9

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 region of the 16S rRNA gene amplified, and the choice of region depends on the desired universality of your primers as well as the read length constraints of ...


4

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 elucidate causal mechanisms. 16s is mostly limited to providing information about the taxonomy of a community. While there are ways of "predicting" the ...


4

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 came from. 16S can be useful for distinguishing between prokaryotes (bacteria), at least to genus level. It will not always give enough information to ...


3

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 one that works for you. I wrote a simple R package for my lab awhile back but there are much better ways to put together Co-occurrence networks (in no ...


2

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/ search that accession nunber selecting "all databases" to get the project page here https://www.ncbi.nlm.nih.gov/bioproject/325650 Under "resources" there is "...


2

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 more complex than the relationships between the stable core elements like ribosomal RNA (see, for example the mosaic genome of Rickettsia felis). Focusing on only ...


2

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 later. That said, there are some potential solutions. Akonni has some kits that don't use any centrifugation and they claim they'll work on soil and stool, so ...


1

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 described. You pro-con list is not far off, in terms of information lost or gained, but I think it overlooks some of the down-stream consequences of losing that ...


1

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, and this is actually a method used in the diagnoses of infectious diseases. Understanding the Promises and Hurdles of Metagenomic Next-Generation Sequencing as ...


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