So, since the time that I started this blog to now, the field I titled the blog to address has virtually exploded. The human microbiome, particularly in its relationship to other microbiomes is still more than a little uncharacterized - but now, people are trying. Process is still a giant mess but pattern is seeing rapid advances.

This is very encouraging in one respect; I am able to give talks about the microbiome and say things that are 'factual.' We are introgressing into the areas where ignorance reigned supreme.

Some of my greatest joy, though, with a bit of schadenfreude, I suppose, is the ability to finally convince the old guard - with their reliance on culture techniques and classic in vitro biochemistry, their vast taxonomies and their stodgy assurance that they knew which pathogens were important, what was merely a clinical 'contaminant' and their oversimplified Koch's postulates, that they not only knew very little - but that most of what they thought/think they know is actually error. Erroneous. False.

Yes, that's the stuff of which revolutions are made. Every microbiologist knew 'how little we know.' How few organisms were named and characterized, how complex biochemistry and genetics was, etc. What they didn't know was how deeply flawed their generalizations were. The assumption was largely that 'refinements' were necessary. That new pathogens would be discovered, for instance, not that the entire mode of pathogenesis would be, for many diseases, overturned; that Koch's postulates and the germ theory would have to be thrown out for 'dybiosis,' that the host-microbiome function would be so sophisticated and genetically interwoven.

We are in a brave new world and much unlearning needs to happen. The next generation of researchers will have little need for the hopelessness that comes from wondering if anything big is yet to be discovered.

Anyway, there are plenty of interesting papers to discuss.

Let's start anew with one of the recent microbiome papers:

Phylogenetic Characterization of Fecal Microbial

Communities of Dogs Fed Diets with or without

Supplemental Dietary Fiber Using 454 Pyrosequencing

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842427/pdf/pone.0009768.pdf

Inflammatory bowel diseases were one of the great unknowns a decade or so ago. Still, the debates about the microbial, genetic, immunologic components rage. There is probably some truth, it turns out, to all three views. Root causes may not, frankly, exist in this case; that is, the disease state may be a result of a spiral, as the immunity and microbiomes, assisted by predispositions, behaviors, environmental exposures, migration events, lead from one state to another until the gut is irreversibly (or near irreversibly) broken. At least now, we can say that the bowel flora is abnormal, that the immune response is abnormal, and that normalizing these things as best we can is helpful. The place of worms in the health-compatible flora is unknown - both for 'primitive' living conditions and 'modern living conditions' and may have something to do with it, but we can't say that for certain.

The results of this paper were generally unsurprising. Diet and flora interact in a repeatable fashion, at least at the phyla level. There was no obvious priority effects/order effects with the diets used in conventional dogs (useful result). The OTUs per dog were ~300; pretty normal. Using V3 gave them enough data to be dangerous but there really isn't much to say about function or anything like that. It's a good first data set and will certainly be foundational for later work on dog GI disease; which appears to be their next step.