in genera level and Bifidobacteriaceae and Prevotellaceae in family level were dominant genus in CT, CKD, and HD groups, while urease containing-, indole- and p-cresol-forming taxa as Escherichia in genera and Enterobacteriaceae , Enterococcaceae in family level was dominated genus in PD group. Number of differential expressed genes in KEGG enrichment pathways were significantly different in PD group in carbohydrate metabolism, amino acid metabolism, energy metabolism, translation, and membrane transport.Conclusion Our results suggest peritoneal dialysis therapy could result in reduced diversity and altered microbial communities, with reduced probiotic butyrate-producing taxa and increased urease containing-, indole- and p-cresol-forming taxa. The disordered intestinal flora can seriously affect the nutrition level in CKD patients with PD therapy.

scholarly journals High-throughput sequencing analysis of intestinal flora changes in elderly hemodialysis CKD patients

2019 ◽  
Author(s):  
yan liu ◽  
Jianguang Hu ◽  
Xiaoshi Zhong ◽  
Jing Yan ◽  
Daoyuan Zhou ◽  
...  
Keyword(s):  
Peritoneal Dialysis ◽  
High Throughput Sequencing ◽  
Intestinal Flora ◽  
Albumin Level ◽  
Control Group ◽  
Sequencing Analysis ◽  
Dominant Type ◽  
Inflammatory Conditions ◽  
Rdna Sequencing ◽  
Family Level

Abstract Background Chronic kidney disease (CKD) disease affects gut flora by causing dysbiosis and lead to systemic inflammatory conditions. Here, we provide intestinal flora changes of CKD patients undertook different hemodialysis therapy.Methods Patients were recruited during 2017-2019 and divided into healthy control group (CT), CKD non-dialysis group (CKD), hemodialysis group (HD) and peritoneal dialysis group (PD). Intestinal flora genome 16S rDNA sequencing and further bio-informatic analysis were performed.Results Decreased diversity and altered communities of intestinal flora in PD patients, in which microbial diversity was positive correlated with the albumin level were observed. A total of 20 intestinal flora phyla were detected in 166 fecal samples, divided into 3 dominant intestinal types including Bacteroides-dominant gut type, Firmicutes-dominant type and Proteobacteria-dominant gut type. Further analyses found 198 genera, the abundance of 86 genera were significantly different. Butyrate-producing taxa as Faecalibacterium in genera level and Bifidobacteriaceae and Prevotellaceae in family level were dominant genus in CT, CKD, and HD groups, while urease containing-, indole- and p-cresol-forming taxa as Escherichia in genera and Enterobacteriaceae , Enterococcaceae in family level was dominated genus in PD group. Number of differential expressed genes in KEGG enrichment pathways were significantly different in PD group in carbohydrate metabolism, amino acid metabolism, energy metabolism, translation, and membrane transport.Conclusion Our results suggest peritoneal dialysis therapy could result in reduced diversity and altered microbial communities, with reduced probiotic butyrate-producing taxa and increased urease containing-, indole- and p-cresol-forming taxa. The disordered intestinal flora can seriously affect the nutrition level in CKD patients with PD therapy.

scholarly journals High-throughput sequencing analysis of intestinal flora changes in elderly hemodialysis CKD patients

2019 ◽  
Author(s):  
yan liu ◽  
Jianguang Hu ◽  
Xiaoshi Zhong ◽  
Jing Yan ◽  
Daoyuan Zhou ◽  
...  
Keyword(s):  
Peritoneal Dialysis ◽  
High Throughput Sequencing ◽  
Intestinal Flora ◽  
Albumin Level ◽  
Control Group ◽  
Sequencing Analysis ◽  
Dominant Type ◽  
Inflammatory Conditions ◽  
Rdna Sequencing ◽  
Family Level

Abstract Background Chronic kidney disease (CKD) disease affects gut flora by causing dysbiosis and lead to systemic inflammatory conditions. Here, we provide intestinal flora changes of CKD patients undertook different hemodialysis therapy.Methods Patients were recruited during 2017-2019 and divided into healthy control group (CT), CKD non-dialysis group (CKD), hemodialysis group (HD) and peritoneal dialysis group (PD). Intestinal flora genome 16S rDNA sequencing and further bio-informatic analysis were performed.Results Decreased diversity and altered communities of intestinal flora in PD patients, in which microbial diversity was positive correlated with the albumin level were observed. A total of 20 intestinal flora phyla were detected in 166 fecal samples, divided into 3 dominant intestinal types including Bacteroides-dominant gut type, Firmicutes-dominant type and Proteobacteria-dominant gut type. Further analyses found 198 genera, the abundance of 86 genera were significantly different. Butyrate-producing taxa as Faecalibacterium in genera level and Bifidobacteriaceae and Prevotellaceae in family level were dominant genus in CT, CKD, and HD groups, while urease containing-, indole- and p-cresol-forming taxa as Escherichia in genera and Enterobacteriaceae, Enterococcaceae in family level was dominated genus in PD group. Number of differential expressed genes in KEGG enrichment pathways were significantly different in PD group in carbohydrate metabolism, amino acid metabolism, energy metabolism, translation, and membrane transport.Conclusion Our results suggest peritoneal dialysis therapy could result in reduced diversity and altered microbial communities, with reduced probiotic butyrate-producing taxa and increased urease containing-, indole- and p-cresol-forming taxa. The disordered intestinal flora can seriously affect the nutrition level in CKD patients with PD therapy.

