Health Articles

The Human Microbiome and Our Health

If you haven’t heard about the connection between the human microbiome and our health yet, you’ve probably been living under a rock – there’s been tons of news articles, blog posts, research studies etc. about this topic in recent years.

Type in ‘human microbiome’ into PubMed (the database for scientific research) and you’ll be rewarded with over 30.000 results!

Although the topic has probably been covered enough, I’d like to offer my own little summary here to use as future reference on my blog and for completeness sake.

What is The Microbiome?

The term microbiome refers to the collective genomes of microbes living in a certain environment, in this case in and on the human body. The term microbiota is often used synonymously and refers to an ecological community of microbes.

When we talk about the human microbiome, we often refer to the gut microbiome as the digestive tract houses the biggest number of microbes. However, other body sites also have their own microbiome – the mouth, genitals, skin, airways and of course the bladder.

Over the course of evolution, humans have co-evolved as ‘superorganisms’ with the microbes living in and on us, especially those living in the gut (the most densely populated body site) [1]. These microbes include bacteria, fungi and other organisms such archae, eukarya, viruses and helminths [12].

More recent methods of DNA sequencing have allowed advances in microbiome research [2], whereas previously we were only able to look at the microbes that can be cultured (grown) in a lab (and 60-80% of microbes can’t be cultured in a lab! [3]).

While there are still many unknowns, it has been estimated that we have 150 times more microbial genes than we have human genes [1] – some say we’re really only 10% human after all! Up to 1000 different species may be present in the gut microbiota and the species vary greatly between individual humans [1] and together they weigh around the same as our brain [3].

The human body with its microbiome has been described as an ‘ecosystem’ [1] that is dynamic and changes and adapts with us.

How Microbiota Develops and Changes

It is believed that our first set of microbes is acquired during birth in the mother’s birth canal and then is ‘boosted’ through breastmilk, which contains food for beneficial Bifidobacteria in the infant’s gut [4]. Additionally, we now know that we may already acquire some microbes in the placenta [10].

The infant’s gut microbiota then develops and matures over the first 3 years of life and especially in the first year [5] until it looks more like an adult’s microbiota.

Mode of delivery and breastfeeding have a huge impact on the development and composition of the gut microbiota and it’s the cessation of breastfeeding that drives the biggest shift towards developing an adult-like gut microbiota [5].

Several other factors impact how the microbiota develops and changes (I’m talking mainly about the gut here, but this could affect all body sites including the bladder):

  • Diet: Both a person’s long term dietary habits but also short term changes in these habits can lead to a shift in the kinds of microbes that live in our gut [1].
  • Antibiotics: Because antibiotics are capable of killing all bacteria and not just the strains targeted, they can be a very powerful factor changing the balance of microbes in our body [6].
  • Genetics: Certain gene mutations may negatively affect the diversity of the gut microbiota as they alter the structure of the mucus layer the microbes adhere to [7].
  • Physiology: Physiological changes such as pregnancy [1] and exercise [8] can alter the composition of the microbiota.
  • Age: The microbiome changes over the course of our lifetime from early infancy to old age and helps exert specific functions associated with a particular age [1].
  • Hygiene: Our modern obsession with hygiene and sanitization, although healthy to some degree, also has an impact on microbial composition and diversity by reducing the environmental microbes we’re exposed to [9]. Plus antibacterial soaps etc can directly kill bacteria on our body.
  • Other changes in Environment: The microbiota can change and adapt to any change in environment (e.g. travel) [1].

The Microbiome and Health

When in good balance, the microbiome can have many positive influences on our health.

Its roles include [1]:

  • Digestion of indigestible fibres
  • Metabolism of carbohydrates
  • Production of vitamins and other nutritional co-factors and metabolites
  • Development of a balanced immune system
  • Immune-balance throughout life
  • Protection against pathogenic microbes
  • Modulation of mood, behaviour and stress response through the ‘gut-brain axis’
  • Production of short-chain fatty acids (SCFAs) that play an important role in energy production, storage and appetite and serving as ‘food’ for cells in the colon, helping to regulate immunity and inflammation


The Microbiome and Disease

While a healthy microbiome can have many health benefits, an unhealthy microbiome can have the opposite effect.

Changes in the composition of the microbiome have been implicated in an array of chronic health conditions, including [11, 12]:

  • Obesity
  • Gastrointestinal cancers
  • Inflammatory Bowel Disease (Crohn’s and Ulcerative Colitis)
  • Skin conditions: Atopic dermatitis, psoriasis, acne, eczema
  • Autoimmune conditions: e.g. Type-1 diabetes, rheumatoid arthritis
  • Atherosclerosis
  • Nervous system conditions: autism, multiple sclerosis, anxiety, depression
  • Allergies, asthma
  • Aggressive bacterial infections (e.g. C. Difficile)
  • IBS [13]
  • Interstitial cystitis [14]

Things that disrupt the Microbiota

You might have already gathered from the information above that the following influences can (negatively) impact the microbiota:

  • Antibiotics [6]
  • Birth via C-section and formula-feeding [5]
  • Excessive hygiene [9]
  • Unhealthy diet low in fibre [1]
  • Lack of exercise [8]

These are just some examples, there are most likely other influences that can also play a role such as stress and other medications.

