The Human Microbiome
3rd Jul, 2019

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Human Microbiome Essentials


The human gut microbiome is a collection of tens of trillions of microorganisms populating the intestine. Bacteria are the predominant organisms, and most research is focused on them due to their high abundance and high diversity (see Figure 1). However, it also includes viruses, phages and fungi. The gut microbiota encompasses all microorganisms inhabiting the intestinal tract and their respective genomes (1).

The microbiome is a complex of interconnected ecological communities that communicate, cross-feed, recombine, and coevolve (2). The gut microbes perform a wide range of useful and health-promoting activities, however, they can also be responsible for the production of harmful molecules related to the development of several diseases (3).

Despite their omnipresence, centrality to life, and clear link to health and disease, we are only beginning to understand how microbes interact with each other and their hosts.

Figure 1. The predominant phyla and genera found in the intestinal microbiota. Adapted from (4) under CC BY 4.0

 Human Micrrobiome Fig 1



Traditional Understanding

Microbiome-based treatments have existed for many years and mostly include dietary recommendations and supplements from fermented milk products. These have evolved into the use of probiotics (5).


Latest Research

The complexity of the microbiota necessitates a movement from reductionist approaches that focus on individual pathogens in isolation to more holistic approaches that focus on interactions among members of the community and their hosts (2). The microbiome is recognised as an increasingly important component of disease prevention and treatment, more recently in the realm of chronic non-communicable diseases (6). Some of the current topics of interest and recent findings, outside of the traditional gastrointestinal disease association, include identification of:


Gut-brain axis

Gut microbiota can play an important role in the brain’s physiological, behavioural, and cognitive function. The microbiota has been implicated in the aetiology and progression of autism spectrum disorder, Parkinson’s, Alzheimer’s, behavioural impairment, anxiety and major depressive disorders (7,8,9)


Gut-lung axis

Microbial dysbiosis in the gut and the lung is increasingly being associated with the incidence and severity of asthma. The gut microbiota can influence immune responses at distant sites (such as the lung) via multiple mechanisms, including histamine release and immune effects of an increase in short chain fatty acids (SCFAs) (10,11)


Gut-liver axis

Growing evidence suggests a connection between alterations in the gut microbial composition and chronic liver diseases. The gut microbiota may modulate alcohol liver disease, non-alcoholic fatty liver disease, cirrhosis, and even hepatic carcinoma (12,13,14).


Gut-bone axis

The gut microbiota is responsible for bone physiology, regulating bone mass via the immune system and promoting bone resorption and formation via SCFA production (10)


Gut-vascular axis

Most cardiovascular disease (CVD) risk factors, including ageing, obesity, certain dietary patterns, and a sedentary lifestyle, have been shown to induce gut dysbiosis. Microbial components and metabolites may facilitate the development of CVD (15)


Gut-kidney axis

Microbiota metabolites influence chronic kidney disease progression, during which the kidney is no longer able to deal with microbial-derived uremic toxins (16)


The microbiome is also being studied in relation to the following areas of health:

  • Cancer - Aetiology, progression and interaction with oncology treatment (12)
  • Metabolic diseases - For example, obesity, diabetes (17,18,19)
  • Cardiovascular disease – For example, the effect on lipid profiles and reducing hypertension (20,21,22,23)
  • Immunomodulation - For example, the effect on vaccinations, allergy and autoimmune disease (11,24,25)
  • Personalised nutrition – Individual differences in nutrient bioavailability, absorption, and even glycaemic response (26,27,28,29)
  • Environmental impact - Environmental exposure, including smoking, impacts the microbiome, and the microbiome plays a role in metabolising environmental chemicals (30,31)
  • Microbiota-drug interactions – The microbiota can affect drug metabolism and may alter drug efficacy (32). Similarly, medications (including non-antibiotics) can alter the microbiome (33)
  • Systemic inflammation (11)
  • Interaction with the human genome - The microbiome is associated with both host genetic variations and host gene expression(5). Host genetics have been shown to have a minor role in microbiome composition, with environmental factors having a greater impact (34)
  • Lifestyle factors - For example, exercise, sleep deprivation, stress and weight loss (11,35,36,37)
  • Circadian rhythms - The composition of the gut microbiome is influenced by circadian rhythm, which also then affects host circadian cycles and alters hormone regulation (11)
  • Pancreatic diseases - Gut microbial dysbiosis is thought to contribute to the pathogenesis of pancreatic diseases such as pancreatitis and pancreatic cancer (38


Treatment Options 



Probiotics are live microorganisms which can boost the abundance of specific microbial species and may be consumed in fermented foods such as yoghurt or as capsulated supplements. Individual strain probiotic supplementation has been shown to be beneficial in many areas (15).