scholarly journals High-throughput sequencing analysis of intestinal flora changes in ESRD and CKD patients

2019 ◽  
Author(s):  
Jianguang Hu ◽  
Xiaoshi Zhong ◽  
Jing Yan ◽  
Daoyuan Zhou ◽  
Danping Qin ◽  
...  
Keyword(s):  
Peritoneal Dialysis ◽  
High Throughput Sequencing ◽  
Intestinal Flora ◽  
Albumin Level ◽  
Control Group ◽  
Sequencing Analysis ◽  
Dominant Type ◽  
Inflammatory Conditions ◽  
Rdna Sequencing ◽  
Family Level

Abstract Background Chronic kidney disease (CKD) disease affects gut flora by causing dysbiosis and lead to systemic inflammatory conditions. Here, we provide intestinal flora changes of CKD patients undertook different hemodialysis therapy.Methods Patients were recruited during 2017-2019 and divided into healthy control group (CT), CKD non-dialysis group (CKD), hemodialysis group (HD) and peritoneal dialysis group (PD). Intestinal flora genome 16S rDNA sequencing and further bio-informatic analysis were performed.Results Decreased diversity and altered communities of intestinal flora in PD patients, in which microbial diversity was positive correlated with the albumin level were observed. A total of 20 intestinal flora phyla were detected in 166 fecal samples, divided into 3 dominant intestinal types including Bacteroides-dominant gut type, Firmicutes-dominant type and Proteobacteria-dominant gut type. Further analyses found 198 genera, the abundance of 86 genera were significantly different. Butyrate-producing taxa as Faecalibacterium in genera level and Bifidobacteriaceae and Prevotellaceae in family level were dominant genus in CT, CKD, and HD groups, while urease containing-, indole- and p-cresol-forming taxa as Escherichia in genera and Enterobacteriaceae , Enterococcaceae in family level was dominated genus in PD group. Number of differential expressed genes in KEGG enrichment pathways were significantly different in PD group in carbohydrate metabolism, amino acid metabolism, energy metabolism, translation, and membrane transport.Conclusion Our results suggest peritoneal dialysis therapy could result in reduced diversity and altered microbial communities, with reduced probiotic butyrate-producing taxa and increased urease containing-, indole- and p-cresol-forming taxa. The disordered intestinal flora can seriously affect the nutrition level in CKD patients with PD therapy.

scholarly journals Role of Tryptophan-Metabolizing Microbiota On Diarrhea Mice Caused by Folium sennae Extracts

2020 ◽  
Author(s):  
Chenyang Zhang ◽  
Haoqing Shao ◽  
Dandan Li ◽  
Nenqun Xiao ◽  
Zhoujin Tan
Keyword(s):  
Cytochrome P450 ◽  
Metabolic Pathways ◽  
High Throughput Sequencing ◽  
Statistical Significance ◽  
Bacterial Flora ◽  
Intestinal Flora ◽  
Shannon Index ◽  
Tryptophan Metabolism ◽  
Control Group ◽  
Sequencing Analysis

