scholarly journals High-throughput sequencing identifies distinct fecal and mucosal gut microbiota correlating with different mucosal proteins

2016 ◽  
Author(s):  
Li-na Dong ◽  
Jun-ping Wang ◽  
Ping Liu ◽  
Yun-feng Yang ◽  
Jing Feng ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Flexible Sigmoidoscopy ◽  
Local Effect ◽  
Chinese People ◽  
Rt Pcr ◽  
Clinical Indices ◽  
16Srrna Gene ◽  
Firmicutes Phylum

The intestinal microbiota is associated with human health. The luminal microbiota (LM) and mucosa-associated microbiota (MAM) are distinct ecosystems with different metabolic and immunological functions. Several studies have examined the correlations between the gut microbiota and clinical indices, but few have investigated the relationships between the microbiota and mucosal proteins. We characterized the intestinal LM and MAM in Chinese people and examined the association between these communities and the expression of mucosal proteins. Fresh fecal samples and distal colonic mucosal biopsies were collected from 32 subjects before (fecal) and during (mucosal) flexible sigmoidoscopy. We used high-throughput sequencing targeting the 16SrRNA gene V3–V4 region to analyze the samples and reverse transcription(RT)–PCR to detect the expression of colonic proteins BDNF, ZO1, TLR2, TLR4, AQP3, and AQP8. Differences in the stool and mucosal microbiota were identified and a correlation network analysis performed. The LM and MAM populations differed significantly. In LM, the microbiota composition correlated significantly positively with host age, and Firmicutes (phylum) correlated positively with body mass index (BMI), but inversely with ZO1.At the genus level, systemic indices, such as age, BMI, and BDNF, correlated predominantly with LM, whereas systemic and local indices, such as TLR2, correlated with both MAM and LM. ZO1 and TLR4 which usually exert a local effect, mainly correlated with MAM. Different bacteria were associated with the expression of different proteins. Our data suggest that The microbial compositions of LM and MAM differed. Different gut bacteria may play different roles by regulating the expression of different proteins.

scholarly journals High-throughput sequencing identifies distinct fecal and mucosal gut microbiota correlating with different mucosal proteins

2016 ◽  
Author(s):  
Li-na Dong ◽  
Jun-ping Wang ◽  
Ping Liu ◽  
Yun-feng Yang ◽  
Jing Feng ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Flexible Sigmoidoscopy ◽  
Local Effect ◽  
Chinese People ◽  
Rt Pcr ◽  
Clinical Indices ◽  
16Srrna Gene ◽  
Firmicutes Phylum

The intestinal microbiota is associated with human health. The luminal microbiota (LM) and mucosa-associated microbiota (MAM) are distinct ecosystems with different metabolic and immunological functions. Several studies have examined the correlations between the gut microbiota and clinical indices, but few have investigated the relationships between the microbiota and mucosal proteins. We characterized the intestinal LM and MAM in Chinese people and examined the association between these communities and the expression of mucosal proteins. Fresh fecal samples and distal colonic mucosal biopsies were collected from 32 subjects before (fecal) and during (mucosal) flexible sigmoidoscopy. We used high-throughput sequencing targeting the 16SrRNA gene V3–V4 region to analyze the samples and reverse transcription(RT)–PCR to detect the expression of colonic proteins BDNF, ZO1, TLR2, TLR4, AQP3, and AQP8. Differences in the stool and mucosal microbiota were identified and a correlation network analysis performed. The LM and MAM populations differed significantly. In LM, the microbiota composition correlated significantly positively with host age, and Firmicutes (phylum) correlated positively with body mass index (BMI), but inversely with ZO1.At the genus level, systemic indices, such as age, BMI, and BDNF, correlated predominantly with LM, whereas systemic and local indices, such as TLR2, correlated with both MAM and LM. ZO1 and TLR4 which usually exert a local effect, mainly correlated with MAM. Different bacteria were associated with the expression of different proteins. Our data suggest that The microbial compositions of LM and MAM differed. Different gut bacteria may play different roles by regulating the expression of different proteins.

