The gut microbiota
Gut microbiota: why is it that important for your health?
We have trillions1 of bacteria that populate our intestine with fascinating powers on the human body. Let’s understand how your intestinal microbiota works and why you should take care of it!
About this article
Table of contents
Table of contents
What is exactly the human gut microbiota?
You probably have already heard about the “gut flora”, well, scientifically, it is called “the intestinal microbiota” or to put it more simply “the gut microbiota”. It consists of trillions1 of (sidenote: Microorganisms Living organisms that are too small to be seen with the naked eye. They include bacteria, viruses, fungi, archaea and protozoa, and are commonly referred to as “microbes”. What is microbiology? Microbiology Society. ) that populate your intestines like bacteria, viruses, fungi (including yeasts), and even parasites.
By the way, microbiota and microbiome are two words often used as one to the other but they have two different meanings while microbiota is used to talk about the microorganism and answer the question “who is there?” basically the “individuals”, the microbiome talks about their genome “what is inside of them”2 to answer the question “what are they doing” meaning their function.
Each one of us has a unique microbiota, like a fingerprint.1 When you’re born, fecal and vaginal microorganisms transmitted by your mother during vaginal delivery, or environmental microorganisms for cesarean delivery,3 induce the start of your gut microbiota colonization4. It takes around three years for the gut microbiota to build up, diversify and stabilize.5 During adulthood,6 the composition is relatively stable until old age when it undergoes profound changes again to become slightly impoverished.7
Why is the gut microbiota a key player for your health?
The gut microbiota can be considered a functional organ of the human body. It works closely with your intestines and have 4 important roles:
by helping with the absorption of nutrients (sugars, amino acids, vitamins…) by intestinal cells or with the fermentation of the small fraction of food. These fermentation processes produce gas and numerous metabolites, including short-chain fatty acids, a real “fuel” for the cells in your colon.8
by having an active role in the production of gastrointestinal mucus, the irrigation of intestinal cells, and the enzymatic activity of the mucosa.9
against pathogens and toxins.10 Furthermore, some bacteria release antimicrobial molecules against the (sidenote: Pathogens A pathogen is a microorganism that causes, or may cause, disease. Pirofski LA, Casadevall A. Q and A: What is a pathogen? A question that begs the point. BMC Biol. 2012 Jan 31;10:6. ) bacteria while others stimulate the production of mucus to protect intestinal cells from attacks and avoid harmful effects on your body.11
in developing the human immune system. Bacteria of the gut flora are involved in the maturation and activation of cells in the intestinal immune system, which protects you from attacks by pathogenic agents like bacteria and viruses. The intestine is the primary reservoir for immune cells in your body. For its part, the immune system influences the composition and diversity of microbiota.12
Unbalanced gut microbiota: what are the associated diseases?
What is an unbalanced gut microbiota?
The composition of the gut microbiota is characterized by its high diversity (number of different species present in an individual) and its abundance (total number of microorganisms present). When the composition is disrupted, the balance is broken, and a (sidenote: Dysbiosis Generally defined as an alteration in the composition and function of the microbiota caused by a combination of environmental and individual-specific factors. Levy M, Kolodziejczyk AA, Thaiss CA, et al. Dysbiosis and the immune system. Nat Rev Immunol. 2017;17(4):219-232. ) emerges,13 which can be associated with several diseases all along the body. Dysbiosis, cause or consequence of these diseases? The question has not yet been answered with certainty by scientific studies.
Let’s have a look to some diseases associated with intestinal dysbiosis: antibiotic associated diarrhea, infantile colic, gastroenteritis, inflammatory bowel diseases (IBS)...:
Infantile colic 14 that affects 20 to 25% of infants between the age of 1 and 4 months
Antibiotics associated diarrhea, which happens between 5 and 35% of patients taking antibiotics15
Traveler’s diarrhea is an infection caused by contaminated food or contaminated. Postinfectious irritable bowel syndrome may occur in 3% to 17% of patients who had this infection16
Gastroenteritis generally benign and most often viral is responsible for over 200,000 deaths of children per year worldwide17
Obesity is a common, costly, and serious chronic disease that affected 13% of the world’s adult population (11% of men and 15% of women) in 201618
IBS is one of the most functional gastrointestinal disorders characterized by abdominal pain and alterations in the host’s bowel habits (constipation, diarrhea, or alternations). The prevalence varies substantially between countries19
Crohn’s disease is an inflammatory bowel disease, where inflammation can be localized at all stages of the digestive system, from the mouth to the anus. Recent studies provide evidence that the gut microbiota plays an important function in the etiopathogenesis of this disease20
Stomach cancer21 and colorectal cancer22 are two gastrointestinal cancers associated with gut microbiota dysbiosis
But the role of the human gut microbiota doesn’t stop at the gut: recent studies have identified that the gut microbiota may play a role beyond the gastrointestinal tract. In fact, gut microbiota has been associated with several extra-intestinal diseases: for example, acne23 , allergies24 , obesity,25 anxiety disorders,26 autism-spectrum disorders26…And that’s not all of it. It seems that gut microbiota can also be associated with neurodegenerative diseases like Alzheimer’s,27 Parkinson’s.28 In fact, there is bidirectional communication between the gut and the brain, named “gut- brain- axis”, and gut microbiota could influence these interactions. That is why your gut is sometimes called your second brain.
