Fecal 16S rRNA Gene Sequencing Analysis of Changes in the Gut Microbiota of Rats with Low-Dose Aspirin-Related Intestinal Injury

Background. The incidence of small intestinal injury caused by low-dose aspirin (LDA) is high, but the pathogenesis and intervention measures of it have not been elucidated. Recent studies have found gut microbiota to be closely associated with onset and development of NSAID-induced intestinal injury. However, studies of the changes in the gut microbiota of rats with LDA-related intestinal injury have been lacking recently. In this study, we investigated fecal 16S rRNA gene sequencing analysis of changes in the gut microbiota of rats with LDA-related intestinal injury. Methods. Sprague-Dawley (SD) rat models of small intestinal injury were established by intragastric administration of LDA. The small intestinal tissues and the fecal samples were harvested. The fecal samples were then analyzed using high-throughput sequencing of 16S rRNA V3-V4 amplicons. The gut microbiota composition and diversity were analyzed and compared using principal coordinate analysis (PCoA), nonmetric multidimensional scaling (NMDS) analysis, the unweighted pair-group method with arithmetic mean (UPGMA) clustering analysis, multivariate statistical analysis (ANOSIM, MetaStats, and LEfSe), and spatial statistics. Results. The LDA rat model was successfully established. Decreased Firmicutes and increased Bacteroidetes abundances in rats with LDA-induced small intestinal injury were revealed. MetaStats analysis between the before administration of LDA (CG) and after administration of LDA (APC) groups showed that the intestinal floras exhibiting significant differences ( P < 0.05 , q < 0.1 ) were Firmicutes, Bacteroides, Cyanobacteria, Melainabacteria, Coriobacteriia, Bacteroidia, Bacteroidales, Eubacteriaceae, and Streptococcaceae. In addition, the bacterial taxa showing significant differences between the control (NS) and APC groups were Firmicutes, Bacteroides, Verrucomicrobiaceae and Peptococcaceae. Conclusions. The alterations in the gut microbiota composition and diversity of rats with LDA-related intestinal injury were found in the present study. The change of gut microbiota in LDA-related intestinal injury will lay the foundation for further research on the function and signaling pathways of the intestinal flora and promote the use of intestinal flora as drug targets to treat LDA-induced small intestinal injury.

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Gut microbiota accelerates cisplatin-induced acute liver injury associated with robust inflammation and oxidative stress in mice

Journal of Translational Medicine ◽

10.1186/s12967-021-02814-5 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Shenhai Gong ◽

Yinglin Feng ◽

Yunong Zeng ◽

Huanrui Zhang ◽

Meiping Pan ◽

...

Keyword(s):

Oxidative Stress ◽

16S Rrna ◽

Gut Microbiota ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Metabolomic Analysis ◽

Rrna Gene Sequencing ◽

And Oxidative Stress

Abstract Background Gut microbiota has been reported to be disrupted by cisplatin, as well as to modulate chemotherapy toxicity. However, the precise role of intestinal microbiota in the pathogenesis of cisplatin hepatotoxicity remains unknown. Methods We compared the composition and function of gut microbiota between mice treated with and without cisplatin using 16S rRNA gene sequencing and via metabolomic analysis. For understanding the causative relationship between gut dysbiosis and cisplatin hepatotoxicity, antibiotics were administered to deplete gut microbiota and faecal microbiota transplantation (FMT) was performed before cisplatin treatment. Results 16S rRNA gene sequencing and metabolomic analysis showed that cisplatin administration caused gut microbiota dysbiosis in mice. Gut microbiota ablation by antibiotic exposure protected against the hepatotoxicity induced by cisplatin. Interestingly, mice treated with antibiotics dampened the mitogen-activated protein kinase pathway activation and promoted nuclear factor erythroid 2-related factor 2 nuclear translocation, resulting in decreased levels of both inflammation and oxidative stress in the liver. FMT also confirmed the role of microbiota in individual susceptibility to cisplatin-induced hepatotoxicity. Conclusions This study elucidated the mechanism by which gut microbiota mediates cisplatin hepatotoxicity through enhanced inflammatory response and oxidative stress. This knowledge may help develop novel therapeutic approaches that involve targeting the composition and metabolites of microbiota.

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

Scientific Reports ◽

10.1038/s41598-021-82726-y ◽

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.

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First case of an invasive Bacteroides dorei infection detected in a patient with a mycotic aortic aneurysm—raising a rebellion of major indigenous bacteria in humans: a case report and review

BMC Infectious Diseases ◽

10.1186/s12879-021-06345-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Takayuki Matsuoka ◽

Takuya Shimizu ◽

Tadanori Minagawa ◽

Wakiko Hiranuma ◽

Miki Takeda ◽

...

