I believe a specific taxa that is usually dominant in the literature is abscent from my data. Is there a way to make sure of this finding using qiime2 or any other software?
Also, how to know the specific abindance of this taxa in my data also using qiime2?
My data is microbiome 16S sequences, and I do the analysis using qiime2 amplicon.
Hi @RanaAbdelaal,
There are a few questions to ask.
-
Can the technique you're using find the organism you want?
For example, my 16S rRNA sequencing won't find Saccharomyces cerevisiae no matter how much I want it to, becasue S. cerevisiae doesn't have a distinct 16S gene to find. A second variation is that sometimes specific primer regions are baised against specific organisms. For example, Ive recently been working with some data amplified with 515F-926R primers and those primers aren't very good at picking up Bifidobacterium. Your organism might also be sensitive to storage or extraction conditions. In some recent FFPE work, we struggled to find an organism we would have expected in the sample type. I can't tell you why we didnt see it, just that every time we tried to find it, it wasn't there. -
Is the organim in your database?
This seems silly, but if the organism isnt in your database, you are unlikely to find it by name. This can be a particular problem for organisms that newly discovered or re-named. So, if you're using Greengenes 13_8, you may be missing taxa because there are more named taxa now than there were in 2013. There are also multiple ways taxonomy has been re-organized over the past several years. And we know that databases don't agree. So, if the name you're looking for isnt in the database either becuase the organism wasnt discovered yet, the database is too specialized, or it has a differnet name, you may not find it. -
Are you looking at the right resolution?
There are things 16S is great at detecting and things it doesn't do so well with. You're unlikely to get strain specific resolution (unless you're really lucky) and should probably settle for either sequence specifi (ASV) or genus. So, if you're looking for a specific species, you may not have the resolution to detect it. Consider moving up the tree and seeing if you have any hits.
If you know the 16S sequence for your reference organism (or have a set of references for the organism from a source you trust), you could also just use BLAST to see if any of your represntative sequences align to that taxa. I would do that in a limited capacity and think about how to manage the data carefully, but it might be a confirmation.
If you have remaining DNA and money, you could also do qPCR for the orgnaism to confirm.
So, lots of reasons, and some potential solutions.
Best,
Justine
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I believe my data lack a specific taxon that is usually dominant in the literature. Is there a way to confirm this finding using qiime2 or any other software?
Also, how do I know this taxa's specific abundance in my data using qiime2?
My data is microbiome 16S sequences, and I do the analysis using qiime2 amplicon. For example, I want to know the percentage of Cutibacterium acnes that is present in my data. How to do so?
Hello!
First of all, 16S rRNA gene amplicons are often not able to provide taxonomy higher than the Genus level. If you are looking for a specific species, their reads may be present in your data but with annotation only at genus or lower ranks.
Another possibility is that specific taxon present under different name or completely missing from the database you are using, so it is worth checking.
If you are missing this taxon in your taxonomy annotations, then you can't calculate its abundance.
If the taxon is present, you can create a taxonomy_barplot.qzv file and download a CSV file with taxa counts from it at the desired rank or collapse your feature table to that rank.
Best,
Timur
Hi @RanaAbdelaal
I merged duplicated topics.
In the future, please avoid duplicating topics, especially if they have already been answered. Moderators work voluntarily (and hard!) to provide support to qiime2 users, and duplicated topics create an unnecessary additional load on them.
Best,
Timur
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