More Microbe Than Human: How the Microbiome Makes Us Superhuman

Once vilified as the root of disease, microbes are now emerging as indispensable allies—extending our genetic capabilities and bestowing us with powers once thought beyond human.

Once considered the cause of most disease, "germs" are now increasingly being recognized as essential to our survival and well-being by extending our genetic capabilities with "supra human" powers

A groundbreaking study published in the journal Nature titled, "Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota," adds to a growing body of microbiome research challenging the prevailing genome-centric story of human evolution, namely, that the extremely gradual changes in the protein-coding nucleotide sequences of our DNA are primarily responsible for the survival of our species over the eons.

The 2010 Nature study found that the Japanese have a strain of bacteria in their gut loaded with both the genes and enzymes required to digest the polysaccharides found in sea vegetation, which are normally indigestible. These genes are absent from the human genome and originate from a strain of marine bacteria that naturally inhabits sea vegetables traditionally consumed in the Japanese diet.

The human genome, across all populations, codes for just 17 carbohydrate-active enzymes (CAZymes), which evolved over millions of years to digest terrestrial plants. In contrast, the average human microbiome is vastly more dynamic, containing orders of magnitude more CAzymes than the human genome could ever produce on its own. One study estimated there are about 16,000 different CAzymes in the human gut microbiome.^[1] The human gut symbiont Bacteroides thetaiotaomicron3, alone, contains 261 carbohydrate-digesting enzymes known as glycoside hydrolases and polysaccharide lyases.

The astounding diversity of CAzymes found within strains like Bacteroides begs the question: how did this immense diversity evolve? The new study provides a novel explanation: the diversity evolved through human gut flora acquiring new genes from microbes living outside the gut, presumably through the well known phenomenon of horizontal gene transfer.

The researchers identified enzymes known as porphyranases in the marine bacterial strain Bacteroidetes, Zobellia galctanivorans; a bacteria which naturally lives on the red marine algae of the genus Porphyra commonly consumed in East Asia as nori.

Porphyranases break down a type of carbohydrate found in marine vegetation known as sulphated polysaccharide. The human body does not produce porphyranases, which is why these marine polysaccharides are generally considered indigestible to humans.

Remarkably, the researchers showed that genes coding for porphyranases, agarases and associated proteins needed to degrade marine vegetation have been transferred to the gut bacterium Bacteroides plebeius isolated from Japanese individuals.

Because comparative gut metagenome analyses show that porphyranases and agarases are frequent in the Japanese population and that they are absent in metagenome datafrom North American individuals, the implication is that the genes from marine bacteria consumed through non-sterilized marine vegetation in the Japanese diet (consumed at a rate of approximately half an ounce per day) were transferred horizontally into already existing bacterial strains in their guts.

The new study reveals that, relative to the glacial pace of our genome's evolution and adaptability to ever-changing environmental and dietary conditions, epigenetic factors and modulators, which include the 100 trillion microbes in our gut and their 4.2 million genes, enable us to rapidly adapt, change, and extend our genetic capabilities, conferring significant advantages to our species for both survival and collective well-being. In theory, these microbiome-mediated epigenetic capabilities enabled humans to radically alter their physiological capabilities, e.g. produce unique enzymes not found in our genome; changes which occurred, in what amounts in biological terms to "real time," relative to the geologic time scale within which the genome of our species evolved.

Another concrete example of this is the discovery of a wide range of bacteria in the gut of Westerners capable of degrading the thousands of hard, if not impossible to digest proteins in modern wheat (there are over 23,000 distinct proteins in the modern wheat proteome). Indeed, without the help of these gluten peptide-degrading microbes, the sudden Neolithic introduction of gluten-containing grains into the human diet may have had even more catastrophic health consequences than I already documented in my essay series, "The Dark Side of Wheat."

Cooperative Evolution: Microbes as Evolutionary Fast-Track Agents

Obviously, the implications of microbiome-mediated enhanced digestion are profound. Whereas it takes millions of years to evolve functional genes that remain coded in the primary DNA sequence of the genome, epigenetic inheritance systems, such as that represented by the human gut microbiome, may take only a fraction of the time to adjust to a radically changing environmental/dietary milieu. This "real time" versus "eonic time" adaptability confers a profound evolutionary survival advantage.

