Friday, 20 February 2015

Microbiology: our changing perception of nature

Recent developments in the field of microbiology (see below), together with advances in epigenetics, horizontal gene transfer by viruses, fungal networks and quantum biology, contribute towards a perception of the biological world very different from that of a selfish-gene-driven machine. Increasingly it is seen to be an intricately interconnected ecosystem with purposeful evolution of immense complexity. The protein coding gene is only 1% of the human genome: the rest is an unfolding mystery. There is miraculous engineering, organisation, data transfer and decision taking from the macroscopic to the microscopic. Whether it is a tropical rain forest or  biochemical pathways within a cell, the characteristic that stands out is one of systems cooperating to produce new systems of larger functionality.

Results of the Human Microbiome Project

A 5 year study involving 80 research institutions and funded mainly by the US government has sequenced the genes present in the bacteria, fungi and viruses, collectively known as microbes, present in and on the human body. Here are the main results as reported in Focus, August 2012, p.12 and The Economist, August 18, p.62-4.
  • The human digestive system alone has 100 trillion bacterial cells, which is 10x the number of body cells and weighing a total of about 1 kilogramme. NB: bacterial cells are typically only about 1/50th the volume of a human cell, which normally has a diameter in the range 5-40 microns. In all the human microbiome contains 3 million genes compared to the 23,000 of the human genome.

  • There are 10,000 different species of bacteria, viruses and fungi which reside on the skin, on the palms, in the nose, intestines, throat, hair and vagina, behind the ears and in other places.

  • The colony present in a person is unique to that person and the variation between people is very large. Despite this variation there are a core set of functions common to all.

  • Disease lies dormant in almost everyone. Pathogens are present all the time and do no harm until for no apparent reason they go on the attack. E.g.: heart disease, diabetes (both 1 and 2), multiple sclerosis, eczema and asthma. Conversely, they can also protect the body from infection, as with clostridium difficile (severe diarrhoea etc.). This arises when antibiotics kill off the beneficial bacteria.

  • The bacteria in the gut breaks down food that cannot be broken down by the digestive enzymes produced by the body, turning it into vitamins. Surprisingly, the gut bacteria varies substantially from person to person yet the function is the same.

 Expanding on this last point, complex carbohydrates are turned into formic, acetic and butyric acid. These are then  passed through the walls of the gut into the bloodstream where a miraculous biochemical pathway converts them into energy or layers of fat.  10-15% of the energy used by an adult is provided in this way.

See also more recently a post dated 17 February 2015 from the Scientific American
 'Microbes in our gut are essential to our well being.'    

The March 2015 issue of Focus has as its cover story ‘How Bacteria change your mood.’

Antibiotic resistance

 The prevailing dogma has been that bacteria mutate in response to modern antibiotics, until they become resistant. No doubt there is some truth in this, although my understanding is that the actual mutations are far from random. But a much wider picture is emerging. It now appears that bacteria present in the biosphere some 4 million years before modern antibiotics were invented were already resistant to them. In other words when ever a new antibiotic is launched on the market the chances are that somewhere on Earth there is a bacteria which can beat it. This will have big implications for drug research and evolutionary theory.

The evidence for this came to light in the discovery of bacteria present in the Lechuguilla caves in New Mexico. These had been isolated from human influences for 4-7 million years. Of those that could be grown in petri dishes over 70% were found to be resistant to antibiotics.


It may be that antibiotic resistance to any conceivable antibiotic is present in bacteria somewhere in the biosphere and it is only a matter of time before it finds its way to a patient under treatment. If so, the effort should be focused on  more robust ways of treating infections.

Possibly complementing this finding there is recent evidence that resistance to penicillin, sulfonamide and tetracycline is present in soil bacteria. See

I am sure there is much more going on in biology than I can possibly keep track of or comprehend but I hope this gives you a taste of just how much our understanding of the biosphere is evolving.


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see also
 Natural technology: the bacterium

Evolution IS progress

Project GENOME turns junk DNA into treasure

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