Delivering a single strain compared to a combination of bacteria in probiotic formulations is an important consideration, as each strain may have a different impact on microbial structure/function or on the host immune response (39,40). Circumstantial evidence supports the use of multistrain probiotics, particularly those with a high number of different strains. It’s possible that more strains convey more chances of success, a broader spectrum of efficacy and multistrain probiotics may provide additive or synergistic effects (41,42). Further research is required to confirm these effects.

Table 1. Recent and current Cochrane Reviews on probiotics

Microbiome Table 1


Prebiotics are non-digestible food ingredients such as dietary fibres and other digestion-resistant carbohydrates, which “feed” the microbiome. Carbohydrate fermentation by the gut microbiota produces SCFAs, which have wide-ranging physiological effects. Future trends may expand beyond fermentable substances to include novel prebiotics, such as bacteriophages, that can modulate the growth of certain bacteria and improve host health (15).



Psychobiotics are probiotics and prebiotics that have the potential to relieve neuropsychiatric symptoms, with compelling evidence for use in mental health (53).



Dietary effects on the human gut microbiome are rapid and driven by quality and quantity of dietary fat and carbohydrates (1). The typical Western diet may permanently reduce the capacity of the gut to support diversity.



Postbiotics refers to soluble factors (products or metabolic by-products) secreted by live bacteria or released after bacterial lysis. They have a clear chemical structure, safe dose parameters and a long shelf life which offer advantages over probiotics. Evidence shows that postbiotics possess antimicrobial, antioxidant, and immunomodulatory properties (54).

Paraprobiotics, also known as “non-viable probiotics”, refer to inactivated (non-viable) microbial cells, which, when administered in sufficient amounts, confer benefits to human health (54).


Faecal microbiota transplantation (FMT)

FMT is a procedure in which healthy donor faecal microbiota are introduced orally or through enemas or colonoscopy into recipient patients (1). They have become increasingly standardised products that are becoming acceptable to mainstream medicine. It has shown to be a promising treatment for recurring C. difficile infections, and current research is exploring its use in other areas of health, such as obesity, type 2 diabetes, inflammatory bowel diseases, non-alcoholic steatohepatitis, and recolonization after heavy antibiotic exposure (5,15).


Takeaway on the Microbiome

The vast body of evidence which is accumulating at a rapid pace is showing some very exciting trends in the field of the human gut microbiome and potential for disease prevention and treatment. Relatively cheap and easy to implement options through diet and probiotic/prebiotic supplements makes this a very promising area of clinical practice which can have an enormous impact on the lives of our clients.