Comparison of high throughput sequencing to standard protocols for virus detection in berry crops

Plant Disease ◽  
2021 ◽  
Author(s):  
Dan Edward Veloso Villamor ◽  
Karen E Keller ◽  
Robert Martin ◽  
Ioannis Emmanouil Tzanetakis
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Wide Spectrum ◽  
Virus Detection ◽  
Rt Pcr ◽  
Host Interactions ◽  
Growing Seasons ◽  
Berry Crops ◽  
Sampling Times ◽  
Better Than

A comprehensive study comparing virus detection between high throughput sequencing (HTS) and standard protocols in 30 berry selections (12 Fragaria, 10 Vaccinium and 8 Rubus) with known virus profiles was completed. The study examined temporal detection of viruses at four sampling times encompassing two growing seasons. Within the standard protocols, RT-PCR proved better than biological indexing. Detection of known viruses by HTS and RT-PCR nearly mirrored each other. HTS provided superior detection compared to RT-PCR on a wide spectrum of virus variants and discovery of novel viruses. More importantly, in most cases where the two protocols showed parallel virus detection, 11 viruses in 16 berry selections were not consistently detected by both methods at all sampling points. Based on these data we propose a four sampling times/two-year testing requirement for berry and potentially other crops to ensure that no virus remains undetected independent of titer, distribution or other virus/virus or virus/host interactions.

scholarly journals High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin

2012 ◽  
Vol 56 (11) ◽  
pp. 5811-5820 ◽  
Author(s):  
Fiona Fouhy ◽  
Caitriona M. Guinane ◽  
Seamus Hussey ◽  
Rebecca Wall ◽  
C. Anthony Ryan ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Antibiotic Treatment ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Short Term ◽  
Parenteral Antibiotic ◽  
Content Type ◽  
Combined Use ◽  
Cessation Of Treatment

ABSTRACTThe infant gut microbiota undergoes dramatic changes during the first 2 years of life. The acquisition and development of this population can be influenced by numerous factors, and antibiotic treatment has been suggested as one of the most significant. Despite this, however, there have been relatively few studies which have investigated the short-term recovery of the infant gut microbiota following antibiotic treatment. The aim of this study was to use high-throughput sequencing (employing both 16S rRNA andrpoB-specific primers) and quantitative PCR to compare the gut microbiota of nine infants who underwent parenteral antibiotic treatment with ampicillin and gentamicin (within 48 h of birth), 4 and 8 weeks after the conclusion of treatment, relative to that of nine matched healthy controls. The investigation revealed that the gut microbiota of the antibiotic-treated infants had significantly higher proportions ofProteobacteria(P= 0.0049) and significantly lower proportions ofActinobacteria(P= 0.00001) (and the associated genusBifidobacterium[P= 0.0132]) as well as the genusLactobacillus(P= 0.0182) than the untreated controls 4 weeks after the cessation of treatment. By week 8, theProteobacterialevels remained significantly higher in the treated infants (P= 0.0049), but theActinobacteria,Bifidobacterium, andLactobacilluslevels had recovered and were similar to those in the control samples. Despite this recovery of totalBifidobacteriumnumbers,rpoB-targeted pyrosequencing revealed that the number of differentBifidobacteriumspecies present in the antibiotic-treated infants was reduced. It is thus apparent that the combined use of ampicillin and gentamicin in early life can have significant effects on the evolution of the infant gut microbiota, the long-term health implications of which remain unknown.

scholarly journals High-Throughput Sequencing Reveals Cyclamen persicum Mill. as a Natural Host for Fig Mosaic Virus

Viruses ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 684 ◽  
Author(s):  
Toufic Elbeaino ◽  
Armelle Marais ◽  
Chantal Faure ◽  
Elisa Trioano ◽  
Thierry Candresse ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Viral Infections ◽  
Small Scale ◽  
Rt Pcr ◽  
Cyclamen Persicum ◽  
Sequence Variations ◽  
Pcr Products ◽  
Complete Sequences ◽  
Fig Mosaic Virus