Things that may boost the Microbiota

Here are some things that may positively impact the microbiota:

  • Prebiotic fibre
  • Exposure to dirt, animals
  • Exercise
  • Probiotic foods
  • Natural birth and breast-milk


When looking at health or disease we can now no longer look at just us, or even just a single organ system – we need to also consider the microbes living in and on us!

While changes in the microbiome are indicated in disease states, there are still many things we don’t know – e.g. is it the disease that drives the change in the microbiome or is it the change in the microbiome that drives the disease.

It also becomes more and more difficult to find a truly ‘unchanged’ microbiome in our modern world so we still don’t know exactly what a ‘healthy’ microbiota necessarily looks like (although we do know about some important key species).

The good news is that because the microbiome is dynamic in nature we have the chance to manipulate it with diet and lifestyle changes.

We also have the chance to use it for therapeutic purposes, for example as faecal microbiota transplants (FMT) and probiotics [15].

For me personally I don’t just consider myself anymore when it comes to what I eat or do, I also think about my little friends!

Now I’d like to hear from you: How do you think your microbiome has impacted your health? Let me know in the comments!

Pin it for later:


  • BioCare Education Series Digestion in Practice 2017
  1. Quercia, S. et al From lifetime to evolution: timescales of human gut microbiota adaptation. Front Microbiol. 2014 Nov 4;5:587
  2. Kim, Y et al Deciphering the human microbiome using next-generation sequencing data and bioinformatics approaches. Methods. 2015 Jun;79-80:52-9.
  3. Warinner, Christina et al. “Ancient Human Microbiomes.” Journal of human evolution 0 (2015): 125–136. PMC. Web. 12 Dec. 2017.
  4. Zivkovic, A et al Human milk glycobiome and its impact on the infant gastrointestinal microbiota PNAS March 15, 2011 [vol. 108 no. Supplement 1]
  5. Baeckhed, F et al Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. Cell Host Microbe. 2015 May 13;17(5):690-703.
  6. Yoon MY, Yoon SS. Disruption of the Gut Ecosystem by Antibiotics. Yonsei Med J. 2018 Jan;59(1):4-12.
  7. Rausch, P et al Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype PNAS November 22, 2011 [vol. 108 no. 47]
  8. O’Sullivan, Orla et al. “Exercise and the Microbiota.” Gut Microbes 6.2 (2015): 131–136. PMC. Web. 12 Dec. 2017.
  9. Ege, Markus The Hygiene Hypothesis in the Age of the Microbiome AnnalsATS Issues Vol. 14, No. Supplement_5 | Nov 01, 2017
  10. Thomas, Sunil et al. “The Host Microbiome Regulates and Maintains Human Health: A Primer and Perspective for Non-Microbiologists.” Cancer research 77.8 (2017): 1783–1812. PMC. Web. 14 Dec. 2017.
  11. Muszer, Magdalena et al. “Human Microbiome: When a Friend Becomes an Enemy.” Archivum Immunologiae et Therapiae Experimentalis 63.4 (2015): 287–298. PMC. Web. 11 Dec. 2017.
  12. Thomas, Sunil et al. “The Host Microbiome Regulates and Maintains Human Health: A Primer and Perspective for Non-Microbiologists.” Cancer research 77.8 (2017): 1783–1812. PMC. Web. 14 Dec. 2017.
  13. Distrutti, Eleonora et al. “Gut Microbiota Role in Irritable Bowel Syndrome: New Therapeutic Strategies.” World Journal of Gastroenterology 22.7 (2016): 2219–2241. PMC. Web. 14 Dec. 2017.
  14. Braundmeier-Fleming, A. et al. Stool-based biomarkers of interstitial cystitis/bladder pain syndrome. Rep. 6, 26083
  15. Ravel, Jacques et al. “Human Microbiome Science: Vision for the Future, Bethesda, MD, July 24 to 26, 2013.” Microbiome 2 (2014): 16. PMC. Web. 14 Dec. 2017.


  • Reply


    December 18, 2017

    Thanks Layla for your research and work so we can educate ourselves and lovingly treat our whole bodies!

    • Reply


      December 19, 2017

      🙂 my pleasure!

  • Reply

    Lina Preszler

    January 2, 2018

    I am constantly on antibiotics for uti. After reading your research I’m sure that antibiotics are ruining my microbiome. I just can’t seem to get off this merry go round! I take a lot of probiotics between my rounds of antibiotics/uti.

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