1Bruce-Keller AJ, Salbaum JM, Berthoud H-R. Harnessing Gut Microbes for Mental Health: Getting From Here to There. Biological Psychiatry. 2018 Feb;83(3):214–23.
2Layeghifard M, Hwang DM, Guttman DS. Disentangling Interactions in the Microbiome: A Network Perspective. Trends in Microbiology. 2017 Mar;25(3):217–28.
3De Filippis F, Vitaglione P, Cuomo R, Berni Canani R, Ercolini D. Dietary Interventions to Modulate the Gut Microbiome—How Far Away Are We From Precision Medicine. Inflammatory Bowel Diseases. 2018 Apr 13.
4Shortt C, Hasselwander O, Meynier A, Nauta A, Fernández EN, Putz P, et al. Systematic review of the effects of the intestinal microbiota on selected nutrients and non-nutrients. Eur J Nutr. 2018 Feb;57(1):25–49.
5Luca F, Kupfer SS, Knights D, Khoruts A, Blekhman R. Functional Genomics of Host–Microbiome Interactions in Humans. Trends in Genetics. 2018 Jan;34(1):30–40.
6Dietert RR. The microbiome-immune-host defense barrier complex (microimmunosome) and developmental programming of noncommunicable diseases. Reproductive Toxicology. 2017 Mar;68:49–58.
7Johnson KV-A, Foster KR. Why does the microbiome affect behaviour? Nature Reviews Microbiology. 2018 Apr 24.
8Lin L, Zheng LJ, Zhang LJ. Neuroinflammation, Gut Microbiome, and Alzheimer’s Disease. Molecular Neurobiology. 2018 Mar 9.
9Zalar B, Haslberger A, Peterlin B. The Role of Microbiota in Depression - a brief review. Psychiatr Danub. 2018 Jun;30(2):136–41.
10Feng Q, Chen W-D, Wang Y-D. Gut Microbiota: An Integral Moderator in Health and Disease. Front Microbiol. 2018 Feb 21;9.
11Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. Current understanding of the human microbiome. Nature Medicine. 2018 Apr 10;24(4):392–400.
12Goodman B, Gardner H. The microbiome and cancer: The microbiome and cancer. The Journal of Pathology. 2018 Apr;244(5):667–76.
13Parker EA, Roy T, D’Adamo CR, Wieland LS. Probiotics and gastrointestinal conditions: An overview of evidence from the Cochrane Collaboration. Nutrition. 2018 Jan;45:125-134.e11.
14Tripathi A, Debelius J, Brenner DA, Karin M, Loomba R, Schnabl B, et al. The gut-liver axis and the intersection with the microbiome. Nat Rev Gastroenterol Hepatol. 2018 Jul;15(7):397–411.
15Battson ML, Lee DM, Weir TL, Gentile CL. The gut microbiota as a novel regulator of cardiovascular function and disease. The Journal of Nutritional Biochemistry. 2018 Jun;56:1–15.
16Cosola C, Rocchetti MT, Cupisti A, Gesualdo L. Microbiota metabolites: Pivotal players of cardiovascular damage in chronic kidney disease. Pharmacological Research. 2018 Apr;130:132–42.
17Davis HC. Can the gastrointestinal microbiota be modulated by dietary fibre to treat obesity? Ir J Med Sci. 2018 May;187(2):393–402.
18Kobyliak N, Conte C, Cammarota G, Haley AP, Styriak I, Gaspar L, et al. Probiotics in prevention and treatment of obesity: a critical view. Nutrition & Metabolism. 2016 Dec;13(1).
19Yao K, Zeng L, He Q, Wang W, Lei J, Zou X. Effect of Probiotics on Glucose and Lipid Metabolism in Type 2 Diabetes Mellitus: A Meta-Analysis of 12 Randomized Controlled Trials. Med Sci Monit. 2017 Jun 22;23:3044–53.
20Khalesi S, Sun J, Buys N, Jayasinghe R. Effect of probiotics on blood pressure: a systematic review and meta-analysis of randomized, controlled trials. Hypertension. 2014 Oct;64(4):897–903.
21Komaroff AL. The Microbiome and Risk for Atherosclerosis. JAMA. 2018 Jun 19;319(23):2381–2.
22Wang L, Guo M-J, Gao Q, Yang J-F, Yang L, Pang X-L, et al. The effects of probiotics on total cholesterol. Medicine (Baltimore). 2018 Feb 2;97(5).
23Wu Y, Zhang Q, Ren Y, Ruan Z. Effect of probiotic Lactobacillus on lipid profile: A systematic review and meta-analysis of randomized, controlled trials. PLoS One. 2017 Jun 8;12(6).
24Lynn DJ, Pulendran B. The potential of the microbiota to influence vaccine responses. Journal of Leukocyte Biology. 2017 Sep 1;jlb.5MR0617-216R.
25Watts AM, Cox AJ, Smith PK, Besseling-van der Vaart I, Cripps AW, West NP. A Specifically Designed Multispecies Probiotic Supplement Relieves Seasonal Allergic Rhinitis Symptoms. The Journal of Alternative and Complementary Medicine. 2018 Aug;24(8):833–40.
26Bashiardes S, Godneva A, Elinav E, Segal E. Towards utilization of the human genome and microbiome for personalized nutrition. Current Opinion in Biotechnology. 2018 Jun;51:57–63.
27Chittim CL, Irwin SM, Balskus EP. Deciphering Human Gut Microbiota-Nutrient Interactions: A Role for Biochemistry. Biochemistry. 2018 08;57(18):2567–77.
28Skrypnik K, Suliburska J. Association between the gut microbiota and mineral metabolism. J Sci Food Agric. 2018 May;98(7):2449–60.
29Zeevi D, Korem T, Zmora N, Israeli D, Rothschild D, Weinberger A, et al. Personalized Nutrition by Prediction of Glycemic Responses. Cell. 2015 Nov;163(5):1079–94.