Abstract (1) Background: Although reports have provided evidence that diarrhea caused by Folium sennae can result in intestinal flora diversity disorder, the intestinal bacterial characteristic and specific mechanism are still unknown. The objective of our study was to investigate the mechanism of diarrhea caused by Folium sennae, which was associated with intestinal bacterial characteristic reshaping and metabolic abnormality. (2) Methods: The intestinal contents of 2 groups of mice, intervened with Folium sennae extracts and distilled water respectively, were collected and its DNA was extracted for high-throughput sequencing analysis. The active compounds of Folium sennae were filtrated, and their diarrhea-related targets and metabolic pathways were predicted. Virtual Metabolic Human (VMH) was utilized to simulated metabolic function of bacteria associated with Folium sennae -induced diarrhea to verified the metabolic pathways of the drug. (3) Results: For the intervention of Folium sennae extracts, Chao1 index and Shannon index were statistical decreased. The Beta diversity clusters of mice interfered by Folium sennae extracts were distinctly separate from control group. Combining PPI network analysis, cytochrome P450 (CYP) enzymes metabolism was the main signaling pathway of diarrhea caused by Folium sennae. Moreover, the abundance of 10 bacterial flora communities had statistical significance with Folium sennae intervention: the abundance of Paraprevotella, streptococcus, Epulopiscium, Sutterella and Mycoplasma were increased significantly; and the abundance of Adlercreutzia, Lactobacillus, Dehalobacterium, Dorea and Oscillospira were reduced significantly. 7 of the 10 intestinal flora communities were related to the synthesis of tryptophan derivatives, which affected the transformation of aminotryptophan into L-tryptophan, leading to abnormal tryptophan metabolism in the host. (4) Conclusions: Folium sennae targeted cytochrome P450 (CYP) 3A4 to alterd intestinal bacterial characteristic and interven the tryptophan metabolism of intestinal microflora, such as Streptococcus, Sutterella and Dorea, which could be the intestinal microecological mechanism of diarrhea caused by Folium sennae extracts.

Effect of Dapagliflozin on Intestinal Flora in MafA-deficient Mice

2018 ◽  
Vol 24 (27) ◽  
pp. 3223-3231 ◽  
Author(s):  
Luyao Li ◽  
Shiyao Xu ◽  
Tingting Guo ◽  
Shouliang Gong ◽  
Chuan Zhang
Keyword(s):  
Blood Glucose ◽  
High Throughput Sequencing ◽  
Fatty Acid Content ◽  
Fasting Blood Glucose ◽  
Intestinal Flora ◽  
Short Chain Fatty Acids ◽  
The Body ◽  
Short Chain ◽  
Control Group ◽  
Deficient Mice

Objective: To investigate the effect of dapagliflozin on intestinal microflora in MafA-deficient mice using an animal model of diabetes. Methods: Male MafA-deficient mice were administered dapagliflozin (1.0 mg/kg/d) intragastrically for 6 weeks. Mouse body weights and fasting blood glucose levels were measured, and intestinal short-chain fatty acids were measured by gas chromatography. A series of methods was used to analyse the number of primary harmful bacteria in the faeces, and high-throughput sequencing was used to sequence the changes in intestinal flora. Results: The weight of the mice decreased after dapagliflozin gavage, and fasting blood glucose was significantly lower than that in the control group (P < 0.001). Acetic acid and butyric acid contents in the intestinal tracts of the mice increased, and the growth of harmful microorganisms, such as Clostridium perfringens, enterococci, Enterobacteriaceae, and intestinal enterococci, was inhibited. Blautia is a species found in the experimental group and was significantly different from the control and blank groups as determined by the LDA score from highthroughput sequencing. Conclusion: Dapagliflozin can reduce fasting blood glucose, decrease body weight, increase short-chain fatty acid content, regulate the intestinal microecological balance of the body and promote blood glucose and energy homeostasis.

scholarly journals High-throughput sequencing analysis of intestinal flora changes in ESRD and CKD patients

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Jianguang Hu ◽  
Xiaoshi Zhong ◽  
Jing Yan ◽  
Daoyuan Zhou ◽  
Danping Qin ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Intestinal Flora ◽  
Sequencing Analysis

scholarly journals Vaginal Microbiota Diversity of Patients with Embryonic Miscarriage by Using 16S rDNA High-Throughput Sequencing

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Linfen Xu ◽  
Lingna Huang ◽  
Chengying Lian ◽  
Huili Xue ◽  
Yanfang Lu ◽  
...  
Keyword(s):  
Pregnant Women ◽  
16S Rdna ◽  
High Throughput Sequencing ◽  
Interleukin 2 ◽  
Life Quality ◽  
Control Group ◽  
Operational Taxonomic Units ◽  
Causative Relationship ◽  
Rdna Sequencing ◽  
And Control

Embryonic miscarriage severely affects the life quality and physical and mental state of pregnant women. However, the detailed mechanism underlying embryonic miscarriage is not fully understood. This study is aimed at analyzing embryonic miscarriage. We collected samples from 25 normal pregnant women and 25 embryonic miscarriage patients of similar age to analyze microbiota isolated from the vagina. Crude examination of the vagina isolates showed that compared with the control group, 80% of the embryonic miscarriage group contained a significantly lower number of Lactobacillus, the major healthy microbe in the vagina. Furthermore, the levels of Th1 and Th2 secreted cytokine interleukin 2 (IL-2) and interleukin10 (IL-10), respectively, were examined. Results showed that the IL2 level was higher, and IL10 level was lower in the embryonic miscarriage group than in the control group, whereas the IL2/IL10 level was higher in the embryonic miscarriage group than in the control group. This finding suggested that the immune response was suppressed in the embryonic miscarriage group. To further dissect the microbiota of the vagina in the two groups, 16S rDNA sequencing was performed. Bioinformatics analysis showed that 1096 and 998 overlapped operational taxonomic units were identified from the embryonic miscarriage and control groups, respectively. At the genus level, the relative abundance of Fam_Finegoldia, Lac_Coprococcus_3, and Lac_Roseburia significantly differed in the embryonic miscarriage group. Overall, our analyses provided potential biomarkers for embryonic miscarriage and elucidated the causative relationship between microbiota and immune responses and may enable the possible diagnosis and therapeutics of early pregnancy loss.

