Hi everyone, In a recent discussion with colleagues we asked ourselves how mitochondrial 16S rRNA (mt16S) is handled. First of all, we verified that mitochondria still have its 16S (it has lost most of its genes). If you wonder, yes it still has a 16S: http://rnacentral.org/rna/URS0000992695/9606 …

Hi @Alban_OTT , It is definitely true that you will sometimes see organelle rRNA sequences in your data, and they will often be classified during taxonomy classification. For example, in Greengenes, mitochondrial rRNA are often classified as: k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; …

Hi @Alban_OTT , Just to add to @gregcaporaso 's advice: if chloroplast or mitochondrial DNA sequences are more/less abundant in different experimental groups that you are comparing, or if you suspect that this would be the case (e.g., because you are comparing host-associated vs. environmental microb…

Thanks @Nicholas_Bokulich , I agree. In any case, it shouldn't hurt to remove these features.

@gregcaporaso @Nicholas_Bokulich I confirm that I have some "k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__mitochondria;" OTUs in my studies. None of the studies I analyzed had differentially abundant "f_mitochondria[...]". So I will just left it in the datasets an…

QIIME 2 2017.10 was just released! There are some new methods in q2-taxa which simplify filtering and a brand new section in the Filtering Tutorial explaining how to filter certain taxa from your data.

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Mitochondrial 16S handling

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