I have to analyse microbial community in sludge after DNA extraction. Can you please tell me the details of 16srRNA primers. Do I have to design them or they are available as universal primers. Please help me in this regard.
Depending on the goals of your study, you have several options. - In the context of amplicon sequencing work, "universal" primer sets refer to primers that universally target some desired group of organisms. For example, universal primer sets for prokaryotes target both bacteria and archaea. There are also more specific universal primer sets, e.g. for bacteria only, so ultimately the choice of which set to use would need to be defined by your study design. - Primer sequences for different universal primer sets are widely available in the literature, so typically there is no need to design your own (unless you are purposefully seeking to develop new primer sets or ones that improve upon existing ones). We would suggest seeking out relevant publications in your field and choosing a suitable primer set based on those. New primer sets are being continuously developed, so it is also worth keeping an eye on recently published articles. For example, the following paper (published in September) details new primers for prokaryotic community surveys that offer improved results in terms of detecting anammox species that are important in wastewater treatment facilities: www.nature.com/articles/s41598-020-72577-4 Hope this helps!
This video has been so helpful thank you!!
I have to analyse microbial community in sludge after DNA extraction. Can you please tell me the details of 16srRNA primers. Do I have to design them or they are available as universal primers.
Please help me in this regard.
Depending on the goals of your study, you have several options.
- In the context of amplicon sequencing work, "universal" primer sets refer to primers that universally target some desired group of organisms. For example, universal primer sets for prokaryotes target both bacteria and archaea. There are also more specific universal primer sets, e.g. for bacteria only, so ultimately the choice of which set to use would need to be defined by your study design.
- Primer sequences for different universal primer sets are widely available in the literature, so typically there is no need to design your own (unless you are purposefully seeking to develop new primer sets or ones that improve upon existing ones). We would suggest seeking out relevant publications in your field and choosing a suitable primer set based on those.
New primer sets are being continuously developed, so it is also worth keeping an eye on recently published articles. For example, the following paper (published in September) details new primers for prokaryotic community surveys that offer improved results in terms of detecting anammox species that are important in wastewater treatment facilities:
www.nature.com/articles/s41598-020-72577-4
Hope this helps!
@@ChipsterTutorials thank u so much for your guidance