scholarly journals High-throughput sequencing reveals miRNA effects on the primary and secondary production properties in long-term subcultured Taxus cells

2015 ◽  
Vol 6 ◽  
Author(s):  
Meng Zhang ◽  
Yanshan Dong ◽  
Lin Nie ◽  
Mingbo Lu ◽  
Chunhua Fu ◽  
...  
Keyword(s):  
High Throughput ◽  
Secondary Production ◽  
High Throughput Sequencing

scholarly journals Avian MHC Evolution in the Era of Genomics: Phase 1.0

Cells ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 1152 ◽  
Author(s):  
Emily A. O’Connor ◽  
Helena Westerdahl ◽  
Reto Burri ◽  
Scott V. Edwards
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Structural Evolution ◽  
Great Depth ◽  
Long Read ◽  
Ecological Patterns ◽  
In The Wild ◽  
The Many ◽  
Avian Mhc

Birds are a wonderfully diverse and accessible clade with an exceptional range of ecologies and behaviors, making the study of the avian major histocompatibility complex (MHC) of great interest. In the last 20 years, particularly with the advent of high-throughput sequencing, the avian MHC has been explored in great depth in several dimensions: its ability to explain ecological patterns in nature, such as mating preferences; its correlation with parasite resistance; and its structural evolution across the avian tree of life. Here, we review the latest pulse of avian MHC studies spurred by high-throughput sequencing. Despite high-throughput approaches to MHC studies, substantial areas remain in need of improvement with regard to our understanding of MHC structure, diversity, and evolution. Recent studies of the avian MHC have nonetheless revealed intriguing connections between MHC structure and life history traits, and highlight the advantages of long-term ecological studies for understanding the patterns of MHC variation in the wild. Given the exceptional diversity of birds, their accessibility, and the ease of sequencing their genomes, studies of avian MHC promise to improve our understanding of the many dimensions and consequences of MHC variation in nature. However, significant improvements in assembling complete MHC regions with long-read sequencing will be required for truly transformative studies.

scholarly journals Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in a Uranium-Contaminated Site after Bioreduction Followed by Reoxidation

2018 ◽  
Vol 84 (9) ◽  
Author(s):  
Bing Li ◽  
Wei-Min Wu ◽  
David B. Watson ◽  
Erick Cardenas ◽  
Yuanqing Chao ◽  
...  
Keyword(s):  
Network Analysis ◽  
High Throughput ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Ecological Niches ◽  
Content Type ◽  
Oak Ridge ◽  
Α Diversity ◽  
Before And After

ABSTRACTA site in Oak Ridge, TN, USA, has sediments that contain >3% iron oxides and is contaminated with uranium (U). The U(VI) was bioreduced to U(IV) and immobilizedin situthrough intermittent injections of ethanol. It then was allowed to reoxidize via the invasion of low-pH (3.6 to 4.0), high-nitrate (up to 200 mM) groundwater back into the reduced zone for 1,383 days. To examine the biogeochemical response, high-throughput sequencing and network analysis were applied to characterize bacterial population shifts, as well as cooccurrence and coexclusion patterns among microbial communities. A pairedttest indicated no significant changes of α-diversity for the bioactive wells. However, both nonmetric multidimensional scaling and analysis of similarity confirmed a significant distinction in the overall composition of the bacterial communities between the bioreduced and the reoxidized sediments. The top 20 major genera accounted for >70% of the cumulative contribution to the dissimilarity in the bacterial communities before and after the groundwater invasion.Castellaniellahad the largest dissimilarity contribution (17.7%). For the bioactive wells, the abundance of the U(VI)-reducing generaGeothrix,Desulfovibrio,Ferribacterium, andGeobacterdecreased significantly, whereas the denitrifyingAcidovoraxabundance increased significantly after groundwater invasion. Additionally, seven genera, i.e.,Castellaniella,Ignavibacterium,Simplicispira,Rhizomicrobium,AcidobacteriaGp1,AcidobacteriaGp14, andAcidobacteriaGp23, were significant indicators of bioactive wells in the reoxidation stage. Canonical correspondence analysis indicated that nitrate, manganese, and pH affected mostly the U(VI)-reducing genera and indicator genera. Cooccurrence patterns among microbial taxa suggested the presence of taxa sharing similar ecological niches or mutualism/commensalism/synergism interactions.IMPORTANCEHigh-throughput sequencing technology in combination with a network analysis approach were used to investigate the stabilization of uranium and the corresponding dynamics of bacterial communities under field conditions with regard to the heterogeneity and complexity of the subsurface over the long term. The study also examined diversity and microbial community composition shift, the common genera, and indicator genera before and after long-term contaminated-groundwater invasion and the relationship between the target functional community structure and environmental factors. Additionally, deciphering cooccurrence and coexclusion patterns among microbial taxa and environmental parameters could help predict potential biotic interactions (cooperation/competition), shared physiologies, or habitat affinities, thus, improving our understanding of ecological niches occupied by certain specific species. These findings offer new insights into compositions of and associations among bacterial communities and serve as a foundation for future bioreduction implementation and monitoring efforts applied to uranium-contaminated sites.

