The Human “omes”

The importance of the microbiome to human health can’t be overstated, but this is only one part of a much vaster biomic whole.  My guess is that because we know more (as little as that is!) about our resident bacteria at the moment – they have been recognized and studied longer than our other old friends – they are what’s trending.  However, already interest in our mycobiome (fungi), our virome (viruses) and our macrobiome (our native animal life) is growing and I believe we’ll see a lot more research on these in the not-very-distant future.

A few examples:

Back in September, I read an article[i] on Science Daily about recent research into fungal, as well as bacterial, alterations in the guts of those with Crohn’s disease.  Researchers compared the bacteria and fungi in those with and without Crohn’s, within the same families, and found marked differences in both bacteria and fungi.  They were actually able to demonstrate that there is interaction between these that can lead to the inflammation found in IBD.[ii]

Last year, I read a similar article[iii] about the virome.  Research on this is just beginning so at this point, we know next-to-nothing.  However, in this study[iv] the scientists did note a large increase in the variety of viruses in those with IBD.  As one researcher involved in the work said, “”This is the tip of the iceberg…A significant portion of the viral DNA we identified in these patients is unfamiliar to us — it comes from newly identified viruses we don’t know much about. We have a great deal of groundwork to do, including sequencing the genetic material of these viruses and learning how they interact with the gut and gut bacteria, before we can determine if changes in the virome cause these conditions or result from them.”

And then there is my own personal favorite “ome” – the macrobiome.  I first learned about the concept in the New York Times, in August 1999.  I read the article “In Pursuit of Autoimmune Worm Cure”[v], and knew without a shadow of a doubt that I was reading about one of the most important factors in our growing epidemic of inflammatory diseases.

All mammals on earth have native animal life resident in their guts, right along with all those microscopic organisms.  The main type of macrobiotic organism is the helminth – intestinal worms.  The vast majority of humans on the planet still have their native helminths, except for those of us in the industrialized world where (by wearing shoes all the time, using toilets, drinking purified water, etc.) we have eradicated our native macrobiomes.  There is a growing body of evidence demonstrating that the loss of the immune stimulation provided by these organisms is largely responsible for our greatly increased tendency toward inflammatory disease.  Helminths stimulate the production of Th2 cytokines, including regulatory ones – the off switch to the inflammatory system.

By the way, two articles were published in the last years which demonstrate that the presence of helminths causes an increase in anti-inflammatory bacteria and a decrease in pro-inflammatory ones.  More on this in a future post.

Back to 1999: I ripped that article out of the newspaper and it still hangs on the wall of my office.  I stare at it every day as I work.  Reading that article was a major turning point in my life.

The complexity of our inner ecosystem is mind-boggling, isn’t it?  It’s like a vast, interlocking puzzle.  I think that’s why I find it so utterly mesmerizing. We, humans, are giant, walking ecosystems, just teeming with other life forms.  We can’t see them or feel them but without our “omes” we wouldn’t be alive.  AMAZING.



[ii] G. Hoarau, P. K. Mukherjee, C. Gower-Rousseau, C. Hager, J. Chandra, M. A. Retuerto, C. Neut, S. Vermeire, J. Clemente, J. F. Colombel, H. Fujioka, D. Poulain, B. Sendid and M. A. Ghannoum. Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease. mBio, September 2016 DOI: 10.1128/mBio.01250-16


[iv] Jason M. Norman, Scott A. Handley, Megan T. Baldridge, Lindsay Droit, Catherine Y. Liu, Brian C. Keller, Amal Kambal, Cynthia L. Monaco, Guoyan Zhao, Phillip Fleshner, Thaddeus S. Stappenbeck, Dermot P.B. McGovern, Ali Keshavarzian, Ece A. Mutlu, Jenny Sauk, Dirk Gevers, Ramnik J. Xavier, David Wang, Miles Parkes, Herbert W. Virgin. Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease. Cell, 2015; DOI: 10.1016/j.cell.2015.01.002


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