In a search for viral infections, double-stranded RNA (dsRNA) were recovered from a diseased cyclamen (Cyclamen persicum Mill.) accession (Cic) and analyzed by high-throughput sequencing (HTS) technology. Analysis of the HTS data showed the presence of Fig mosaic emaravirus (FMV) in this accession. The complete sequences of six FMV-Cic RNA genomic segments were determined from the HTS data and using Sanger sequencing. All FMV-Cic RNA segments are similar in size to those of FMV from fig (FMV-Gr10), with the exception of RNA-6 that is one nucleotide longer. The occurrence of FMV in cyclamen was investigated through a small-scale survey, from which four plants (out of 18 tested) were found RT-PCR positive. To study sequence variations of cyclamen isolates of FMV, RT-PCR products generated through the amplification of the partially RNA-dependent RNA polymerase (RdRp, RNA-1), glycoprotein (GP, RNA-2), and nucleocapsid (NCP, RNA-3) genes were explored. The nucleotide sequence identities for cyclamen isolates ranged between 86% and 99% in RNA-1, 93% and 99% in RNA-2, and 98% and 99% in RNA-3, while lower identity levels were observed with the sequences of fig isolates. Based on the phylogenetic tree obtained with a 304-nt fragment of RNA3, all FMV isolates from cyclamens were assigned to a single cluster close to fig isolates from the Mediterranean. FMV was graft-transmitted to healthy cyclamens eliciting symptoms similar to those observed in the Cic accession, thus suggesting a causal role of FMV in the symptoms that prompted the investigation. This is the first report of FMV in a non-fig host, Cyclamen persicum, a finding that may help in the control of the mosaic and mosaic-like diseases of fig and cyclamen, respectively.

scholarly journals Association Study of Gut Flora in Coronary Heart Disease through High-Throughput Sequencing

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Li Cui ◽  
Tingting Zhao ◽  
Haibing Hu ◽  
Wen Zhang ◽  
Xiuguo Hua
Keyword(s):  
Coronary Heart Disease ◽  
Heart Disease ◽  
Gut Microbiota ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Group Method ◽  
Gut Flora ◽  
Unifrac Distance ◽  
Pair Group ◽  
The Impact

Objectives.We aimed to explore the impact of gut microbiota in coronary heart disease (CHD) patients through high-throughput sequencing.Methods.A total of 29 CHD in-hospital patients and 35 healthy volunteers as controls were included. Nucleic acids were extracted from fecal samples, followed byαdiversity and principal coordinate analysis (PCoA). Based on unweighted UniFrac distance matrices, unweighted-pair group method with arithmetic mean (UPGMA) trees were created.Results.After data optimization, an average of121312±19293reads in CHD patients and234372±108725reads in controls was obtained. Reads corresponding to 38 phyla, 90 classes, and 584 genera were detected in CHD patients, whereas 40 phyla, 99 classes, and 775 genera were detected in controls. The proportion of phylum Bacteroidetes (56.12%) was lower and that of phylum Firmicutes was higher (37.06%) in CHD patients than those in the controls (60.92% and 32.06%,P<0.05). PCoA and UPGMA tree analysis showed that there were significant differences of gut microbial compositions between the two groups.Conclusion.The diversity and compositions of gut flora were different between CHD patients and healthy controls. The incidence of CHD might be associated with the alteration of gut microbiota.

scholarly journals Evaluation on the Characteristics of Gut Microbiome in Polycystic Ovary Syndrome Rats Induced by Dihydrotestosterone or Letrozole

2020 ◽  
Author(s):  
Yanhua Zheng ◽  
Hongxia Ma ◽  
Ying Xu ◽  
Chengjie Liang ◽  
Tong Yang
Keyword(s):  
Polycystic Ovary Syndrome ◽  
Gut Microbiota ◽  
Aromatase Inhibitor ◽  
16S Rdna ◽  
High Throughput ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Polycystic Ovary ◽  
Molecular Ecology ◽  
Ovary Syndrome

Abstract The etiology of polycystic ovary syndrome (PCOS) is unclear. Recent reports indicated that the gut microbiome of PCOS patients and rodents has changed. In this study, we induced the nonaromatizable androgen dihydrotestosterone (DHT) or the aromatase inhibitor letrozole (LET) to induce PCOS model rat to compare the bacterial diversity distribution within and between the two groups. The molecular ecology of the fecal gut microbiota was analyzed by 16S rDNA high-throughput sequencing. Our study found that DHT can reduce the microbial richness in rats. PCoA plots confirmed that DHT group was statistically significantly separated from C group and LET group. At phylum level, DHT led to a decrease in Bacteroidetes as well as an increase in Cyanobacteria, Tenericutes, Actinobacteria, Spirochaetae and Saccharibacteria. At genus level, LEfSe analysis showed that genus of Bifidobacteriales, Vibro, Peptococcus and Turicibacter played roles in the letrozole induced PCOS rats. And Lachnospiraceae_NK4A136_group, Ruminococcus_1, Ruminiclostridium, Anaerotruncus and Anaeroplasma played vital roles in the intestine of DHT induced PCOS rats.

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