New tools for discovering and characterizing microbial diversity

Cardenas, Erick; Tiedje, James M.

doi:10.1016/j.copbio.2008.10.010

Cited by 146 publications

(86 citation statements)

References 47 publications

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“…Next Generation Sequencing (NGS) is a good method to study the richness and evenness of a prokaryotic community. Illumina-sequencing platform allows a full characterization of the bacterial community, with the major advantage of obtaining thousands of gene sequences [25]. However, this new technology is limited by the short length of the reads.…”

Section: Introductionmentioning

confidence: 99%

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes

López-Fernández

Cherkouk²,

Vílchez-Vargas

et al. 2015

Microb Ecol

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The long-term disposal of radioactive wastes in a deep geological repository is the accepted international solution for the treatment and management of these special residues. The microbial community of the selected host rocks and engineered barriers for the deep geological repository may affect the performance and the safety of the radioactive waste disposal. In this work the bacterial population of bentonite formations of Almeria (Spain), selected as reference material for bentonite engineered barriers in the disposal of radioactive wastes, was studied. 16S rRNA gene-based approaches were used to study the bacterial community of the bentonite samples by traditional clone libraries and Illumina-sequencing. By both techniques the bacterial diversity analysis revealed similar results, with phylotypes belonging to 14 different bacterial phyla:

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Section: Introductionmentioning

confidence: 99%

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes

López-Fernández

Cherkouk²,

Vílchez-Vargas

et al. 2015

Microb Ecol

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“…Culture-independent molecular techniques like denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP) and PCR cloning and sequencing have been currently applied, and this revolutionised the perception of the microbial communities [5,6,[12][13][14]. However, only the predominant microorganisms were identified by using these methods, leaving in the dark most of the microbial diversity [15]. High-throughput sequencing has made accessible the in-depth analysis of microbial communities.…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of the Intestinal Bacterial Communities in Different Species of Carp by Pyrosequencing

et al. 2014

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Gut microbiota is increasingly regarded as an integral component of the host, due to important roles in the modulation of the immune system, the proliferation of the intestinal epithelium and the regulation of the dietary energy intake. Understanding the factors that influence the composition of these microbial communities is essential to health management, and the application to aquatic animals still requires basic investigation. In this study, we compared the bacterial communities harboured in the intestines and in the rearing water of grass carp (Ctenopharyngodon idellus), crucian carp (Carassius cuvieri), and bighead carp (Hypophthalmichthys nobilis), by using 454-pyrosequencing with barcoded primers targeting the V4 to V5 regions of the bacterial 16S rRNA gene. The specimens of the three species were cohabiting in the same pond. Between 6,218 and 10,220 effective sequences were read from each sample, resulting in a total of 110,398 sequences for 13 samples from gut microbiota and pond water. In general, the microbial communities of the three carps were dominated by Fusobacteria, Firmicutes, Proteobacteria and Bacteroidetes, but the abundance of each phylum was significantly different between species. At the genus level, the overwhelming group was Cetobacterium (97.29±0.46 %) in crucian carp, while its abundance averaged c. 40 and 60 % of the sequences read in the other two species. There was higher microbial diversity in the gut of filterfeeding bighead carp than the gut of the two other species, with grazing feeding habits. The composition of intestine microbiota of grass carp and crucian carp shared higher similarity when compared with bighead carp. The principal coordinates analysis (PCoA) with the weighted UniFrac distance and the heatmap analysis suggested that gut microbiota was not a simple reflection of the microbial community in the local habitat but resulted from species-specific selective pressures, possibly dependent on behavioural, immune and metabolic characteristics.

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“…But this technique is expensive and time-consuming, which is why it is not widely used. Second-generation DNA sequencing is a promising alternative to clone library sequencing (Cardenas and Tiedje, 2008). Masoud et al (2011) studied the bacterial populations in Danish raw milk cheeses by pyrosequencing of tagged amplicons of the V3 and V4 regions of the 16S rRNA gene.…”

Section: Pcr-based Methods For Microbial Diversity Investigationmentioning

confidence: 99%

Application of PCR-Based Methods to Dairy Products and to Non-Dairy Probiotic Products

Monnet¹,

Matijašić²

2012

Polymerase Chain Reaction

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New tools for discovering and characterizing microbial diversity

Cited by 146 publications

References 47 publications

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes

Comparative Analysis of the Intestinal Bacterial Communities in Different Species of Carp by Pyrosequencing

Application of PCR-Based Methods to Dairy Products and to Non-Dairy Probiotic Products

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