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 Capturing noroviruses circulating in the population: sewage surveillance in Guangdong, China (2013-2018)

2020 ◽  
Author(s):  
Jing Lu ◽  
Ling Fang ◽  
Jinju Peng ◽  
Lilian Zeng ◽  
Huifang Lin ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Local Population ◽  
Operational Taxonomic Unit ◽  
Viral Origin ◽  
Critical Part ◽  
Origin And Evolution ◽  
Viral Loads ◽  
Dynamic Correlation

Noroviruses (NoVs) are the leading cause of acute gastroenteritis outbreaks. The specific geographical distribution and expanding diversity of NoVs has posed a challenge to NoV surveillance and interventions. Here, we describe the long-term dynamic correlation between NoV distribution in sewage and in the local population by using high-throughput sequencing and operational taxonomic unit (OTU) analysis. The NoV viral loads in sewage were closely associated with the number of NoV outbreaks in the population. Compared with the viral distributions in outbreaks, the dominance of the newly emerged variants, such as GII.P17-GII.17 and GII.P16-GII.2, could be detected two months ahead in sewage. In addition, the dynamics of pre-epidemic variants, which were rarely detected from clinics, could be captured through sewage surveillance, thus improving our understanding of the viral origin and evolution. Our data highlight that the high-throughput environmental screening should become a critical part of the response to infectious diseases.

scholarly journals Change the original microbial community structure in the hydrolysis acidification tank to enhance the COD removal performance of oily wastewater

2021 ◽  
Vol 84 (6) ◽  
pp. 1477-1486
Author(s):  
Mengshi Zhao ◽  
Qiang Fu ◽  
Yu Yang ◽  
Li Zhang ◽  
Si Shan
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Bioinformatics Analysis ◽  
Oxygen Demand ◽  
Pseudomonas Stutzeri ◽  
Oily Wastewater ◽  
Sequencing Technology ◽  
Term Operation ◽  
Hydrolysis Acidification

Abstract The hydrolysis acidification tank mainly relies on microorganisms to treat oily sewage, but in many cases the chemical oxygen demand (COD) of the effluent from the hydrolysis acidification tank does not decrease or even increase. In this work, about 50 L of oily wastewater is treated in a facultative anaerobic hydrolysis acidification tank with a temperature of 29 °C, pH 6, high-throughput sequencing technology analyzes found that after long-term operation of the hydrolysis and acidification tank, the dominant bacterial Pseudomonas accounted for only 2.87%, at this time, the effluent COD of the hydrolysis and acidification tank was 450 mg/L. Pseudomonas stutzeri LH-42 a strain screened in the laboratory, was domesticated and colonized in the hydrolysis acidification tank. High-throughput sequencing and bioinformatics analysis showed that the proportion of Pseudomonas in the hydrolysis acidification tank reached 5.89%, the effluent COD of the hydrolysis and acidification tank was 200 mg/L. The above results indicate the importance of the proportion of Pseudomonas in the hydrolysis and acidification tank for the COD degradation of oily wastewater.

scholarly journals Study of Periplaneta Americana Microbial Community Structure and Diversity by 16S rRNA High-Throughput Sequencing

2017 ◽  
Vol 2 (4) ◽  
pp. 350
Author(s):  
Zhuang Zhi Chen ◽  
Xiu Mei Wu ◽  
Yong Mei Shen ◽  
Cheng Gong Li ◽  
Kai Ge Xu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
Microbial Communities ◽  
High Throughput ◽  
Microbial Community Structure ◽  
Periplaneta Americana ◽  
High Throughput Sequencing ◽  
Shannon Index

<p><strong><em>Objective: </em></strong><em>The present study probes into the microbial community structure in Periplaneta americana under different breeding conditions, using 16S rRNA high-throughput sequencing technique, in the hope of finding the microbial community structure in Periplaneta americana and their diversity under different breeding conditions. </em></p><p><strong><em>Methods:</em></strong><em> In this study, we extract the microbial metagenomic DNA of 5 groups of Periplaneta americana which under different breeding conditions. Using lllumina Miseq sequencing platform, two-terminal sequencing of V3-V4 regions of 16S rRNA were sequenced; diversity of community structure was analyzed using the softwares such as fastqc, </em><em>QIIME, </em><em>PyNAST, fasttree and R language.</em></p><p><strong><em>Results: </em></strong><em>Shannon index of samples in SG group was lower than that of the other four groups, significantly lower than that of DB group (P&lt;0.05), but not significantly different from other groups. This suggested that the intake of a mixed fodder with high sugar, high fat and high protein by Periplaneta americana can reduce the diversity of microbial communities. Our findings showed that breeding intervention with different fodders may cause differences in the contents of Bacteroidetes, Proteobacteria and Firmicutes in Periplaneta americana. Results showed that long-term intake of lots of sucrose and fat may increase the proportion of Bacteroidetes in Periplaneta americana; and long-term intake of lots of sucrose may reduce the proportion of Proteobacteria in Periplaneta americana; and long-term intake of lots of fat may reduce the proportion of Firmicutes in Periplaneta americana. Two major dominant bacterial genera in all samples were Blattabacterium and Rickettsiella. But different feeding interventions can change the proportions of Blattabacterium and Rickettsiella.</em></p><p><strong><em>Conclusion:</em></strong><em> Periplaneta americana has a complex microbial community structure. Different feeding conditions may change the microbial community structure of Periplaneta americana. An important bacterial genus in Periplaneta americana, Blattabacterium is positively correlated with the intake of sucrose- and fat-rich fodder. In the breeding process of Periplaneta americana, adding sucrose and fat to fodder may increase the content and proportion of Blattabacterium in microbial communities.</em></p>

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