scholarly journals Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing

BMC Genomics ◽  
2013 ◽  
Vol 14 (Suppl 5) ◽  
pp. S16 ◽  
Author(s):  
Suparna Mitra ◽  
Karin Förster-Fromme ◽  
Antje Damms-Machado ◽  
Tim Scheurenbrand ◽  
Saskia Biskup ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Intestinal Microbiota ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Shotgun Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

scholarly journals Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Francesco Durazzi ◽  
Claudia Sala ◽  
Gastone Castellani ◽  
Gerardo Manfreda ◽  
Daniel Remondini ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Shotgun Sequencing ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Experimental Conditions ◽  
Rrna Gene Sequencing

AbstractIn this paper we compared taxonomic results obtained by metataxonomics (16S rRNA gene sequencing) and metagenomics (whole shotgun metagenomic sequencing) to investigate their reliability for bacteria profiling, studying the chicken gut as a model system. The experimental conditions included two compartments of gastrointestinal tracts and two sampling times. We compared the relative abundance distributions obtained with the two sequencing strategies and then tested their capability to distinguish the experimental conditions. The results showed that 16S rRNA gene sequencing detects only part of the gut microbiota community revealed by shotgun sequencing. Specifically, when a sufficient number of reads is available, Shotgun sequencing has more power to identify less abundant taxa than 16S sequencing. Finally, we showed that the less abundant genera detected only by shotgun sequencing are biologically meaningful, being able to discriminate between the experimental conditions as much as the more abundant genera detected by both sequencing strategies.

scholarly journals A Correlation Study between Clinical Efficacy of Weifuchun on Precancerous Lesions of Gastric Cancer and Intestinal flora

2021 ◽  
Author(s):  
Yanqin Bian ◽  
Xi Chen ◽  
Hongyan Cao ◽  
Dong Xie ◽  
Meiping Zhu ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Intestinal Microbiota ◽  
Roc Analysis ◽  
Precancerous Lesions ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Abstract BackgroudWeifuchun(WFC), a Chinese herbal prescription consisting of Red Ginseng, Isodon amethystoides and Fructus Aurantii, is commonly used in China to treat a variety of chronic stomach disorders. The aim of the paper is to determine the effect of WFC on intestinal microbiota changes in precancerous lesions of gastric cancer (PLGC) patients. MethodsPLGC patients of H.pylori negative were randomly divided into two groups received either WFC tablets at a dose of 1.44g 3 times a day or vitacoenzyme tablets at a dose of 0.8g 3 times a day. All patients were treated for 6 months, consecutively. Gastroscopy and histopathology were used to assess the histopathological changes in the gastric tissues before and after treatment. 16S rRNA gene sequencing was carried out to assess the effects WFC on intestinal microbiota changes in PLGC patients. Receiver Operating Characteristics(ROC) analysis was used to assess the sensitivity and specificity of different intestinal microbiota in distinguishing between PLGC patients and healthy control. ResultsGastroscopy and histopathological results indicated that WFC could improve the pathological condition of PLGC patients, especially in the atrophy or intestinal metaplasia. The results of 16S rRNA gene sequencing indicated that WFC could regulate the microbial diversity, microbial composition, and abundance of the intestinal microbiota of PLGC patients. Following WFC treatment, the relative abundance of Parabacteroides was decreased in WFC group when compared with the control group. ROC analysis found that the Parabacteroides could effectively distinguish PLGC patients from healthy individuals with sensitivity of 0.79 and specificity of 0.8. ConclusionsWFC could slow down the progression of PLGC by regulating intestinal microbiota abundance. Trial registrationNCT03814629. Name of registry: Randomized Clinical Trial: Weifuchun Treatment on Precancerous Lesions of Gastric Cancer. Registered 3 August 2018-Retrospectively registered, https://register.clinicaltrials.gov/ NCT03814629.

scholarly journals Effects of probiotics and prebiotics on intestinal microbiota in mice with acute colitis based on 16S rRNA gene sequencing

2019 ◽  
Vol 132 (15) ◽  
pp. 1833-1842 ◽  
Author(s):  
Ya-Nan Wang ◽  
Xiang-Chen Meng ◽  
Yi-Fan Dong ◽  
Xin-Hua Zhao ◽  
Jia-Ming Qian ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Intestinal Microbiota ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Acute Colitis ◽  
Rrna Gene Sequencing

scholarly journals A correlational study of Weifuchun and its clinical effect on intestinal flora in precancerous lesions of gastric cancer

