Thursday, 24 November 2016

Gut Microbes Influence Our Evolution

Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues | Molecular Cell:

We need to stop thinking of the higher animals (and maybe plants) as a single species with a single genome as the unit on which natural selection operates.

We, along with all higher animals, are colonies of more-or-less cooperating species each of which has it's own evolutionary 'agenda' but each of which, like us, is inextricably bound up with the evolution of the colony as a whole. In effect, what is evolving is the colony with its distributed genome. This also has damaging implications for creationism and its dressed up little brother, intelligent (sic) design.

Evidence of how this works was published yesterday in Molecular Cell by a team of researchers from the University of Wisconsin-Madison. They have shown how the microbiota of mice can interact with their cells and change their epigenome through a group of small-chain molecules derived from the food the mice were fed. Sadly, The publishers, Elsevier, want £24.05 for me to reprint even the abstract here. (When is publicly funded research going to be made freely available online?) However, the full paper is available online, as is a press release from the University of Wisconsin-Madison.

The epigenome is the system of regulatory mechanisms that activate and deactivate genes, so acting as switches to turn different genes on or off as appropriate the the current activity of different cells. Part of this mechanism depends on the availability of small molecules that are derived from food, in particular from the polysaccarides in food such as cellulose.

The problem is that many animals cannot digest cellulose, present in fibrous plants, and depend on gut microbes to do the digesting for them. Some ruminants have elaborate digestive systems which acts like a fermentation vat to cope with a diet high in cellulose, for example, but even omnivorous species like mice and humans require plant fibre in their diet to provide their gut microbes with the raw material to produce these small molecules to make their epigenome work efficiently.

A good diet translates to a beautifully complex microbiome, and we see that the gut microbiome affects the host epigenome in a diet-dependent manner. A plant-based diet seems to favor host-microbe communication.

So, our cell genetic activity depends on our gut microbiota which in turn is dependent on our diet, and that has profound implications, particularly for our low-fibre Western diet.

The team demonstrated this by a simple yet elegant experiment in which 'germ free' mice were fed different diets and their epigenomes were then compared to those of mice with a normal microbiota fed the same diet. The 'healthiest' epigenomes were found in the normal mice fed on a high fibre/low sugar and fat diet. Moreover, the deficiency found in the 'germ free' mice could be rectified by including the small molecules normally produced by bacterial fermentation in their diet.

One of the findings here is that microbial metabolism or fermentation of plant fiber results in the production of short-chain fatty acids. These molecules, and potentially many others, are partially responsible for the communication with the epigenome.

So here we have a mechanism by which signals about our diet can be passed to our genomes and this depends on a healthy, varied diet which in turn produces a healthy and rich gut microbiota. Incidentally, the evidence that we are more healthy with a diet rich in plant matter and low in sugars and fats suggests were are still dependent on a system evolved early in our ancestry when our diet was mainly plant matter - like that of our great ape cousins.

Biologically, of course, this concept is not a problem for biologists. Nor is it for nature which doesn't have a rule book and has no need to conform to our classification systems. We think in terms of humans, mice, Escherichia coli, etc., but nature 'thinks' in terms of ecosystems and colonies because that is the reality of nature.

So how does this translate to a creationist view of biology?

Firstly, and something that is almost guaranteed to send any creationist into either deep denialism or a frenzy of abuse and condescension, is the idea of there only being two (or seven) of every species on the mythical Noah's Ark, an essential part of every creationists' Bible-literalist creed. The animals could not have survived, nor been healthy enough to survive long afterwards, with such a tiny number of gut bacteria, populations of which are normally in the tens of billions or more. But then the authors of that tale knew nothing of microorganisms, let alone their role in digestion and maintaining a healthy host.

Yet any supposed creator/designer of this system would be even more aware than we are today with our sophisticated microscopes and chemical analysis, but there is no hint whatsoever of any awareness of it in any ancient holy book and the Noah's Ark 'solution' would be untenable and not an option open to some assumed divine, genocidal god with an obsession with sex and sin and ashamed of its creation.

And why would an intelligent designer give us a gut microbiota which is unsuited to our Western modern diet (and not helped in the least by Biblical dietary taboos), if indeed it would have given us a microbiota-dependent digestive system in the first place when it would not have been beyond it to design a digestive system which can digest cellulose.

But then this is just another example of how modern science in general and modern biology in particular is showing just how inadequate and primitive the early understanding of biology was by the simple people who wrote the Bible in the almost complete absence of any understanding of the real world and no more understanding of the very small than they had of the very large. Such understanding would not have been lost on the creator of it all, if such a creator ever existed.

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