Gut bugs (aka microbiota)!


We are not alone

Gut microbiota is the term for the bacterial, fungal and yeast populations that reside in our gut. The microbiota are symbiotic (we benefit from them and they benefit from us) and have been shown to help with energy uptake from food sources as well as help with the fermentation of starchy foods.

It has been shown that the microbe population can be altered within a day from changes in diet. It has been proposed that this could have been advantageous for when people were day-to-day foragers and had diets that differed not only daily, but from season-to-season. Changes in microbiota have also been linked to obesity, where germ-free mice that are fed a high fat diet are protected from changes to adipose tissues and insulin response.

Some microbes will only produce metabolites based on the consumption of certain foods. An example is vegans vs. meat eaters. And, in the example of the obesity studies, mice given the gut microbes from obese mice only showed problems when fed the high fat diet, indicating that it is the diet that has the greatest effect on the microbes.

The microbiota are highly sensitive to changes in the diversity of the populations of microbes. Generally, certain strains are found to co-colonise the gut, however pathogenic strains can compete for food sources, which promotes the expansion of these colonies thereby reducing the number of “good microbes”.

Gut microbiota also have effects on immunity and can either contribute to or reduce inflammation in the gut, encourage resistance to or promote the growth of pathogenic bacteria, as well as influence foods allergies, particularly to dairy.

It is now also known dramatic changes in gut microbiota are linked to neurological behaviour in mice. This is due to small molecules that microbes release that can influence the release of neurotransmitters such as serotonin.

They are everywhere!

Studies of neonates have shown that the uterus is not in fact sterile, but that there are microbiota present in the umbilical cord and meconium.  It is thought that this is one way infants are first exposed to microbiota. The diversity of the post-birth microbiota, including which strains are dominant, is linked to ethnicity. However, many premature births can be triggered by intrauterine infection and microbiota present in amniotic fluid.

Certain strains are found in breast milk, which provide a defensive mechanism against pathogens in the gut while infants are still developing an immune system. Eventually, however, the microbiota introduced in breast milk are out-competed and by age 3 children have a microbiome resembling an adult. However, at the same time, an infant’s microbiome is also affected by their external environment, showing that breast milk is not the only source. An interesting observation has been that even sucking on a dummy (pacifier) can change an infant’s oral microbiome!

As mentioned, diet can alter the population, as can inflammation, which changes the absorbance and availability of nutrients required by the microbiota, however the biggest affect by far is antibiotics.

The cure and the cause

Antibiotics are without a doubt, one of the most important discoveries of the modern age. However, it is only just being realised that certain problems can arise from the over-use of antibiotics. Antibiotic treatment can reduce the diversity of gut microbes, as well as promote the expansion of pathogenic microbes. So how do we prevent the drastic effects of antibiotics on gut microbe populations, when in some cases, antibiotics are absolutely necessary?

Probiotics are now widely available and claim to introduce “good bacteria” into the gut. While these strains are found to be introduced into the gut, the overall diversity is not changed, meaning that the “good bacteria” have not become the ‘dominant’ strain.

Supplementation of infant formula milk with pre-or probiotics is becoming increasingly common despite the lack of data supporting their efficacy. The effects of the probiotics on paediatric diseases, including allergies, obesity, gastrointestinal infections or colic have been extensively studied but the benefits still remain controversial. Some interesting studies have investigated administrating probiotics to neonates undergoing emergency surgery, where the risk of infection is high and have found that the probiotics had no effect. It was found that the gut microbiota was altered from the pre- and post-operative procedures, but was restored some time after the surgery. This is complemented by mouse studies that have shown that surgical procedures can cause fluctuation in the microbiota but the diversity does not differ.

Despite this, there is some evidence that probiotics can have a positive on people suffering from inflammatory bowel disease, although the location of the inflammation influences the response.

Final thought?

So what is the take home message from this? I suppose it could be ‘you are what you eat’? But in terms of that what you eat can influence your gut microbiota that has an influence on immunity, obesity, as well as neurological responses. For me, I think it is that the human body relies heavily on our environment and symbiotic relationships to function properly.

Post script: although there is the evidence that antibiotics can have a negative effect on gut microbiome, we should not forget the beneficial effect that antibiotics have. People should simply remember that it is overuse of antibiotics is the danger.




Bruce-Keller, Annadora J., et al. “Obese-type gut microbiota induce neurobehavioral changes in the absence of obesity.” Biological psychiatry 77.7 (2015): 607-615.

Heijtz, Rochellys Diaz, et al. “Normal gut microbiota modulates brain development and behavior.” Proceedings of the National Academy of Sciences 108.7 (2011): 3047-3052.

Murakami, Hiroshi, et al. “Intestinal microbiota in neonates requiring urgent surgery: assessing the role of probiotics using fecal DNA sequencing.” Pediatric surgery international 32.1 (2016): 37-43.

Sheehan, Donal, Carthage Moran, and Fergus Shanahan. “The microbiota in inflammatory bowel disease.” Journal of gastroenterology 50.5 (2015): 495-507.

Sommovilla, J., et al. “Small bowel resection induces long-term changes in the enteric microbiota of mice.” Journal of Gastrointestinal Surgery 19.1 (2015): 56-64.

Tamburini S, Shen N, Wu HC, Clemente JC. The microbiome in early life: implications for health outcomes. Nature Medicine. 2016;22:713-22.


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