The human microbiome is all the rage in this day and age. It’s at the forefront of modern science and medicine and features prominently in newspaper articles, health & wellness magazines, and diet books. But despite being so visible and scrutinized, the microbiome is frequently perceived as being a mystery – something that it’s difficult to get a handle on/make sense of. This is undoubtedly largely because much of the information that’s currently available is highly heterogeneous with respects to the messages and ideas that are expressed, with different studies and reports communicating different – and sometimes conflicting – things. Couple that with the fact that microbiomes are highly variable, complex, and malleable, and one can quickly understand why there’s so much confusion and uncertainty in this area.
I’ve long argued that Darwinian science can help us navigate our way out of this “mess” by providing us with invaluable insights pertaining to the evolution and nature of symbiotic relations. It’s arguably fundamentally required in the context of microbiome research. Without it, we’re fumbling in the dark. This is not to say that invoking evolutionary theory is going to rapidly reveal the correct answers to all the questions microbiome explorers are currently asking themselves; however, there’s no doubt that it can help guide us towards those answers.
Some shrewd investigators have made this realization, two of which recently published an insightful article in the Yale Journal of Biology and Medicine entitled Natural Selection, The Microbiome, and Public Health…
Darwinian microbial medicine
Over the years I’ve read a great number of scientific papers on the human microbiome, and I’ve also conducted some original research myself. Naturally, I’ve found some of the articles I’ve read to be better and more enjoyable than others. The aforementioned paper, which I read as recently as yesterday, gets a very high score in this respect. It’s one of the best reviews on the microbiome I’ve ever read, and I’d highly recommend it to others, in particular to researchers, medical professionals, and health aficionados who are trying to unravel human-microbe connections and figure out what it takes to build a truly healthy microbiota.
In the article, investigators Holly A. Swain Ewald and Paul W. Ewald start by exploring and describing the continuum at which symbiotic relationships exists, before they proceed to look into the relevance of this concept to modern medicine and public health. They don’t get into a lot of specifics or talk about a long list of concepts or diseases; rather, they focus their attention on certain key biological principles that can be applied pretty much across the board with respects to symbiotic relations in nature, and provide a couple of examples that highlight the relevance of these principles to health and medicine.
What really appeals to me about the piece is that it’s essentially one long argument, expertly guided by evolutionary logic. From a bird’s eye perspective, the authors, who come across as reasonable and thoughtful, bring evolutionary science, the human microbiome, and medicine together into a unified whole. Basically, they intertwine various elements of science that are often explored separately, despite being inseparable in terms of their true relation. For example, oftentimes, the prebiotic concept is discussed without any appreciation or mentioning of evolutionary theories, in spite of the fact that it’s absolutely critical to invoke such theories in order to make sense of why we humans have come to require a ‘steady’ influx of fermentable fibers (“prebiotics”) in order to stay healthy, as well as what compounds we should ideally take in, and in what form.
The people who’ve followed my writings here on the site will undoubtedly recognize the main concepts discussed in the article, which all fall under the umbrella of what may be called Darwinian microbial medicine; however, they will undoubtedly also discover/learn something new. I know I did.
I know well that a paper of this calibre is unlikely to “come out of nowhere”; hence, immediately after having devoured the review, I went online to have a look at some of the other papers the Ewalds have put out. Of note, I discovered that Paul Ewald is listed as one of the authors of Evolutionary Health Promotion – a great review paper that deals with the evolutionary health concept. That helps explain why this new article is so good.
Some important takeaway messages from the paper
Below, I’ve included some segments of the paper that stood out to me. If they catch your attention, then I’d recommend that you head on over to PubMed and read the whole article, which is freely available.
On the importance of evolutionary science to microbiome research…
Natural selection has shaped host-microbiome interactions, but is dependent on the environmental context. Application of evolutionary and ecological principles may therefore provide essential insights into the composition, maintenance, and restoration of gut microbiomes and effects on human health.
On the evolution of mutalism…
Although the conflict of interest between host and symbiont imposes constraints on the evolution of mutualisms, a large number of the microbes in the zone of commensalism should be mutualistic. The main reason is that the diversity of threats posed by pathogens is ever changing and unbounded. The immune system has adapted to counter a large portion of these threats by lymphocyte diversity, which is bounded by the make-up of each host’s genome. The reliance of somatic mutation of lymphocytes and the variation in MHC from one individual to another, however, suggest that the diversity of threats cannot be defended against by a single host genome relying on recombinatorial diversity. Mutualist gut microbes evolve to defend themselves against parasitic microbes and have short generation times with virtually unbounded evolutionary potential. It seems reasonable, therefore, to expect that they can offer a complementary defensive system that can respond to unpredictable changes in parasites in the gut lumen, which is relatively inaccessible to immunological defenses.
On the causes and implications of microbial evolutionary mismatch…
The microbial community in the gut is composed of hundreds of different species interacting with each other and with the host; thus, co-evolution and arms races dynamically shape the gut landscape. Many of the problems perceived as epidemic—obesity, type 2 diabetes, autism, childhood allergies—are linked to the microbiome. The evolutionary mismatch of a diet low in fiber and high in sugar and fat and the radical increase in formula feeding have led to near global disturbance of the human gut microbiome with shifts in species diversity and proportions. The spreading embrace of the Western diet and the influence of companies such as Nestlé on formula feeding help explain the long reach of microbiome disturbance and sequelae.
One the problems with genetically modified “probiotics”…
Evolutionary logic would caution against the use of genetically modified probiotic strains because host-organism interactions have neither been tested over time nor shaped into mutualisms by natural selection. These considerations apply as well to interactions between introduced organisms and existing gut mutualists.
On the importance of microbiome restoration to public health…
Public health efforts to counter negative effects of the Western diet, support breastfeeding, and assure access to high-fiber, low-sugar, and low-fat foods may have an outsized effect on seemingly unrelated widespread diseases such as diabetes, autism, and childhood allergies. The broad sweep of these effects suggests that health promotion by the microbiome may involve broad-based benefits such as the enhancement of immunological function and/or the protection by microbial mutualists against pathogens that would otherwise cause damage specifically to gut tissues as well as systemically. The evidence relative to diabetes may illustrate this breadth because the Western diet appears to shift the microbiome towards species that directly antagonize insulin in a pathological process that is preventable and treatable.
It is fascinating to consider. Microbes have co-evolved with animals and plants. These microbes have their own genetics that would interplay with the genetics of other species. We already know the powerful affect microbes can have over biological functioning, not to mention mind and mood and much else.
Here is where it could get even more interesting. It’s not merely genetics since genetic expression is determined by epigenetics. Maybe epigenetics plays a role in microbes as well. However epigenetics may or may not influence genetic expression of microbial genetics, it’s quite possible that microbes themselves could alter the epigenetics of their host species.