How to take care of your microbiota? You can have a direct influence on it
You know by now the central role of the gut microbiota in human health. So how should you take care of your own microbiota? Many scientific studies raised the question of how to avoid any disruption in its composition and keep it as balanced as possible.29 The answer is not as simple as bring in good bacteria or yeast to fill or enrich the existing microbiota or replace the bad ones. In fact, the idea is to influence the microbiota to help it to function smoothly thereby improving host health.30
How? You have several ways of positively affecting the balance and the diversity of the gut microbiota and each of them has its own specific features:
Diet: the diversity and quality of what we eat contribute to the balance in our intestinal microbiota.31,32 On the other hand, a poorly balanced diet can affect the composition of our gut and lead to some conditions.33 It is important to know what type of food has a beneficial effect or a negative one to keep our gut in shape!34
Probiotics: Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host.35,36 Check for more information here how they work on our microbiota to improve health
Prebiotics: Prebiotics are specific non-digestible dietary fibers conferring a health benefit, they are selectively utilized by beneficial microorganisms in the host’s microbiota.37,38 Some foods are particularly rich in prebiotics, that’s why it is important to pay attention to our diet. When they are added to probiotics in some specific products, we call them symbiotics.39
Transplant: as for the organs, gut microbiota can be transferred to an individual in an attempt to restore equilibrium amongst the gut microbial ecosystem.32 Known as fecal microbiota transplant (FMT), this therapeutic approach is only validated to cure recurrent Clostridioides difficile–associated disease32 and is still under active research to evaluate its effect on other specific health conditions such as Crohn's disease, ulcerative colitis, irritable bowel syndrome, or metabolic disease32… Check for more information here.
The Biocodex Microbiota Institute is dedicated to education about human Microbiota for General Public and Healthcare Professionals, it doesn't give any medical advice.
We recommend you to consult a healthcare professional to answer your questions and demands.
1 Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell. 2006 Feb 24;124(4):837-48.
2 Ursell LK, Metcalf JL, Parfrey LW, et al. Defining the human microbiome. Nutr Rev. 2012;70 Suppl 1(Suppl 1):S38-S44.
3 Callaway E. C-section babies are missing key microbes [published online ahead of print, 2019 Sep 18]. Nature. 2019;10.1038/d41586-019-02807-x.
4 Sandall J, Tribe RM, Avery L, et al. Short-term and long-term effects of caesarean section on the health of women and children. Lancet. 2018;392(10155):1349-1357.
5 Bäckhed F, Roswall J, Peng Y, et al. Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. Cell Host Microbe. 2015;17(5):690-703.
6 Yatsunenko T, Rey FE, Manary MJ, et al. Human gut microbiome viewed across age and geography. Nature. 2012 May 9;486(7402):222-7.
7 Ragonnaud E, Biragyn A. Gut microbiota as the key controllers of "healthy" aging of elderly people. Immun Ageing. 2021 Jan 5;18(1):2.
8 Jandhyala SM, Talukdar R, Subramanyam C, et al. Role of the normal gut microbiota. World J Gastroenterol. 2015 Aug 7;21(29):8787-803.
9 Tomas J, Wrzosek L, Bouznad N, B, et al. Primocolonization is associated with colonic epithelial maturation during conventionalization. FASEB J. 2013 Feb;27(2):645-55.
10 Caballero S, Pamer EG. Microbiota-mediated inflammation and antimicrobial defense in the intestine. Annu Rev Immunol. 2015;33:227-56.
11Sokol H. Microbiota and barrier effect. In: Marteau P, Dore J, eds. Gut Microbiota: A Full-Fledged Organ. Paris: John Libby Eurotext; 2017:65-71.
12 Brandtzaeg P. Role of the Intestinal Immune System in Health. In: Baumgart, Daniel C, eds. Crohn's Disease and Ulcerative Colitis: From Epidemiology and Immunobiology to a Rational Diagnostic and Therapeutic Approach. Springer International Publishing; 2017
13 Levy M, Kolodziejczyk AA, Thaiss CA, et al. Dysbiosis and the immune system. Nat Rev Immunol. 2017;17(4):219-232.
14 Perceval C, Szajewska H, Indrio F, et al. Prophylactic use of probiotics for gastrointestinal disorders in children. Lancet Child Adolesc Health. 2019 Sep;3(9):655-662.
15 McFarland LV. Antibiotic-associated Diarrhea: Epidemiology, Trends and Treatment. Future Microbiol. 2008 Oct;3(5):563-78.
16 Steffen R, Hill DR, DuPont HL. Traveler's diarrhea: a clinical review. JAMA. 2015 Jan 6;313(1):71-80.
17 Stuempfig ND, Seroy J. Viral Gastroenteritis. In: StatPearls. Treasure Island (FL): StatPearls
18 WHO. Fact sheets on obesity and overweight June 2021
19 Oka P, Parr H, Barberio B, et al. Global prevalence of irritable bowel syndrome according to Rome III or IV criteria: a systematic review and meta-analysis. Lancet Gastroenterol Hepatol. 2020 Oct;5(10):908-917.