scholarly journals Illumina-based sequencing analysis of pathogenic microorganisms in dental caries patients of different Chinese ethnic groups

2019 ◽  
Vol 47 (10) ◽  
pp. 5037-5047
Author(s):  
Chen Yun ◽  
Li Zhiyan ◽  
Zhao Chong ◽  
Liu Jing ◽  
Zhang Xin ◽  
...  
Keyword(s):  
Dental Caries ◽  
Ethnic Groups ◽  
High Throughput Sequencing ◽  
Community Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Control Group ◽  
Sequencing Analysis ◽  
Pathogenic Microorganisms ◽  
Effective Prevention

Objective To analyze the pathogenic community diversity of dental caries patients from Tu, Hui, Tibetan, and Han Chinese ethnic groups. Methods Forty saliva samples were collected from the following patients with dental caries: Tu from Huzhu County (n = 10), Hui from Ping’an County (n = 10), Han from Xining city (n = 10), and Tibetan from Yushu (n = 10). High-throughput sequencing of bacterial 16S rRNA genes (V3-V4) was performed using the Illumina MiSeq sequencing platform. Results Based on 97% similarity clustering, operational taxonomic units of Tu, Hui, Tibetan, and Han ethnic groups were 181, 210, 38, and 67, respectively. In Tu patients, 11 phyla, 19 classes, and 89 genera were identified, compared with 13 phyla, 21 classes, and 113 genera in Hui patients, two phyla, four classes, and 21 genera in Tibetan patients, five phyla, nine classes, and 34 genera in Han patients, and four phyla, five classes, and 12 genera from the control group. The main pathogens of dental caries included Veillonella, Aggregatibacter, Leptotrichia, Bacteroides, Granulicatella, Streptococcus, and Prevotella. Conclusion The pathogenic microorganisms of dental caries differ greatly among Tu, Hui, Tibetan, and Han ethnic groups. These findings provide a theoretical basis for the effective prevention and treatment of dental caries in different Chinese populations.

scholarly journals Ginger Alleviates DSS-Induced Ulcerative Colitis Severity by Improving the Diversity and Function of Gut Microbiota

2021 ◽  
Vol 12 ◽  
Author(s):  
Shanshan Guo ◽  
Wenye Geng ◽  
Shan Chen ◽  
Li Wang ◽  
Xuli Rong ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Gut Microbiota ◽  
Pathogenic Bacteria ◽  
Intestinal Flora ◽  
Experimental Models ◽  
Intestinal Microbiome ◽  
Control Group ◽  
Therapeutic Effects ◽  
Sequencing Analysis ◽  
And Function

The effects of ginger on gastrointestinal disorders such as ulcerative colitis have been widely investigated using experimental models; however, the mechanisms underlying its therapeutic actions are still unknown. In this study, we investigated the correlation between the therapeutic effects of ginger and the regulation of the gut microbiota. We used dextran sulfate sodium (DSS) to induce colitis and found that ginger alleviated colitis-associated pathological changes and decreased the mRNA expression levels of interleukin-6 and inducible nitric oxide synthase in mice. 16s rRNA sequencing analysis of the feces samples showed that mice with colitis had an intestinal flora imbalance with lower species diversity and richness. At the phylum level, a higher abundance of pathogenic bacteria, Proteobacteria and firmicutes, were observed; at the genus level, most samples in the model group showed an increase in Lachnospiraceae_NK4A136_group. The overall analysis illustrated an increase in the relative abundance of Lactobacillus_murinus, Lachnospiraceae_bacterium_615, and Ruminiclostridium_sp._KB18. These increased pathogenic bacteria in model mice were decreased when treated with ginger. DSS-treated mice showed a lower abundance of Muribaculaceae, and ginger corrected this disorder. The bacterial community structure of the ginger group analyzed with Alpha and Beta indices was similar to that of the control group. The results also illustrated that altered intestinal microbiomes affected physiological functions and adjusted key metabolic pathways in mice. In conclusion, this research presented that ginger reduced DSS-induced colitis severity and positively regulated the intestinal microbiome. Based on the series of data in this study, we hypothesize that ginger can improve diseases by restoring the diversity and functions of the gut microbiota.

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