text: user17054: I'm a beginner in bioinformatics working with environmental metabarcoding, and while reading up on different marker genes, I understand that COI is preferably used for animals thanks to its higher variability over 18S (although it depends on which taxonomic resolution fits best and which reference data is available). What I don't understand though, and can't find an answer to, is why COI metabarcoding isn't used for bacteria and archaea as well. Why is 16S preferred, although bacteria and archaea clearly have the COI gene? Is it not variable enough? Or are the primer binding sites too variable? Something else?
  
  user3848: The exact answer to your question is bacteria do not have a mitochondrion, therefore cox1 is not a universal gene combining both Archaebacteria and bacteria. In contrast 16S is universal for these two kingdoms AND it is also single copy. Moreover, bacteria have diverse tropisms beyond the Krebs or Calvin cycles. Extensive studies have been performed on 16S and it provides an excellent taxonomic target in bacteria.
  18S is a problematic target in eukaryotes because it can paralogous and that is not an ideal target in taxonomic studies, but has nicely conserved primer site: thus single copy genes are required/preferred. In addition, 18S is prone to indels (insertions/deletions) and these are difficult to model, align and understand the underlying molecular mechanism or selection advantage.
  Every animal on earth has a mitochondrion and therefore cox1. Mitochondrion genes are guaranteed to be single copy in higher eukaryotes and cox1 has been extensively sequenced throughout metazoans. Thereby barcoding is appropriate because there's an exact reference to identify a given species is usually available. It has been extremely successful in insects which are the most biodiverse and species rich taxonomic Class on earth: there are more insects than all other higher eukaryotic species combined.
  
  In answer to the comments ...
  
  Whether mitochondrion were originally bacteria is a very difficult question and remains a theory (compartmentalisation theory - very old). I have not seen any rigorous phylogenetic support for this.
  
  cox1 (COI) or cox2 (COI) is not universal to bacteria, e.g. here. Its primary use is for aerobic organisms (oxygen consuming). Thus cox1 has a strong Krebs cycle association but there are a multitude of anaerobic pathways.
  
  
  Anaerobic bacteria don't necessarily need cox1/cox2 and there are a lot of obligate anaerobic bacteria in addition to non-obligatory anaerobic bacteria (which can do both).
  Marine metazoan are obligate aerobic organisms.
  
  There is no reason to suppose bacteria  are strictly  single copy cox1. mtDNA is tiny and hence copy number heavily constrained, bacterial genomes by contrast are much larger and could easily accommodate duplication events.
  
  There isn't much work on bacterial cox1, it has been pursued to attempt to augment antibiotic therapy. Degli Esposti (2020) is the closest I know to a comprehensive discussion on the bacterial cox genes.
  
  
  
original_text: 17054: <p>I'm a beginner in bioinformatics working with environmental metabarcoding, and while reading up on different marker genes, I understand that COI is preferably used for animals thanks to its higher variability over 18S (although it depends on which taxonomic resolution fits best and which reference data is available). What I don't understand though, and can't find an answer to, is why COI metabarcoding isn't used for bacteria and archaea as well. Why is 16S preferred, although bacteria and archaea clearly have the COI gene? Is it not variable enough? Or are the primer binding sites too variable? Something else?</p>
   3848: <p>The exact answer to your question is bacteria do not have a mitochondrion, therefore <em>cox1</em> is not a universal gene combining both Archaebacteria and bacteria. In contrast 16S is universal for these two kingdoms AND it is also single copy. Moreover, bacteria have diverse tropisms beyond the Krebs or Calvin cycles. Extensive studies have been performed on 16S and it provides an excellent taxonomic target in bacteria.</p>
  <p>18S is a problematic target in eukaryotes because it can paralogous and that is not an ideal target in taxonomic studies, but has nicely conserved primer site: thus single copy genes are required/preferred. In addition, 18S is prone to indels (insertions/deletions) and these are difficult to model, align and understand the underlying molecular mechanism or selection advantage.</p>
  <p>Every animal on earth has a mitochondrion and therefore <em>cox1</em>. Mitochondrion genes are guaranteed to be single copy in higher eukaryotes and <em>cox1</em> has been extensively sequenced throughout metazoans. Thereby barcoding is appropriate because there's an exact reference to identify a given species is usually available. It has been extremely successful in insects which are the most biodiverse and species rich taxonomic Class on earth: there are more insects than all other higher eukaryotic species combined.</p>
  <hr />
  <p>In answer to the comments ...</p>
  <ul>
  <li><p>Whether mitochondrion were originally bacteria is a very difficult question and remains a theory (compartmentalisation theory - very old). I have not seen any rigorous phylogenetic support for this.</p>
  </li>
  <li><p><em>cox1</em> (COI) or <em>cox2</em> (COI) is not universal to bacteria, e.g. <a href="https://www.sciencedirect.com/science/article/pii/S0005272820301547" rel="nofollow noreferrer">here</a>. Its primary use is for aerobic organisms (oxygen consuming). Thus <em>cox1</em> has a strong Krebs cycle association but there are a multitude of anaerobic pathways.</p>
  </li>
  </ul>
  <p>Anaerobic bacteria don't necessarily need <em>cox1</em>/<em>cox2</em> and there are a lot of obligate anaerobic bacteria in addition to non-obligatory anaerobic bacteria (which can do both).</p>
  <p>Marine metazoan are obligate aerobic organisms.</p>
  <ul>
  <li><p>There is no reason to suppose bacteria  are strictly  single copy <em>cox1</em>. mtDNA is tiny and hence copy number heavily constrained, bacterial genomes by contrast are much larger and could easily accommodate duplication events.</p>
  </li>
  <li><p>There isn't much work on bacterial <em>cox1</em>, it has been pursued to attempt to augment antibiotic therapy. <a href="https://www.sciencedirect.com/science/article/pii/S0005272820301547" rel="nofollow noreferrer">Degli Esposti (2020)</a> is the closest I know to a comprehensive discussion on the bacterial <em>cox</em> genes.</p>
  </li>
  </ul>
  