Nutrimicrobiomics & Epimicrobiomics: Two new frontiers in human health & nutrition thinkering

(Above: Dennis Green, former head coach of the Arizona Cardinals, talking about human biology dogma prior to recent advances in genomics and in microbiomics)

Turns out, we aren't who we thought we were.

Awhile back, like in 2003, the central dogma of biology (DNA --> RNA --> Protein) still ruled the day and Lamarck was considered crazy. Like most extant models of homeostasis (physiologies are nonlinear and fractal, in reality), this cellular reasoning followed linearly.

And then the flood gates opened.

Finally.

From the Human Genome Project (hat tip to Dave Lull) and associated efforts, we realized that this genetics business is a bit more complicated and messy than we predicated a priori. We realized that we are still human beings trying to understand our own beings, our own biological underpinnings. We realized that trying to understand physiology is humbling, yet exciting and empowering. And that's a good thing.

And we were just looking at our own genomes, our own DNA.

Fast forward a few years to today, and it appears that experts from various disciplines are starting to say more regularly and persuasively that we'd be wise to examine those symbiotic micro-organisms (or anti-symbiotic "weeds") that inhabit and interact with our bodies. In short, the central dogma of biology is evolving rapidly as we speak. And we're responding swiftly, I think. Recently, fields like nutrigenomics and epigenetics have emerged with promising perspectives, offering insights on how our environments and other external factors interact with our primal blueprint genetic makeups to produce body tissues and regulate biochemical functioning. In parallel, from the Human Microbiome Project and associated efforts, we are realizing that those micro-organisms in our bodies that outnumber us 10:1 (based on cell count) determine our phenotypic destinies quite dramatically. From this view, the Personal Genome encompasses both human and non-human genomics because we carry all these other cells (and their DNA/RNA) around with us all the time.

Here are a few working definitions for this area of inquiry:

Microbiota: The collection of micro-organisms in a particular environment, such as the human body, e.g. the human gut microbiota.

Microbiome: The collection of genetic material (all the genomes) in a particular microbiota.

Gnotobiotic: Describes a microbiota with a known set of micro-organisms.

Agnotobiotic: Describes a microbiota of unknown or poorly defined composition.

In an anti-Dennis Green fashion, these threads suggest that we aren't who we thought we were. It appears that we really are meritages of cells that change dynamically across our lifespans (just consider how antibiotics wipe out our gut microflora or how the atoms that constitute our bodies turn over entirely every seven years or so).

So, to this list of terms, I would like to add the following memes:

1. Nutrimicrobiomics: The study of the multi-directional interactions between microbiomes and diets.
2. Epimicrobiomics: The study of the multi-directional interactions between microbiomes and environments.

That's a start, at least, to defining these new fields of inquiry (which may fall under the umbrella term "Functional Microbiomics"). I'm imagining things like metabolomic profiling for microbiomes too. For example, inulin is a fermentable fiber that acts as a prebiotic that 'feeds' gut flora. As inulin is metabolized in a person's body, it influences that person's 'human' genome and his/her 'non-human' microbiome simultaneously. This simple interaction with our intimate micro-organism neighbors represents nutrimicrobiomics in action. Chris Kresser of The Healthy Skeptic (who recently conducted an awesome interview with Stephan Guyenet), has an excellent series on 'acid stopping drugs' that speaks to this too. I've long stood against widespread use of Proton Pump Inhibitors (PPIs) as pharmacological agents because they increase susceptibility to Clostridium difficile infections dramatically (thanks to Dave Lull) and create grounds for extensive bacterial overgrowth in the lower intestinal tract. Clearly, the choices that we make about dietary intake shape the environments of our microbiomes directly (see Dr. Ayer's recent Cooling Inflammation post on human milk as prebiotics) and thus influence our n=1 set of micro-organisms through epimicrobiomics in the process.

Which adds another layer of plasticity to our health optimization functions!

So, when it comes to optimizing health, given both the inherent variability in people's genomes and microbiomes and the plasticity considerations of epigenetics and epimicrobiomics, it seems reasonable to conclude that we each won't be who we think we are going to be in the future because our experiences today will lead us down unpredictable phenotypic expression paths in powerfully fractal ways.

Embrace this uncertainty and listen to your body respectfully to see where this path may lead you serendipitously (and, I suspect, nonlinearly).

On this Memorial Day weekend, I'm thankful for where my path has meandered unexpectedly.

Find peace as a deductivist by recognizing that you don't have to be all things to all people at all times: be yourself (in harmony with all those micro-organisms you carry around with you as co-pilot allies) and be your best.

That's the best we can do.

That's what I (try to) do.

To good health,

Brent

PS. One of my favorite prebiotic/probiotic/synbiotic meals is onions (inulin source), mushrooms (fungi source), and meats cooked in cultured pasture butter with FAGE Greek yogurt (bacteria source) as a side. That 'feeds' my GI system symbiotically! While alive, animals work actively to remove toxins from their bodies (save rare evolved examples like tetrodotoxin depositing), so we benefit from their efforts when we eat their tissues. On the flipside, while alive, many plants and fungi actively produce and store toxins in their tissues to deter herbivory. The takeaway: we each, individually, have to work strategically (via self-experimentation, as one mechanism) to figure out which types of tissues and in what amounts and with what constituents we should eat and drink to mesh well with our own distinct beings (and to enjoy while living). That's my working conjecture, at least, that I'm trying to falsify actively.