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People are not just people. They are an awful lot of microbes too.

This quote from The Economist (2012) reflects the realisation that human gastrointestinal microbiota (HGM) is not just a collection of icky bugs lounging around in our guts. In fact, scientists now think that HGM should be classified as a human organ – many endocrinologists (specialists in hormonal disorders) certainly view the HGM as an organ in its own right after discovering hormones produced by HGM can affect the body, brain and the enteric nervous system (ENS, our body’s second brain).

Influential HGM-produced hormones include serotonin, dopamine, noradrenaline, gamma-aminobutyric acid, acetylcholine, histamine, etc. The hormones are not produced by single strains of bacteria either – as an illustration, dopamine is output by bacteria such as Bacillus cereus, B. mycoides, B. subtilis, Proteus vulgaris, Serratia marcescens, S. aureus, etc.

Not all kinds of bacteria can survive in the HGM, being restricted to four specialised groups called Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. A recent revision indicates there are about 100 billion (instead of the oft-quoted 100 trillion) bacteria in adult human guts and there are probably over a thousand species and sub-species of bacteria.

Investigating HGM bacteria is difficult as many are so specialised that they survive only in intestines and cannot be cultured. They are crucial for various digestive processes – without HGM, many foods are simply indigestible. For example, humans have no enzymes for digesting most complex carbohydrates – these can only be processed by HGM. The outputs from HGM include vitamins, minerals, short chain fatty acids (SCFA) and other nutrients which are passed through the gut walls into the bloodstream – it also supplies between 10% and 15% of the energy for adults.

HGM also enhances the immune system; intestinal bacteria produce antimicrobial compounds which help attack and destroy pathogens (disease-causing microorganisms) present in the intestines and these compounds can be adopted by the body – an example is anti-inflammatory compounds produced by Faecalibacterium prausnitzii.

Cohabiting bacteria within HGM do not attack each other – they manage themselves via a fascinating mechanism called quorum sensing.

How quickly things change

The microbial balance of HGM can change quickly, within a day or less, and this is a direct result of what the body has ingested. Problem foods are not always obvious and can mutate over time – what is easily tolerated before may trigger severe issues later, and nobody is really certain why. Idiosyncratic human differences mean that problem foods are not always the same between people, even if they share the same diet.

In Taiwan, my intestinal cramps were so severe that I thought I had developed gluten intolerance. Later, it seemed the Taiwanese buns and noodles made from heavily-processed white flour were a more likely cause – and I never had problems with flour before.

HGM is loosely divided into three enterotypes (effectively a catalogue of the types of bacteria within the HGM), and enterotypes are influenced by diet. The three types are simply classed as Type 1 (where the genus Bacteroides dominate the HGM), Type 2 (where Prevotella is prevalent), and Type 3 (where Ruminococcus is plentiful). Other genera of bacteria always exist within each enterotype – the Types simply indicate the largest bacterial group by proportion.


Problem foods are not always obvious and can mutate over time.

Enterotypes can alter over time, normally due to prolonged dietary changes. Type 1 is associated with digestion of proteins and saturated fats. Type 2 is linked with carbohydrates and simple sugars while Type 3 prefers complex carbohydrates and insoluble fibres – note that these types are only fuzzy classifications which can overlap substantially. A sudden change in diet can promote certain bacteria temporarily (though in general the original enterotype will revert eventually) – but while the enterotype is disrupted, the event may manifest itself as bodily discomfort and/or diarrhoea or constipation.

Other enterotype disruptive agents include tobacco, medications (especially antibiotics), alcohol, stress, pesticides, pollution, bacterial invasion, etc.

Persistent disruption of HGM balance via long-term exposure to problem diets and disruptive agents will simply end up with HGM deterioration.

The effect of a dysfunctional HGM

Dysbiosis (impairment of the HGM) manifests itself in ways which may not appear connected to dietary issues – this is the disconcerting peculiarity: certain health problems do not seem linked to the probable root cause. However it is still too early to confirm direct causal relationships between HGM and disease – but, as an example, some findings about Parkinson’s Disease (PD) are worth noting.

Compared to normal people, patients with PD have much higher concentrations of E. coli bacteria in their guts, along with more bacteria associated with the production of lipopolysaccharides, an endotoxin which aggravates tissue inflammation. PD is also associated with constipation and “leaky gut” syndrome, where intestinal walls are weakened, allowing the dangerous interchange of pathogens and toxins between the intestines and the blood stream – this may be due to degradation of the intestinal mucus lining caused by excessive numbers of bacteria such as Akkermansia muciniphila. An initial major event during the development of PD appears to be damage to the neurons in the ENS which then spreads to the central nervous system and motor neurons in the brain.

Pathologies of other disorders such as autism, kidney disease, liver disease, metabolic syndromes (such as diabetes, obesity, heart disease) and gastrointestinal issues (such as Irritable Bowel Syndrome, Crohn’s Disease, Clostridium difficile infection, etc) now also appear traceable to dysbiosis. Whether a malfunctioning HGM is always the prime cause of these conditions is debatable – but regardless of the root cause, it is indisputable that dysbiosis can be a contributing factor in the progression of many diseases.

Oops – now what?

So if a bout of overindulgence or encounter with a disruptive agent distresses your HGM, there are some things to consider. Firstly, chances are good that balance will be restored over time, though recovery is affected by age – older people take longer to restore their normal enterotypes. However, in some cases, the HGM may never recover if the disruptive event is overwhelming – more on this later.

Next is awareness of the symptoms of disruption, and avoiding things which may further aggravate matters. As a personal example, a sense of unease and constipation are signals which prompt abstinence from alcohol and rich foods. It is now time for fructans and dietary oligosaccharides (insoluble fibres used as food by HGM), eg. inulin (found in leeks, okra, etc) and galacto-oligosaccharides (lentils, chickpeas, etc). By weight, the HGM in adults weigh around 500g – and normal daily excretion removes up to 20% of this mass. With this amount of attrition, HGM needs to feed well to propagate itself, especially after some trauma.

Third point is drink lots of water, particularly if suffering from alcoholic dehydration. Insoluble fibre also needs water to progress through the gut better.


Aged cheeses and natural cheese rinds contain lots of good bacteria and can help counter HGM. Photo: The Star/Yap Chee Hong

Yoghurts and drinks fermented with probiotic bacteria are sold in many supermarkets. However, in almost all cases, over 99% of the bacteria (usually from the genera Bifidus and Lactobacillus) are killed by stomach acids before it reaches the intestines – so an alternative may be pills of bacterial spores which can survive stomach acids. Or ingest aged cheeses and natural cheese rinds which contain lots of good bacteria. Whichever option you choose, eat some insoluble fibre beforehand.

Recovering from dysbiosis

Frankly, some people may never recover fully from dysbiosis. Once gut pathogens are firmly established or the intestinal lining is severely compromised, there is no easy return to a harmonious gut environment – for example, treatments such as medications/antibiotics would likely damage the remaining good bacteria as much as the pathogens. Faecal transplants from healthy donors appear thus far the best option to treat dysbiosis-related gastrointestinal problems.


As for other diseases now qualitatively linked to faulty HGM, the best preventive options are care and vigilance as reliable diagnostics are presently unavailable. Paying attention to your HGM may really save your life.

I enjoy overindulging occasionally with family and friends, and I do not intend to stop – however I am aware of the obligation to my HGM afterwards and this is something I then manage fastidiously via a temperate diet, or else risk damage and dysbiosis.

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