The implications go even deeper as far as our dependency on microbial genetic capabilities. There are deep-seated "mutations," or SNPs (single nucleotide polymorphisms) in our genome, some of which do things like limit the production of the active form of folate, known as 5-methylenetetrahydrafolate. Presumably, these defects can have a multifocal effects that is associated with a wide range of health problems related to 5-methylenetetrahydratefolate deficiency. There is, however, a well known strain of Lactobacillus helviticus found in fermented dairy products that produce the missing folate metabolite for us in our gut. Examples like this show that the microbiome can fill genetic lacunae within our bodies, literally plugging holes with "epigenetic glue" in what would be the sinking ship of our glacial like adaptability of the human genome.

Challenging Human Limits: Microbial Miracles in Vitamin C and Solar Energy

Moreover, Stephanie Seneff and I located truly remarkable research last year showing that there is a human strain of bacteria in the microbiome capable of synthesizing vitamin C, essentially challenging the prevailing view that humans are incapable of producing vitamin C. Also last year, a chlorophyll metabolite found in the gut known as pyropheophorbide-a was found to "super charge" our mitochondria in producing ATP (without the concomitant increase in reactive oxygen species), essentially disproving the long-held assumption that humans can not directly harvest sunlight and convert it into metabolic energy like plants; it turns out we can! So many apple carts are being overturned, thanks to our growing awareness of the seeming miraculous capabilities of the microbiome and its metabolites.

Tending the Invisible Garden: Microbial Care as Self-Care

Clearly, if this is true, creating conditions that protect and nourish the microbiome, is as important as the effort we make to prevent insults to DNA in our bodies, i.e. reducing exposure to genotoxic chemicals and radiation. As important as oxygen, nutriment, sunlight, is living food, grown in healthy soil, and prepared with cultural practices (recipes: literally a French word meaning "medical prescriptions") passed down for generations! The way we are born into the world, vaginally or by C-section, whether or not the mother has been exposed to antibiotics, before conception, during, and even after when breastfeeding – these factors become extremely important as far as establishing the microbially-dependent infrastructure and superstructure of our health.

Again, I believe the Nature study indicates that the seemingly "supra human" genetic capabilities of our gut microbiome may have been the primary determinant in our species' survivability to this present day because they allowed our species to adapt quickly to changing environmental and dietary niches. Undoubtedly, the ability to produce marine vegetation specific polysaccharide-digesting enzymes is only the tip of the iceberg as far as how the microbiome's genetic-extension capabilities.

This notion that (microbiome-mediated) adaptability and not simply natural selection of primary DNA sequences was essential to our survival as a species is perhaps echoed in the theory of evolution's original architect Charles Darwin, to which the following quote was attributed:

"It is not the strongest of the species that survives, nor the most intelligent; it is the one most adaptable to change."

Increasingly, research on the microbiome and its ability to extend our genetic/epigenetic capabilities giving us "supra human" powers, such as profoundly enhanced digestion, assimilation, immunity, synthesis of vitamins, is accumulating in the biomedical literature.

The human genome, after all, contains approximately 23,000 protein-coding genes, while the human microbiome contributes about 4,200,000 such genes. And this, of course, is still using the outdated metric of comparing the number of protein-coding genes to protein-conding genes; the vast swaths of information-containing nucleotides, such as non-coding RNA molecules, and transposable genetic elements, contributed by the trillions of bacteria, viruses, together exert far more influence via epigenetic mechanisms than the primary sequences in our DNA.

Ultimately, this should humble us to a startling truth: we are more microbe than man—both in cell count and in genetic capability. To learn more about the Copernican-type paradigm shift inaugurated by the discovery of the microbiome's central role in both our species self-definition and health and well-being, read my recent article on the topic, "How The Microbiome Destroyed the Ego, Vaccine Policy, and Patriarchy."