30Savin Z, Kivity S, Yonath H, Yehuda S. Smoking and the intestinal microbiome. Arch Microbiol. 2018 Jul;200(5):677–84.
31Tun MH, Tun HM, Mahoney JJ, Konya TB, Guttman DS, Becker AB, et al. Postnatal exposure to household disinfectants, infant gut microbiota and subsequent risk of overweight in children. CMAJ. 2018 Sep 17;190(37):E1097–107.
32Wilkinson EM, Ilhan ZE, Herbst-Kralovetz MM. Microbiota-drug interactions: Impact on metabolism and efficacy of therapeutics. Maturitas. 2018 Jun;112:53–63.
33Maier L, Typas A. Systematically investigating the impact of medication on the gut microbiome. Current Opinion in Microbiology. 2017 Oct;39:128–35.
34Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D, et al. Environment dominates over host genetics in shaping human gut microbiota. Nature. 2018 Feb 28;555(7695):210–5.
35Allen JM, Mailing LJ, Niemiro GM, Moore R, Cook MD, White BA, et al. Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans: Medicine & Science in Sports & Exercise. 2018 Apr;50(4):747–57.
36Durk RP, Castillo E, Márquez-Magaña L, Grosicki GJ, Bolter ND, Lee CM, et al. Gut Microbiota Composition is Related to Cardiorespiratory Fitness in Healthy Young Adults. International Journal of Sport Nutrition and Exercise Metabolism. 2018 Jul 10;1–15.
37Muñiz Pedrogo DA, Jensen MD, Van Dyke CT, Murray JA, Woods JA, Chen J, et al. Gut Microbial Carbohydrate Metabolism Hinders Weight Loss in Overweight Adults Undergoing Lifestyle Intervention With a Volumetric Diet. Mayo Clinic Proceedings. 2018 Aug;93(8):1104–10.
38Akshintala VS, Talukdar R, Singh VK, Goggins M. The Gut Microbiome in Pancreatic Disease. Clin Gastroenterol Hepatol. 2019 Jan;17(2):290–5.
39Markowiak P, Śliżewska K. Effects of Probiotics, Prebiotics, and Synbiotics on Human Health. Nutrients. 2017 Sep 15;9(9).
40Martinez KB, Leone V, Chang EB. Western diets, gut dysbiosis, and metabolic diseases: Are they linked? Gut Microbes. 2017 04;8(2):130–42.
41Basso PJ, Câmara NOS, Sales-Campos H. Microbial-Based Therapies in the Treatment of Inflammatory Bowel Disease – An Overview of Human Studies. Frontiers in Pharmacology. 2019 Jan 10;9.
42Ouwehand AC, Invernici MM, Furlaneto FAC, Messora MR. Effectiveness of Multi-strain Versus Single-strain Probiotics: Current Status and Recommendations for the Future. Journal of Clinical Gastroenterology. 2018;52:S35–40.
43Guo Q, Goldenberg JZ, Humphrey C, Dib RE, Johnston BC. Probiotics for the prevention of pediatric antibiotic‐associated diarrhea. Cochrane Database of Systematic Reviews. 2019;(4).
44Hao Q, Dong BR, Wu T. Probiotics for preventing acute upper respiratory tract infections. Cochrane Acute Respiratory Infections Group, editor. Cochrane Database of Systematic Reviews. 2015 Feb 3.
45Schwenger EM, Tejani AM, Loewen PS. Probiotics for preventing urinary tract infections in adults and children. Cochrane Kidney and Transplant Group, editor. Cochrane Database of Systematic Reviews. 2015 Dec 23.
46Dalal R, McGee RG, Riordan SM, Webster AC. Probiotics for people with hepatic encephalopathy. Cochrane Hepato-Biliary Group, editor. Cochrane Database of Systematic Reviews. 2017 Feb 23.
47Goldenberg JZ, Yap C, Lytvyn L, Lo CK-F, Beardsley J, Mertz D, et al. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane IBD Group, editor. Cochrane Database of Systematic Reviews. 2017 Dec 19.
48Xie HY, Feng D, Wei DM, Mei L, Chen H, Wang X, et al. Probiotics for vulvovaginal candidiasis in non-pregnant women. Cochrane STI Group, editor. Cochrane Database of Systematic Reviews [Internet]. 2017 Nov 23.
49Scott AM, Clark J, Julien B, Islam F, Roos K, Grimwood K, et al. Probiotics for preventing acute otitis media in children. Cochrane Database of Systematic Reviews. 2019;(6).
50Coffey MJ, Garg M, Homaira N, Jaffe A, Ooi CY. Probiotics for people with cystic fibrosis. Cochrane Cystic Fibrosis and Genetic Disorders Group, editor. Cochrane Database of Systematic Reviews. 2018 Feb 12.
51Okesene-Gafa KA, Brown J, McCowan L, Crowther CA. Probiotics for treating women with gestational diabetes for improving maternal and fetal health and well-being. Cochrane Pregnancy and Childbirth Group, editor. Cochrane Database of Systematic Reviews. 2018 Feb 26.
52Barajas‐Nava LA, Sánchez AC, Castilla‐Peon M-F, Pizarro‐Castellanos MP, Frias RV. Probiotics for the treatment of irritable bowel syndrome in children. Cochrane Database of Systematic Reviews. 2018 (8).
53Sarkar A, Lehto SM, Harty S, Dinan TG, Cryan JF, Burnet PWJ. Psychobiotics and the Manipulation of Bacteria–Gut–Brain Signals. Trends in Neurosciences. 2016 Nov;39(11):763–81.
54Aguilar-Toalá JE, Garcia-Varela R, Garcia HS, Mata-Haro V, González-Córdova AF, Vallejo-Cordoba B, et al. Postbiotics: An evolving term within the functional foods field. Trends in Food Science & Technology. 2018 May;75:105–14.