[HN Gopher] Catalog of viruses from human metagenomes reveals ch...
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       Catalog of viruses from human metagenomes reveals chronic disease
       associations
        
       Author : rch
       Score  : 132 points
       Date   : 2021-06-05 14:58 UTC (8 hours ago)
        
 (HTM) web link (www.pnas.org)
 (TXT) w3m dump (www.pnas.org)
        
       | contingencies wrote:
       | _It should be stressed that association does not necessarily
       | imply causation, and a variety of associative relationships
       | between viruses and a given disease state are possible. For
       | instance, virus abundance might simply be an epiphenomenon
       | reflecting bacterial host abundance, the human genetics that
       | predispose people to a disease might also provide a more
       | favorable environment for the virus or its bacterial host, the
       | external causes of a disease may create a more favorable
       | environment for the virus, or the virus may contribute to the
       | disease presentation in some way but ultimately does not cause
       | the disease in isolation from other important factors. Verifying
       | the associations we have detected with independent studies of the
       | same diseases in additional populations will be key to
       | understanding the extent to which the findings presented here are
       | generalizable._
        
       | AlexCoventry wrote:
       | > Read data were downloaded from the National Center for
       | Biotechnology Information's (NCBI's) Sequence Read Archive (SRA),
       | including data from the Human Microbiome Project (34) and several
       | other studies (25 Bioprojects in total) pursuing massively
       | parallel sequencing of human metagenomic samples
       | 
       | Don't you need a statistical model accounting for possible
       | sequencing batch effects, in that case? They may have been
       | batched according to some scheme which correlates with the
       | chronic diseases, and variations in the sequencing chemistry
       | between batches could cause spurious associations.
        
       | COGlory wrote:
       | If anyone is interested in other work on this topic, here is an
       | article by one of my mentors, Mark Young:
       | 
       | https://pubmed.ncbi.nlm.nih.gov/27573828/
       | 
       | They found bacteriophages (viruses that infect bacteria) that
       | were more common in people without IBS than with.
        
       | wpasc wrote:
       | With all the excitement around the study of the microbiome, its
       | connection to the other organs (even brain), and role in a wide
       | variety of diseases, I find it a bit daunting how little is
       | understood about the other components of the microbiome beyond
       | bacteria. The presence or absence of a specific phage or any
       | other organism could be just as important if not more than
       | relative balance of bacterial species.
       | 
       | I'm glad that these catalogs are growing and we are getting more
       | datasets like this and the human protein atlas.
       | 
       | Remember when we thought the human genome project was going to
       | "solve biology" :)
        
         | imglorp wrote:
         | And what about non-organisms like prions, which we barely grasp
         | in terms of gray matter. What other types are there and what
         | other havoc do they cause?
        
         | alexfromapex wrote:
         | Agreed, especially available information around archaea and
         | fungi
        
       | alexfromapex wrote:
       | It explains the benefit of having a diverse microbiome because of
       | increased adaptability of the bacteria to fighting off viruses
        
       | zeeshanqureshi wrote:
       | The author, Michael J. Tisza also shared some details in this
       | twitter thread
       | https://twitter.com/MikeTisza/status/1400528027285557248
        
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       (page generated 2021-06-05 23:01 UTC)