Wednesday, July 12, 2017


Source: Teach the Microbiome

For a long time now THE GENERALIST has been curious to know more about what is now referred to as the human microbiome - the entire ecosystem of bacteria (and other organisms) that we carry on us and inside our bodily containers. 99% of the bacteria are found in the gut.

I find this whole area of science incredibly powerful and it is clear from the research for this post that many discoveries are revealing a whole new world of medical investigation.

Published by Scribe 2016

My first main source is this highly accessible book by a young German scientist which is a great place to start understanding this remarkable new paradign shift in our thinking about our own bodies.

It seems we're built of three main tubes: the cardiovascular system with the heart at its centre; the nervous system, running in parallel, with the spinal cord, our brain at the top and nerve networks across our entire body. The third is the intestinal tube running through us from end to end via the mouth, oesophagus, stomach, small and large intestines and anus.

This is where it gets real interesting. Something called the vagus nerve serves as a fast and direct link between our gut and our brain. It runs from the diaphragm, between the lungs and the heart, up along the oesophagus  and through the neck to the brain. As the brain is insulated from the rest of the body, it needs information from the gut to form a picture of how the body is doing. Enders writes:
'The gut has not only a remarkable system of nerves to gather all this information, but also a huge surface area. That makes it the body's largest sensory organ...a huge matrix, sensing our inner life and working on the subconscious mind,'
Here are other things I learnt from this book:
  • 'Stress is thought to be among the most important stimuli discussed by the brain and the gut' writes Enders. One theory is that the 'altered circumstances stress creates in the gut allow different bacteria to survive there than in periods of low stress. We could say that stress changes the weather in the gut.'
  • 'Anyone who suffers from anxiety or depression should remember that an unhappy gut can be the cause of an unhappy mind.'
  • 'Our gastrointestinal tract is home to more than a thousand different species of bacteria - plus minority populations of viruses and yeats, as well as fungi and various other single-celled organisms.
  • 'Our gut's microbiome can weigh up to 2 kilos and contain about 100 trillion bacteria. One gramme of faeces contains more bacteria than there are people on the Earth.
  • 80% of our immune system is in the gut.
  • 'We are influenced by the microscopic world that lives in us. This is all the more interesting when we realise that every person's inner world is unique to him and her.'
  • 'While 100 per cent of the cells that make us up when we start life are human cells, we are soon colonised by so many micro-organisms that only 10 per cent of our cells are human, with microbes accounting for the remaining 90 per cent.
  • 'Our lifestyle, random acquaintances, illness, or hobbies all influence the shape of the populations inside our bodies...It is generally accepted that the first population to colonise out gut lay the main foundations for the future of our entire body.
  • In the April 2011 issue of Nature, scientists cliamed to have discovered three main enterotypes - bacteriological ecosystems - which appear in humans of all ages, genders, body weight and nationality. Type 1 is domninated by high-levels of Bacteroides, Type 2 by Prevotella and Type 3 by Ruminococcus. There are indication that long-term diet influences these enterotypes. Bacteroides seem to like meat and saturated fatty acids; Prevotellas are more common in the guts of vegetarians; Ruminococcus feed on the cell walls of plants.
  • Some scientists now support the theory that our gut microbiota can be considered an organ


The Human Microbiome Project (HMP), involving some 200 scientists, was a US National Institutes of Health (NIH) initiative with the goal of identifying and characterizing the microorganisms which are found in association with both healthy and diseased humans. The results were published in June 2012.

The Human Microbiome
The Human Microbiome is the collection of all the microorganisms living in association with the human body. These communities consist of a variety of microorganisms including eukaryotes, archaea, bacteria and viruses. Bacteria in an average human body number ten times more than human cells, for a total of about 1000 more genes than are present in the human genome. Because of their small size, however, microorganisms make up only about 1 to 3 percent of our body mass (that's 2 to 6 pounds of bacteria in a 200-pound adult). These microbes are generally not harmful to us, in fact they are essential for maintaining health. For example, they produce some vitamins that we do not have the genes to make, break down our food to extract nutrients we need to survive, teach our immune systems how to recognize dangerous invaders and even produce helpful anti-inflammatory compounds that fight off other disease-causing microbes. An ever-growing number of studies have demonstrated that changes in the composition of our microbiomes correlate with numerous disease states, raising the possibility that manipulation of these communities could be used to treat disease.

