Sediment-associated bacterial community and predictive functionalities are influenced by choice of 16S ribosomal RNA hypervariable region(s): An amplicon-based diversity study.

  title={Sediment-associated bacterial community and predictive functionalities are influenced by choice of 16S ribosomal RNA hypervariable region(s): An amplicon-based diversity study.},
  author={Meora Rajeev and T. J. Sushmitha and Subba Rao Toleti and Shunmugiah Thevar Karutha Pandian},

Microbial community and predictive functionalities associated with the marine sediment of Coastal Gujarat.

Marine sediments are complex ecosystems where structures and functions constantly change due to natural and anthropogenic influences. In this investigation, a comprehensive and comparative analysis

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Biased Diversity Metrics Revealed by Bacterial 16S Pyrotags Derived from Different Primer Sets

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Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys

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The latest developments of 454 and Illumina technologies offered higher resolution compared to their previous versions, and showed relative consistency with each other, but the majority of the Illumina reads could not be classified down to genus level due to their shorter length and higher error rates.

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The PacBio system generated sequences with a significantly higher level of deletions than datasets generated by other platforms, with an abnormally high proportion of sequences assigned to the phylum Proteobacteria.

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

The results of this study may be used as a guideline for selecting primer pairs with the best overall coverage and phylum spectrum for specific applications, therefore reducing the bias in PCR-based microbial diversity studies.

Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment

Community composition is very similar for both tags at the class level, but very different at the level of 97% similar OTUs, and class-level diversity and community composition of water-column samples are very similar at each water depth between the Atlantic and Pacific.

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data

The results indicate that Tax4Fun provides a good approximation to functional profiles obtained from metagenomic shotgun sequencing approaches, and is a software package that predicts the functional capabilities of microbial communities based on 16S rRNA datasets.

Comparison of Species Richness Estimates Obtained Using Nearly Complete Fragments and Simulated Pyrosequencing-Generated Fragments in 16S rRNA Gene-Based Environmental Surveys

Regression analysis indicated that observed discrepancies in species richness estimates within various regions could readily be explained by the proportions of hypervariable, variable, and conserved base pairs within an examined fragment.