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Yanqin Bian ◽  
Xi Chen ◽  
Hongyan Cao ◽  
Dong Xie ◽  
Meiping Zhu ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Intestinal Microbiota ◽  
Roc Analysis ◽  
Precancerous Lesions ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Abstract Background Weifuchun (WFC), a Chinese herbal prescription consisting of Red Ginseng, Isodon amethystoides and Fructus Aurantii, is commonly used in China to treat a variety of chronic stomach disorders. The aim of the paper was to determine the effect of WFC on intestinal microbiota changes in precancerous lesions of gastric cancer (PLGC) patients. Methods PLGC patients of H. pylori negative were randomly divided into two groups and received either WFC tablets for a dose of 1.44 g three times a day or vitacoenzyme (Vit) tablets for a dose of 0.8 g three times a day. All patients were treated for 6 months consecutively. Gastroscopy and histopathology were used to assess the histopathological changes in gastric tissues before and after treatment. 16S rRNA gene sequencing was carried out to assess the effects WFC on intestinal microbiota changes in PLGC patients. Receiver Operating Characteristics (ROC) analysis was used to assess the sensitivity and specificity of different intestinal microbiota in distinguishing between PLGC patients and healthy control group. Results Gastroscopy and histopathological results indicated that WFC could improve the pathological condition of PLGC patients, especially in the case of atrophy or intestinal metaplasia. The results of 16S rRNA gene sequencing indicated that WFC could regulate microbial diversity, microbial composition, and abundance of the intestinal microbiota of PLGC patients. Following WFC treatment, the relative abundance of Parabacteroides decreased in WFC group when compared with the Vit group. ROC analysis found that the Parabacteroides could effectively distinguish PLGC patients from healthy individuals with sensitivity of 0.79 and specificity of 0.8. Conclusions WFC could slow down the progression of PLGC by regulating intestinal microbiota abundance. Trial registration NCT03814629. Name of registry: Randomized Clinical Trial: Weifuchun Treatment on Precancerous Lesions of Gastric Cancer. Registered 3 August 2018-Retrospectively registered, https://register.clinicaltrials.gov/ NCT03814629.

Copper Changes Intestinal Microbiota of the Cecum and Rectum in Female Mice by 16S rRNA Gene Sequencing

2019 ◽  
Vol 193 (2) ◽  
pp. 445-455
Author(s):  
Sufang Cheng ◽  
Huirong Mao ◽  
Yezhao Ruan ◽  
Cong Wu ◽  
Zheng Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Intestinal Microbiota ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Female Mice ◽  
Rrna Gene Sequencing

scholarly journals Determination of the protective effects of Hua‐Zhuo‐Jie‐Du in chronic atrophic gastritis by regulating intestinal microbiota and metabolites: combination of liquid chromatograph mass spectrometer metabolic profiling and 16S rRNA gene sequencing

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Pingping Zhou ◽  
Xinyu Hao ◽  
Yu Liu ◽  
Zeqi Yang ◽  
Miaochan Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Intestinal Microbiota ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Chronic Atrophic Gastritis ◽  
Rrna Gene ◽  
Liquid Chromatograph ◽  
Daily Dose ◽  
Rrna Gene Sequencing

Abstract Background Hua-Zhuo-Jie-Du (HZJD), a Chinese herbal prescription consisting of 11 herbs, is commonly used in China to treat chronic atrophic gastritis (CAG). We aimed to determine the effect of HZJD on the microbiome-associated metabolic changes in CAG rats. Methods The CAG rat models were induced by 1-methyl-3-nitro-1-nitrosoguanidine (MNNG) combined with irregular fasting and 2% sodium salicylate, which was intragastrically administrated in fasted animals for 24 weeks. The CAG rats in the Chinese medicine (CM) group were administered a daily dose of 14.81 g/kg/day HZJD, and the vitacoenzyme (V) group were administered a daily dose of 0.08 g/kg/day vitacoenzyme. All animals were treated for 10 consecutive weeks, consecutively. Hematoxylin and eosin (H&E) staining was used to assess the histopathological changes in the gastric tissues. An integrated approach based on liquid chromatograph mass spectrometer (LC-MS) metabolic profiling combined with 16S rRNA gene sequencing was carried out to assess the effects of HZJD on CAG rats. Spearman analysis was used to calculate the correlation coefficient between the different intestinal microbiota and the metabolites. Results The H&E results indicated that HZJD could improve the pathological condition of CAG rats. The LC–MS results indicated that HZJD could significantly improve 21 gastric mucosal tissue perturbed metabolites in CAG rats; the affected metabolites were found to be involved in multiple metabolic pathways, such as the central carbon metabolism in cancer. The results of 16S rRNA gene sequencing indicated that HZJD could regulate the diversity, microbial composition, and abundance of the intestinal microbiota of CAG rats. Following HZJD treatment, the relative abundance of Turicibacter was increased, and the relative abundance of Desulfococcus and Escherichia were decreased in the CM group when compared with the M group. Spearman analysis revealed that perturbed intestinal microbes had a strong correlation with differential metabolites, Escherichia exhibited a negative correlation with l-Leucine, Turicibacter was negatively correlated with urea, and Desulfococcus exhibited a positive correlation with trimethylamine, and a negative correlation with choline. Conclusions HZJD could protect CAG by regulating intestinal microbiota and its metabolites.

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