The Human Microbiome Project

The NIH Common Fund Human Microbiome Project (HMP) was established in 2008, with the mission of generating resources that would enable the comprehensive characterization of the human microbiome and analysis of its role in human health and disease.
Traditional microbiology has focused on the study of individual species as isolated units. However the vast majority of microbial species have never been successfully isolated as viable specimens for analysis, presumably because their growth is dependent upon a specific microenvironment that has not been, or cannot be, reproduced experimentally. Advances in DNA sequencing technologies have created a new field of research, called metagenomics, allowing comprehensive examination of microbial communities, without the need for cultivation. Instead of examining the genome of an individual bacterial strain that has been grown in a laboratory, the metagenomic approach examines the collection of genomes derived from microbial communities sampled from natural environments. In the HMP, this method will complement genetic analyses of known isolated strains, providing unprecedented information about the complexity of human microbial communities.
Source: It's OK to be Smart

In 'Tending the Human Body's Microbial Garden' by Carl Zimmer [New York Times / July 1 2012], he writes that, for more than a century doctors have been waging war against bacteria with antibiotics. Now a new approach known as 'medical ecology' suggests that by nurturing our 'garden' of gut flora we may discover entirely new approaches to infectious diseases that have previously been treated with antibiotics. Tending the microbiome may also help in treating obesity and diabetes. Many of bacteria have co-evolved and work to maintain the health of our bodies.


'Germs Are Us' by Michael Specter [New Yorker / 22nd Oct 2012] quotes David A. Relman, the first scientist to sequence the genomes of a human bacterial community - which happened to come from his own mouth. 

He tells Specter: "We have to stop looking at medicine as a war between invading pathogens and our bodies". He believes we need to employ a "sort of stewardship which has more in common with park mangement than it does with the current practice of kill microbes."

'Looked upon this way,' writes Specter, 'the human body turns out to be a vast, highly mutable ecosystem - each of us seems more like a farm than like an individual assembled from a rulebook of genetic instructions. Medicine becomes a matter of cultivation, as if our bacterial cells were crops in a field.'

Specter also refers to a 2009 paper entitled 'What Are the Consequences of the Disappearing Human Microbiome'  written by Martin J. Blaser and fellow microbiologist Stanley Fallow which focused on a loss of diversity in our biomes due to antibiotics. In a theoretical case a woman born at the start of the 20th century might have 10,000 species of bacteria, From the 1930s on, most people would have  one or two courses of antibiotics in their lives and will thus have lost some species. Her child will take many more antibiotice and will lose more species. Blaer says:
"A lot of things are happening at once. The rise in obesity, celiac disease, asthma, allergy syndromes and Type 1 diabetes. Bad eating habits are not sufficient to explain the worldwide explosion in obesity...We are not talking about illnesses that are increasing by ten per cent. They are doubling and tripling and qudrupling. With each generation there is a heavier impact on the early-life microbiome. And it means we are less and less able to metabolize the food we eat.'
'I had the Bacteria in my Gut analysed. And this may be the Future of Medicine' by Andrew Anthony [The Observer Review / 9th Feb 2014]
'Humans are first colonised by microbes during birth. Then through breast milk, which contains both probiotics ( beneficial microbes) and prebiotics (compounds that foster the growth of probiotics).
"There is strengthening evidence ", says microbiologist Paul O'Toole, " that the explosion of auto-immune diseases and immune disregulation diseases in Western society may be due to suppression of gut bacteria from infancy onwards."
'It takes about two years from birth...for a child to attain a mature microbiome. There are several factors that may contribute to childhood microbial dimishment. One is the increase in caesarian sections...Another is a lack of breast milk and a third is the increased use of antibiotics.
'In fact there are many studies around the globe ...which point up connections between the microbiota and diseases and complaints as diverse as  irritable bowel syndrome, inflammatory bowel disease, Type 2 diabetes, Parkinson's. Alzheimer's, autism, depression, cardiovascvular disease and colon cancer.'
Source: Wikipedia
'Why modern life is bad for the gut' by Clive Cookson [Financial Times / 25th April 2015]
 reports on two studies on the microbiomes of remote human communities to compare their diversity with those in the US. One was a isolated Yanomami tribe in the Amazonian forest, the other subsitence farmers in Papua New Guinea. Both had considerably more diverse microbiomes than  Americans. The team leader of the Amazonian project said:

"Our results bolster a growing body of data suggesting a link between, on the one hand, decreased bacterial diversity, industrialised diets and modern antibiotics, and on the other, immunological and metabolic diseases such as obesity, asthma, allergies and diabetes, which have drastically increased since the 1970s.We believe there is something environmental occuring in the paset 30 years driving these diseases. The microbiome could be involved."

In an article by Chloe Lambert entitled 'Gut Thinking' [New Scientist. 21st Nov 2015]:

In 2014, scientists at the University of New Mexico published a review of reasearch on human microbiomes and came to tthis intriguing solution: 'gut microbes don't just flourish on certain diets, they may also control our food cravings and preferences to serve their own purpose'

This raises the intriguing possibility that through the spread of microbes, person to person,  those cravings could become contagious. Lambert says: 'We already know people are much more likely to become obese if they have a friend who is obese.'

According to Tony Goldstone, an endocrinologist at Imperial College, London: 'There's evidence that gut hormones modify not only reward and consumption of food but also any drug of abuse - such as nicotine, cocaine and alcohol.'

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