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Gut Microbiome


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Gut Microbiome

December 6, 2023

It is widely known that the human microbiome has influence on all organ systems and is vital in regulating human development, immunity, and nutrition. There are many topics and themes that could be written about the gut microbiome and how it interacts with its host, a human(!), but this blog will focus on what the gut microbiome is, how it functions, and future research opportunities.


The human microbiome is a newly identified organ and in adults, weighs around 2.8 Kg (6 lbs)4. The human microbiome is collectively inside and outside of the body, covering the skin, in the mouth,vaginal canal, and in the digestive system/gut4. The highest concentration of the human microbiome is held in the gut and weighs about 2 Kg(3.5 lbs) in adults and is commonly known as the gut microbiome or gutmicrobiota4. The gut microbiome is made up of many different types of microbes and their genetic material, these include bacteria, fungi, protozoa, and viruses4. The gut microbiome in most humans is a harmonious and thriving community with all the microbes working together with the host (the human)4. This a commensal relationship because one is not harmful to the other. The gut microbiome predominantly lives in the colon because the conditions are near perfect for all the different microbes4.There are slight changes in pH (the acid base scale) in the different segments of the colon where you’ll find different microbes. It is estimated there is 5000different types of species (bacteria, fungi, protozoa and viruses) with a total of over 100 trillion microbes within the gut microbiome4. All the microbes that live in the gut microbiome specifically, are anaerobic which means they survive in an environment without oxygen.


From a dietary perspective, eating complex carbohydrates such as dietary fibres from both soluble and in-soluble fibre sources provide energy to the gut microbiome1. The gut microbiota metabolises, by fermentation, the fibre particles which then transform into short chain fatty acids (SCFA)1-4. Different foods produce different types of SCFA’s enzymes, such as acetate and butyrate1-4. These different SCFA enzymes work in partnership with the different microbes, regulating the gut brain axis, hormonal processes, and keeping the lumen or inner layer of the intestine healthy and strong1-4. The partnership between the microbes and the different SCFA enzymes each play a large role in the maintenance of insulin, body weight, and how energy is distributed and used within the body. The various types of SCFA enzymes originate from different foods that are minimally processed such as fruits, vegetables, whole grains and seeds. The human body requires a good supply of all the different types of SCFA so eating a variety of complex carbohydrates that contain soluble and insoluble fibre is best1-4.


Other than food, there are many other factors that influence and change the gut microbiome and are mostly from the environment. An example of factors that influence the gut microbiome include but are notlimited to, changes in extreme temperatures, location and level of exposure to soils and animals, exposure to alcohol, smoking, and antibiotics3.There is a lot of research going into exposure levels to these factors to seewhat levels increase and decrease activity of the gut microbiome2,3. It cannot be overestimated how much food and environmental exposures play a role and influence not only the gut microbiome but the human microbiome and careful consideration about what we putin our bodies and environments we live in, and visit, is paramount.


The scientific community used to think there was a correlation between the gut microbiome and how diseases develop but new research completed in the last decade has increasingly shown that certain microbes, within the gut microbiome, may be the cause of some diseases3. With current technology, this is a hard theory to definitively prove due to every single human having a different sequence of DNA (that makes them unique).Coupled with this, each human’s immediate environment, environmental temperature and foods they eat are different from the next human. Additionally, ethnic differences greatly influence a gut microbiome and how each microbe interacts with each human may be different to the next3. This may seem overwhelming but multinational research scientific groups have undertaken this challenge. The human genome project ended in 2006 where all the DNA base pairs were recorded and categorised4. Once this multinational project finished, the human microbiome project started in 2007 and finished in 2015 from the combined effort of research teams from the United Kingdom and the United States of America documenting all the human microbiome colonies4. The human genome project and the human microbiome project are complimentary and have enabled large advances, opened new research pathways and the opportunity for personalised medicine to develop to overcome all the barriers listed above4.These targeted medicines work with a person’s own gut microbiome to improve or resolve diseases. There will continue to be great leaps forward in understanding and knowledge around the gut microbiome over the next decade.


Chyme reinfusion therapy with The Insides System enables the gut microbiome to continue to flourish while a person has a high output double barrel enterostomy or enteroatmospheric fistula.

Written by

Emma Ludlow

CNS Stomal Therapist

PG Dip. Stomal Therapy, MNurs (Hons)

1. Armet, A., Deehan, E., O’Sullivan, A., Mota, J., Field, C., Prado, C., Lucey, A. and Walter, J. (2022). Rethinking healthy eating in light of the gut microbiome. Cell Host and Microbe, 30(June 8). 764-785. Doi: 10.1016/j.chom.2022.04.016

2. Baaziz, H., Baker, Z., Franklin, H. & Hsu, B. (2022). Rehabilitation of a misbehaving microbiome: phages for the remodeling of bacterial composition and function. IScience Review, 25(April 15). 1-12. Doi: 10.1016/j.isci.2022.104146

3. De Vos, W., Tilg, H., Van Hul, M. & Cani, P. (2022). Gut microbiome and health: mechanistic insights. Gut, 71. 1020-1032. Doi: 10.1136/gutjnl-2021-326789

4. The Center for Ecogenetics and Environmental Health. Fast Facts about the Human Microbiome. The University of Washington. Retrieved 16 October, 2023, from,

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