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  • How to interpret correctly this metagenomics results

    Hi guys,

    I have some metageonmics sequencing from environmental microbial samples and I did some analyses. I have found some of housekeeping functions (related to DNA replication etc.) are overabundant.

    I would like to interpret that this may suggest high activities in microbial reproduction in situ.

    My friend told me that this is only DNA, not necessarily being expressed. So, I shouldn't say that. Reviewers might not like it.

    Do you guys have suggestions? I read some papers and a lot of people write as what I did. It seems not that bad. I know it is metagenomics from DNA and it is not metatranscriptomics from RNA. All of the over-representative functions/genes that I found may not be able to express.

    Thanks,

  • #2
    That sounds pretty fishy.

    If you found a high abundance of, say, sulphate-reducing genes, you might be able to infer something about the community. But for housekeeping genes? Maybe it shows that the organisms have the potential to reproduce quickly... and maybe, housekeeping genes are just better annotated and thus easier to find than more specific genes... but there's absolutely no evidence of high levels of reproduction, any more than the generally high fertility a college dorm indicates a high level of reproduction. College dorms actually tend to have a very low rate of reproduction.
    Last edited by Brian Bushnell; 07-16-2015, 10:58 AM.

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    • #3
      You can imagine that if all the bacteria share housekeeping functions, but other functions are distributed across the species, then housekeeping will look "enriched". Gene ontology/functional enrichment is very easy to turn into a "just so" story with post hoc handwaving.
      Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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