What is The Gut Microbiome? – Dysbiosis and Care in the Community

The gastrointestinal system is home to a thriving and diverse microbial ecosystem otherwise known as the gut microbiome.

This community represents an estimated 100 trillion microorganisms, and while the microbiome can consist collectively of up to 1,000 different species, a few dominant bacterial species are the major inhabitants.

Comprising 99% bacteria, the microbiome also harbours some yeast, viruses and pathogens that can impact on the wider community. External environmental factors (in particular diet), directly influence microbial balance. Poor nutrition reduces the diversity and alters the finely tuned balance of this gut ecosystem, leading to what is medically termed, dysbiosis.

The gut microbiome is increasingly appreciated for the role it plays in health and disease, so much so that it has been referred to as the ‘Forgotten Organ’.

A concentrated effort by European and US scientific consortiums to study the genetic diversity of the human microbiome has revealed considerable complexity and person-person variability in gut microflora.

Scientists are striving to understand how the contribution of specific species, their abundance and/or the interplay of microorganisms within a community, can influence health. What is clear is that the gut microbiome and its human host can work together, symbiotically, to avoid microbial imbalance, and the more diverse an individual’s gut microflora are, the better for that person’s wellbeing.

Gut bacteria.

Representation of gut bacteria.

A microbiome containing too many so-called ‘bad’ bacteria and not enough (or the right combinations) of ‘good’ bacteria has been connected with an increasing number of common diseases, including but not limited to: colorectal and gastro-intestinal cancers, immune-based inflammatory diseases such as inflammatory bowel disease, rheumatoid arthritis and multiple sclerosis; cardiometabolic disease including obesity, type II diabetes and hypertension; and increased risk of allergies such as asthma.


While diet has the largest impact on the gut microbiome in children and adults, the earliest inhabitants of this microbial community are established at birth and during the first few years of life, representing a critical phase in the ‘training’ of the immune system that can have life-long consequences for health and disease.

The colonisation of an infant’s gut microbiome is impacted by various factors, including the mode of delivery (vaginal vs. Caesarean), which affects the source of maternal microbes the baby is exposed to, and feeding type (breast vs. formula), which can significantly impact on the diversity of the child’s gut microbiome.

Regular contact with dogs can benefit the gut microbiome. Owning a dog alters the gut microbiome, with all members of the household sharing similar microbiomes, and it is proposed that early infant exposure to dogs may lead to greater gut microbiome diversity and a lowered risk of certain allergies.

In adults, the gut microbiome is associated with a range of morbidities, some of which are unexpectedly far reaching.

The ‘gut-brain axis’ describes chemical signalling between intestinal microorganisms and the brain. Studies have linked altered gut microflora composition with brain disorders including Alzheimer’s, Parkinson’s, and mental health illnesses, although this research is very much in its infancy.

Of potential interest to shift workers or those that travel frequently, reduced sleep causing disrupted Circadian rhythm, negatively influences the gut microbial balance, which is linked to increased inflammation and risk of cardiometabolic disease and obesity.

While the connection between high caloric intake and obesity is well established, a new concept is emerging that describes a relationship between diet, gut microbial balance and energy metabolism. Gut microbes support digestion and the release of nutrients and energy from food. However, too high a balance of energy harvesting bacteria, dictated by the types of food consumed, can strongly affect energy metabolism and the potential to gain weight.

Building a Thriving Community

So what measures can be taken to modulate the gut microbiome?

In extreme cases, faecal transplantation for the treatment of Clostridium difficile infection can be highly effective and involves the re-colonisation of the gastrointestinal system with microflora from a healthy donor; however the jury is still out on the effectiveness of this procedure in treating other chronic inflammatory-related bowel disorders.

Rather more palatably, supplementing diet with probiotic cultures, commonly containing strains of Lactobacillus and Bifidobacterium, may reduce dysbiosis-associated inflammation and be beneficial when the gut microbiome balance is compromised.

However in the long-term, nutrition is key, and the more diverse a diet is, the more diverse and healthy the microbiome will be.

This is of particular relevance for patient cohorts in long-term care. For example, it is shown that those older adults in long-term residential care with an unvaried diet have decreased gut microflora diversity and are frailer, compared to their counterparts still residing in the community.

Thus, diet should be considered an important factor in long-term care plans.

Whilst taking into account that the causal vs. associative effect of the gut microbiome on health outcomes are not fully teased out, our gut microorganisms do appear to have an important part to play in keeping us well, and caring for this community should not be underestimated in healthcare.

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Further Reading

  • Claesson, MJ, Brennan, L, Coakley, M, Conde, S, Cusack, S, Deane, J, Fitzgerald, AP, Fitzgerald, GF, Harnedy, N, Harris, HMB, Hill, C, Jeffery, IB, Lakshminarayanan, B, Marchesi, JR, O’Conner, EM, O’Conner, M, O’Connor, K, O’Mahony, D, O’Sullivan, O, O’Toole, PW, Power, SE, Ross, RP, Shanahan, F, Stanton, C, Van Sinderen, D & Wallace, M 2012, ‘Gut Microbiota Composition Correlates With Diet and Health in the Elderly’, Nature, vol. 488, pp. 178-184, viewed 22 September 2016, nature.com
  • Turnbaugh, PJ, Ley, RE, Mahowald, MA, Magrini, V, Mardis, ER & Gordon, JI 2005, ‘An Obesity-Assocaited Gut Microbiome with Increased Capacity for Energy Harvest’, Nature, vol. 444, pp. 1027-31, viewed 22 September 2016, http://www.nature.com/nature/journal/v444/n7122/abs/nature05414.html
  • Walsh, CJ, Guinane, CM, O’Toole, PW & Cotter, PD 2014, ‘Beneficial Modulation of the Gut Microbiome’, FEBS Letters, vol. 588, pp. 4120-30, viewed 22 September 2016, http://www.ncbi.nlm.nih.gov/pubmed/24681100
  • Xu, Z & Knight, R 2015, ‘Dietary Effects on Human Gut Microbiome Diversity’, British Journal of Nutrition, vol. 113, no. 0, pp. S1-5, viewed 22 September 2016, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405705/

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