20 Aldars-García L, Marin AC, Chaparro M, et al. The Interplay between Immune System and Microbiota in Inflammatory Bowel Disease: A Narrative Review. Int J Mol Sci. 2021 Mar 17;22(6):3076.
21 Nasr R, Shamseddine A, Mukherji D, et al. The Crosstalk between Microbiome and Immune Response in Gastric Cancer. Int J Mol Sci. 2020 Sep 9;21(18):6586.
22 Ranjbar M, Salehi R, Haghjooy Javanmard S, et al. The dysbiosis signature of Fusobacterium nucleatum in colorectal cancer-cause or consequences? A systematic review. Cancer Cell Int. 2021;21(1):194.
23 Dreno B, Dagnelie MA, Khammari A, et al. The Skin Microbiome: A New Actor in Inflammatory Acne. Am J Clin Dermatol. 2020 Sep;21(Suppl 1):18-24.
24 Houghteling PD, Walker WA. From Birth to "Immunohealth," Allergies and Enterocolitis. J Clin Gastroenterol. 2015 Nov-Dec;49 Suppl 1(0 1):S7-S12
25 Ley RE, Turnbaugh PJ, Klein S, et al. Microbial ecology: human gut microbes associated with obesity. Nature. 2006 Dec 21;444(7122):1022-3.
26 Maiuolo J, Gliozzi M, Musolino V, et al. The Contribution of Gut Microbiota-Brain Axis in the Development of Brain Disorders. Front Neurosci. 2021 Mar 23;15:616883.
27 Qian XH, Song XX, Liu XL, et al. Inflammatory pathways in Alzheimer's disease mediated by gut microbiota. Ageing Res Rev. 2021 Mar 9;68:101317.
28 Lorente-Picón M, Laguna A. New Avenues for Parkinson's Disease Therapeutics: Disease-Modifying Strategies Based on the Gut Microbiota. Biomolecules. 2021 Mar 15;11(3):433.
29 ILSI Europe, 2013 Probiotics, Prebiotics and the Gut Microbiota. ILSI Europe Concise Monograph. 2013:1-32.
30 Quigley EMM. Prebiotics and Probiotics in Digestive Health. Clin Gastroenterol Hepatol. 2019;17(2):333-344.
31 Tap J, Furet JP, Bensaada M, et al. Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults. Environ Microbiol. 2015 Dec;17(12):4954-64.
32 Quigley EMM, Gajula P. Recent advances in modulating the microbiome. F1000Res. 2020;9:F1000 Faculty Rev-46. Published 2020 Jan 27.
33 Zmora N, Suez J, Elinav E. You are what you eat: diet, health and the gut microbiota. Nat Rev Gastroenterol Hepatol. 2019 Jan;16(1):35-56
34 Wilson AS, Koller KR, Ramaboli MC, et al. Diet and the Human Gut Microbiome: An International Review. Dig Dis Sci. 2020;65(3):723-740.
35 FAO/OMS, Joint Food and Agriculture Organization of the United Nations/ World Health Organization. Working Group. Report on drafting guidelines for the evaluation of probiotics in food, 2002.
36 Hill C, Guarner F, Reid G, et al. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol. 2014;11(8):506-514.
37 Gibson GR, Roberfroid MB. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics .J Nutr, 1995; 125:1401-12.
38 Gibson GR, Hutkins R, Sanders ME, et al. Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol. 2017;14(8):491-502.
39 Markowiak P, Śliżewska K. Effects of Probiotics, Prebiotics, and Synbiotics on Human Health. Nutrients. 2017;9(9):1021.
40 Bay L, Barnes CJ, Fritz BG, et al. Universal Dermal Microbiome in Human Skin. mBio. 2020;11(1):e02945-19.
41 Neugent ML, Hulyalkar NV, Nguyen VH, et al. Advances in Understanding the Human Urinary Microbiome and Its Potential Role in Urinary Tract Infection. mBio. 2020 Apr 28;11(2):e00218-20.
42 Greenbaum S, Greenbaum G, Moran-Gilad J, et al. Ecological dynamics of the vaginal microbiome in relation to health and disease. Am J Obstet Gynecol. 2019 Apr;220(4):324-335.
43 Radaic A, Kapila YL. The oralome and its dysbiosis: New insights into oral microbiome-host interactions. Comput Struct Biotechnol J. 2021 Feb 27;19:1335-1360.
44 Xu Q, Gill S, Xu L, et al. Comparative Analysis of Microbiome in Nasopharynx and Middle Ear in Young Children With Acute Otitis Media. Front Genet. 2019;10:1176.
45 Mathieu E, Escribano-Vazquez U, Descamps D, et al. Paradigms of Lung Microbiota Functions in Health and Disease, Particularly, in Asthma. Front Physiol. 2018 Aug 21;9:1168.