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Assessment Of 16S RRNA Gene Primers For Studying Bacterial Community Structure And Function Of Aging Flue-cured Tobaccos

Fan Wang, Xiao Shuang Men, Ge Zhang, K. C. Liang, Yuhua Xin, Juan Wang, Aijun Li, Haibo Zhang, Haobao Liu, Lijun Wu
Published 2018 · Biology, Medicine
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Selection of optimal primer pairs in 16S rRNA gene sequencing is a pivotal issue in microorganism diversity analysis. However, limited effort has been put into investigation of specific primer sets for analysis of the bacterial diversity of aging flue-cured tobaccos (AFTs), as well as prediction of the function of the bacterial community. In this study, the performance of four primer pairs in determining bacterial community structure based on 16S rRNA gene sequences in AFTs was assessed, and the functions of genes were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Results revealed that the primer set 799F–1193R covering the amplification region V5V6V7 gave a more accurate picture of the bacterial community structure of AFTs, with lower co-amplification levels of chloroplast and mitochondrial genes, and more genera covered than when using the other primers. In addition, functional gene prediction suggested that the microbiome of AFTs was involved in kinds of interested pathways. A high abundance of functional genes involved in nitrogen metabolism was detected in AFTs, reflecting a high level of bacteria involved in degrading harmful nitrogen compounds and generating nitrogenous nutrients for others. Additionally, the functional genes involved in biosynthesis of valuable metabolites and degradation of toxic compounds provided information that the AFTs possess a huge library of microorganisms and genes that could be applied to further studies. All of these findings provide a significance reference for researchers working on the bacterial diversity assessment of tobacco-related samples.
This paper references
Prokaryotic photosynthesis and phototrophy illuminated.
Donald A. Bryant (2006)
Isolating "Uncultivable" Microorganisms in Pure Culture in a Simulated Natural Environment
T Kaeberlein (2002)
Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis
Niranjan Nitin Parulekar (2017)
Organismal Systems; Endocrine System
Comparison on the structure and function of the rhizosphere microbial community between healthy and root-rot Panax notoginseng
Zhaoxiang Wu (2016)
Progesterone-mediated oocyte maturation
Species Diversity and Functional Prediction of Surface Bacterial Communities on Aging Flue-Cured Tobaccos
Fan Wang (2018)
Decreased tobacco-specific nitrosamines by microbial treatment with Bacillus amyloliquefaciens DA9 during the air-curing process of burley tobacco.
Xuetuan Wei (2014)
Human Diseases
Diversity and heritability of the maize rhizosphere microbiome under field conditions
Jason Peiffer (2013)
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Morgan G I Langille (2013)
[Parkinson's disease].
Houeto Jean-Luc (2005)
Structure and function of the global ocean microbiome
S. Sunagawa (2015)
The Endocrine System
Susanne Hiller-Sturmhöfel (1998)
Combining gene expression and genetic analyses to identify candidate genes involved in cold responses in pea.
Sylvain Legrand (2013)
Changes in chloroplast DNA during development in tobacco, Medicago truncatula, pea, and maize
J M Shaver (2005)
IMG: the Integrated Microbial Genomes
VM Markowitz (2012)
QIIME allows analysis of high-throughput community sequencing data
J. Caporaso (2010)
Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies
Bram Beckers (2016)
Biased Diversity Metrics Revealed by Bacterial 16S Pyrotags Derived from Different Primer Sets
Lin Cai (2013)
Regional variations in the diversity and predicted metabolic potential of benthic prokaryotes in coastal northern Zhejiang, East China Sea
Kai Wang (2016)
The identification of carbamazepine biodegrading phylotypes and phylotypes sensitive to carbamazepine exposure in two soil microbial communities.
Jean-Rene Thelusmond (2016)
Organismal Systems; Digestive System
Search and clustering orders of magnitude faster than BLAST
Robert C. Edgar (2010)
Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria
Pious Thomas (2016)
Biosynthesis of Other Secondary Metabolites
Human Diseases; Immune System Diseases
QIIME allows analysis
C Gregory (2010)
Human Diseases; Neurodegenerative Diseases
IMG: the integrated microbial genomes database and comparative analysis system
Victor M. Markowitz (2012)
Ancient Invasions: From Endosymbionts to Organelles
S. Dyall (2004)
Nicotinedegrading microorganisms and their potential applications
JL Liu (2015)
Antepartum Antibiotic Treatment Increases Offspring Susceptibility to Experimental Colitis: A Role of the Gut Microbiota
Peris M Munyaka (2015)
Community dynamics of prokaryotic and eukaryotic microbes in an estuary reservoir
Zhen Sun (2014)
Nicotine-degrading microorganisms and their potential applications
Jianli Liu (2015)
Multiple approaches to characterize the microbial community in a thermophilic anaerobic digester running on swine manure: a case study.
Nguyen Ngoc Tuan (2014)
A European Database of Fusarium graminearum and F. culmorum Trichothecene Genotypes
M. Pasquali (2016)
Optimisation of methods for bacterial skin microbiome investigation: primer selection and comparison of the 454 versus MiSeq platform
Madhura Castelino (2017)
Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica
Hyunmin Koo (2017)
Bacterial diversities on unaged and aging flue-cured tobacco leaves estimated by 16S rRNA sequence analysis
Jingwen Huang (2010)
Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing
Shunsuke Takahashi (2014)
Genetic Information Processing; Folding, Sorting and Degradation
Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica.
Hyunmin Koo (2017)
KEGG: Kyoto Encyclopedia of Genes and Genomes
Hiroyuki Ogata (1999)
Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis
R. E. Tyx (2016)
Progesterone-mediated oocyte maturation Propanoate metabolism 306168 284655 Metabolism
Impacts of the Three Gorges Dam on microbial structure and potential function
Qingyun Yan (2015)
Culture-independent methods for studying environmental microorganisms: methods, application, and perspective
Can Su (2011)
Structural and functional differentiation of the root-associated bacterial microbiomes of perennial ryegrass
Lin Chen (2016)
Genetic Information Processing; Folding, Sorting and Degradation; Proteasome Protein digestion and absorption
Human Diseases; Cancers; Pathways in cancer Penicillin and cephalosporin biosynthesis 16519 16531
Organismal Systems; Digestive System; Protein digestion and absorption Protein export
Pantothenate and CoA biosynthesis 157710 153263 Metabolism; Metabolism of Cofactors and Vitamins; Pantothenate and CoA biosynthesis Parkinson's disease 24533
A multiple origin for plastids and mitochondria.
David L. Taylor (1970)
Endophytic Bacterial Diversity in Rice (Oryza sativa L.) Roots Estimated by 16S rDNA Sequence Analysis
L. Sun (2007)
Errors in ribosomal sequence datasets generated using PCR-coupled 'panbacterial' pyrosequencing, and the establishment of an improved approach.
Erica M. Prosdocimi (2013)
Metagenomic analysis of the bacterial communities and their functional profiles in water and sediments of the Apies River, South Africa, as a function of land use.
Akebe Luther King Abia (2018)
Pathogenic Escherichia coli infection 2 0 Human Diseases
Analysis of bacterial communities on aging flue-cured tobacco leaves by 16S rDNA PCR–DGGE technology
M. Zhao (2007)

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