What is a variable region in a 16S rRNA gene?
Bacterial 16S ribosomal RNA (rRNA) genes contain nine “hypervariable regions” (V1 – V9) that demonstrate considerable sequence diversity among different bacteria. Species-specific sequences within a given hypervariable region constitute useful targets for diagnostic assays and other scientific investigations.
What are V1 to V9 regions of the 16S rRNA?
The 16S rRNA gene is approximately 1600 base pairs long and includes nine hypervariable regions of varying conservation (V1-V9)1–3. Most current work is based on the Illumina platform11, which produces single-end reads only up to 350 bp and paired-end reads up to 2 × 300–350 bp.
Why is V4 region of 16S rRNA?
The main reason for using V3/V4 region in majority of the cases that these regions contain the maximum nucleotide heterogeneity and displays the maximum discriminatory power. However, it should be noted that no single region can differentiate among all bacteria.
What is the V4 region of 16S rRNA?
approximately 254 bp
For taxonomic classification, it is sufficient to sequence individual hypervariable regions instead of the entire gene length6,7. In most microbial species, the 16S fourth hypervariable (V4) region is approximately 254 bp, and only deviates from this length by a few basepairs.
What is 16S rRNA sequence?
16s rRNA sequencing refers to sequencing the 16s rRNA gene that codes for the small subunit (SSU) of the ribosome found in prokaryotes such as Bacteria and Archaea. There are several factors that make the 16s rRNA gene the perfect target to complete your taxonomy or phylogeny studies.
What is the V3 region of 16S rRNA?
Table 2.
| Region | Number of fragments | Size (range) |
|---|---|---|
| V3 | 486,589 | 152.33 – 197.84 |
| V4 | 478,491 | 281.48 – 284.61 |
| V5 | 483,462 | 137.44 – 144.37 |
| V6 | 489,859 | 150.00 – 159.06 |
What is 16S rRNA amplicon sequencing?
The 16S rRNA amplicon sequencing technique is a microbiome analysis where different samples are analyzed at the same time using multiplexing. The results can be used to evaluate microbial diversity at genus, family, order, class, and phylum levels. The resolution is normally insufficient to evaluate the species level.
What is V3 V4 region?
The V3-V4 region of the 16S rRNA gene was amplified in order to characterize the gut microbiota profile. Overall, the major phyla identified were Bacteroidetes 42%, Firmicutes 32%, and Spirochaetes 9%.
What 4 steps are involved in 16S rRNA sequencing?
Steps in Ribosomal RNA Sequencing:
What is V3 V4 hypervariable region?
The V3/V4 region identifies community state types with characteristic species lacking in the V1/V2 region. We observe a total of six community state types (CSTs) present in the data set using the V1/V2 region.
Is 16S rRNA next generation sequencing?
Next-Generation Sequencing (NGS) of 16S rRNA gene is now one of the most widely used application to investigate the microbiota at any given body site in research. Since NGS is more sensitive than traditional culture methods (TCMs), many studies have argued for them to replace TCMs.
Are there any hypervariable regions in 16S rRNA?
Unfortunately, 16S rRNA hypervariable regions exhibit different degrees of sequence diversity, and no single hypervariable region is able to distinguish among all bacteria.
What is the significance of the s in 16S rRNA?
16S rRNA (16S ribosomal RNA), is a component of the prokaryotic ribosome 30S subunit. The “S” in 16S is a sedimentation coefficient, that is, an index reflecting the downward velocity of the macromolecule in the centrifugal field. The higher the value, the greater the molecule.
Are there primers for the whole 16S rRNA gene?
Primers are far from being universal: Current primers for amplifying the whole 16S rRNA gene (e.g., 8F and 1492R [ 13 ]) significantly improve resolution, compared to sequencing a short region; however, they are highly non-universal. To increase universality, some mix of primer pairs is required.
Which is part of the Shine-Dalgarno sequence does 16S RNA bind to?
16S ribosomal RNA (or 16 S rRNA) is the component of the 30S small subunit of a prokaryotic ribosome that binds to the Shine-Dalgarno sequence. The genes coding for it are referred to as 16S rRNA gene and are used in reconstructing phylogenies, due to the slow rates of evolution of this region of the gene.