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9 votes
Accepted

Limitations of 16S rRNA sequencing

There is simply no variation in the 16S rRNA gene between different species/strains that it would be useful to tell apart for a more accurate analysis. The amount of sequence variation depends on the ...
acvill's user avatar
  • 8,296
5 votes

Limitations of 16S rRNA sequencing

In my experience, the primary impetus is number 3 on your list, but it's also related to number 1. There's a lot you can learn from 16s sequencing, but reviewers want functional data that can help ...
MikeyC's user avatar
  • 4,744
4 votes
Accepted

Methods for microbial identification in soil

16S and ITS techniques try to identify organisms in your samples by amplifying short, 'barcode' sequences from each organism's DNA, and using those short sequences to try to identify the organism they ...
Jay Moore's user avatar
  • 827
3 votes

identifying OTU interactions / hubs

I am going to assume you have a count table that you are starting with. Every tool you decide to use is going to have its own respective instructions so let me get you pointed in a direction to find ...
jtclaypool's user avatar
2 votes

How to download omic data from ncbi? (SRA data or any suggestion?)

I had a look, I can see the data in FASTA format. The accession number is for a project with 50 samples, each of them a sequencing run. First I went to genbank at https://www.ncbi.nlm.nih.gov/ ...
Polypipe Wrangler's user avatar
2 votes

Limitations of 16S rRNA sequencing

Other answers are excellent by and large. One point that is left out: 16S copy number itself varies among organisms, which leads to significant analytic complexity for trying to really estimate ...
Maximilian Press's user avatar
2 votes

Limitations of 16S rRNA sequencing

In addition to the points raised in the other answers, organisms like bacteria frequently engage in horizontal transfer of genetic material. This means that the relationships between organisms are ...
jakebeal's user avatar
  • 6,987
2 votes

DNA extraction kit for microbial mats, rocks, and soil in a remote area

Those are some pretty tough samples to get high-quality DNA from, even in a lab. Your best option is probably to place samples in a nucleic acid preservation buffer and carry them out for extraction ...
MikeyC's user avatar
  • 4,744
1 vote
Accepted

16S sequencing: pooled or individual samples?

Ultimately, it depends on what insights you are trying to glean from your sequencing data, but from a purely scientific perspective, there's almost never a reason to pool samples in the the way you ...
MikeyC's user avatar
  • 4,744
1 vote

Could bacteria and phages be found in tissues?

Per my comment to the question, here is an answer to the same question asked on ResearchGate: Whole genome sequencing of human tissue samples often results in reads aligning to bacterial references, ...
acvill's user avatar
  • 8,296

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