Keyword(s):

Aortic Aneurysm ◽

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Resected Specimen ◽

Rrna Gene ◽

Sequencing Analysis ◽

First Case ◽

Rrna Gene Sequencing

Abstract Background Bacteroides dorei is an anaerobic gram-negative bacterium first described in 2006. Because of the high similarity in mass spectra between B. dorei and Bacteroides vulgatus, discriminating between these species is arduous in clinical practice. In recent decades, 16S rRNA gene sequencing has been a complementary method for distinguishing taxonomically close bacteria, including B. dorei and B. vulgatus, at the genus and species levels. Consequently, B. dorei has been shown to contribute to some diseases, including type 1 autoimmune diabetes mellitus and atherosclerotic diseases. However, there are no reports on invasive infectious diseases caused by B. dorei. This report describes the first case of direct invasion and colonisation of human tissue by B. dorei, thus providing a warning regarding the previously proposed application of B. dorei as a live biotherapeutic for atherosclerotic diseases. Case presentation A 78-year-old Japanese man complained of intermittent chest/back pain and was diagnosed with a mycotic thoracic aortic aneurysm by enhanced computed tomography on admission. Despite strict blood pressure control and empirical antibiotic therapy, the patient’s condition worsened. To prevent aneurysmal rupture and eliminate infectious foci, the patient underwent surgical treatment. The resected specimen was subjected to tissue culture and 16S rRNA gene sequencing analysis to identify pathogenic bacteria. A few days after the surgery, culture and sequencing results revealed that the pathogen was B. dorei/B. vulgatus and B. dorei, respectively. The patient was successfully treated with appropriate antibacterial therapy and after improvement, was transferred to another hospital for rehabilitation on postoperative day 34. There was no recurrence of infection or aneurysm after the patient transfer. Conclusions This report describes the first case of invasive infectious disease caused by B. dorei, casting a shadow over its utilisation as a probiotic for atherosclerotic diseases.

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The protective effects of yellow tea extract against loperamide-induced constipation in mice

Food & Function ◽

10.1039/d0fo02969f ◽

2021 ◽

Author(s):

Pei-Qin Cao ◽

Xiu-Ping Li ◽

Jian Ou-Yang ◽

Rong-Gang Jiang ◽

Fang-Fang Huang ◽

...

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Protective Effects ◽

Rrna Gene Sequencing ◽

Tea Extract

We evaluated the effects of yellow tea extract on relieving constipation induced by loperamide and evaluated the changes of gut microbiota based on 16S rRNA gene sequencing.

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Intervening Effects of Total Alkaloids of Corydalis saxicola Bunting on Rats With Antibiotic-Induced Gut Microbiota Dysbiosis Based on 16S rRNA Gene Sequencing and Untargeted Metabolomics Analyses

Frontiers in Microbiology ◽

10.3389/fmicb.2019.01151 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 4

Author(s):

Xi Liu ◽

Hua Zheng ◽

Rigang Lu ◽

Huimin Huang ◽

Hongjia Zhu ◽

...

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Untargeted Metabolomics ◽

Rrna Gene ◽

Total Alkaloids ◽

Rrna Gene Sequencing ◽

Gut Microbiota Dysbiosis

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Effect of Massa Medicata Fermentata on the Gut Microbiota of Dyspepsia Mice Based on 16S rRNA Technique

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/7643528 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10

Author(s):

Xiaorui Zhang ◽

Hongling Zhang ◽

Qinwan Huang ◽

Jilin Sun ◽

Renchuan Yao ◽

...

Keyword(s):

16S Rrna ◽

Intestinal Microflora ◽

Intestinal Flora ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Blank Group ◽

Intestinal Microorganisms ◽

Specific Pathogen ◽

Rrna Gene Sequencing ◽

Aseptic Conditions

Massa Medicata Fermentata (MMF) is a traditional Chinese medicine (TCM) for treating indigestion and its related disorders. This study analyzes the effect of MMF on intestinal microorganisms in dyspepsia mice based on 16S rRNA technology. We take a dyspepsia model caused by a high-protein, high-calorie, high-fat diet. The 60 specific-pathogen free Kunming (SPF KM) mice were randomly divided into a model group n=12, an MMF group (LSQ group, n=12), a Jianweixiaoshi group (JWXS group, n=12), a domperidone group (DP group, n=12), and a blank group n=12. On the seventh day of administration, mice were fasted and deprived of water. After 24 h, take the second feces of stress defecation in mice under strict aseptic conditions and quickly transfer them to a sterile cryotube. This study comprehensively evaluates the α-diversity, β-diversity, flora abundance and composition of each group of miceʼs intestinal microorganisms, and their correlation with functional dyspepsia based on the 16S rRNA gene sequencing technology. After modeling, some dyspepsia reactions, proximal gastric relaxation reduction, and intestinal microflora changes were noted. Dyspepsia mice showed dyspepsia reactions and proximal gastric relaxation reduction, characterized by a significant decrease of contents of gastrin P<0.01 and cholinesterase P<0.01. MMF can improve dyspepsia symptoms and promote proximal gastric relaxation. Significant intestinal flora disorders were found in dyspepsia mice, including downregulation of Bacteroidetes, Lactobacillus, and Prevotellaceae and upregulation of Proteobacteria, Verrucomicrobia, Epsilonbacteraeota, Firmicutes, Lachnospiraceae NK4A136 group, and Lachnospiraceae. MMF could alleviate intestinal microflora disturbance, and the regulation effect of MMF on Bacteroidetes, Verrucomicrobia, and Epsilonbacteraeota was more reliable than that of Jianweixiaoshi tables and domperidone. The intestinal microflora may be correlated with the promoted digestion of MMF.

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16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones

Urolithiasis ◽

10.1007/s00240-018-1037-y ◽

2018 ◽

Vol 46 (6) ◽

pp. 503-514 ◽

Cited By ~ 38

Author(s):

Ruiqiang Tang ◽

Yonghua Jiang ◽

Aihua Tan ◽

Juan Ye ◽

Xiaoying Xian ◽

...

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

16S Rrna Gene ◽

Kidney Stones ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Rrna Gene Sequencing

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Variations in gut microbiota and fecal metabolic phenotype associated with Fenbendazole and Ivermectin Tablets by 16S rRNA gene sequencing and LC/MS-based metabolomics in Amur tiger

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2018.03.158 ◽

2018 ◽

Vol 499 (3) ◽

pp. 447-453 ◽

Cited By ~ 15

Author(s):

Fengping He ◽

Jiancheng Zhai ◽

Le Zhang ◽

Dan Liu ◽

Yue Ma ◽

...

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Metabolic Phenotype ◽

Rrna Gene ◽

Amur Tiger ◽

Rrna Gene Sequencing

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Glycomic profiling of the gut microbiota by Glycan-seq

10.1101/2021.06.30.450488 ◽

2021 ◽

Author(s):

Lalhaba Oinam ◽

Fumi Minoshima ◽

Hiroaki Tateno

Keyword(s):

Flow Cytometry ◽

16S Rrna ◽

Gut Microbiota ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Appropriate Technology ◽

Fluorescence Labeling ◽

Rrna Gene ◽

Rrna Gene Sequencing

Background: There has been immense interest in studying the relationship between the gut microbiota and human health. Bacterial glycans modulate the cross talk between the gut microbiota and its host. However, little is known about these glycans because of the lack of appropriate technology to study them. Methods: We previously developed a sequencing-based glycan profiling method called Glycan-seq, which is based on the use of 39 DNA-barcoded lectins. In this study, we applied this technology to analyze the glycome of the intact gut microbiota of mice. Fecal microbiota was incubated with 39 DNA-barcoded lectins exposed to UV, and the number of released DNA barcodes were counted by next-generation sequencing to obtain a signal for each lectin bound to the microbiota. In parallel, the bacterial composition of the gut microbiota was analyzed by 16S rRNA gene sequencing. Finally, we performed a lectin pull-down experiment followed by 16S rRNA gene sequencing to identify lectin-reactive bacteria. Results: The evaluation of cultured gram-positive (Deinococcus radiodurans) and gram-negative (Escherichia coli) bacteria showed significantly distinct glycan profiles between these bacteria, which were selected and further analyzed by flow cytometry. The results of flow cytometry agreed well with those obtained by Glycan-seq, indicating that Glycan-seq can be used for bacterial glycomic analysis. We thus applied Glycan-seq to comparatively analyze the glycomes of young and old mice gut microbiotas. The glycomes of the young and old microbiotas had significantly distinct glycan profiles, which reflect the different bacterial compositions of young and old gut microbiotas based on 16S rRNA gene sequencing. Therefore, the difference in the glycomic profiles between young and old microbiotas may be due to their differing bacterial compositions. α2-6Sia-binders bound specifically to the young microbiota. Lectin pull-down followed by 16S rRNA gene sequencing of the young microbiota identified Lactobacillaceae as the most abundant bacterial family with glycans reacting with α2-6Sia-binders. Conclusion: The Glycan-seq system can, without any prior culturing and fluorescence labeling, reveal the glycomic profile of the intact bacterial gut microbiota. A combination of lectin pull-down and 16S rRNA gene sequencing can identify lectin-reactive bacteria.

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