Posted on by Rosanna

What is a microbiome?

I think I must have been one of the last people on the planet to have heard about the concept of a “microbiome”. I mean, I’ve been familiar with the idea of “good bacteria” in the gut, and the genital tract, for years as part of generally accepted medical knowledge. And any health professional who has ever needed to send swabs or samples looking for possible infection in any part of the body will know how common it is to have a report come back with “normal commensals” or “normal flora”, whether you are talking about a skin swab or a sputum sample (stuff you’ve coughed up).

So I have known that your body is covered, inside and out, with “bugs”, most of which do no harm most of the time, and may even help to protect you against invasion of some of the “bad” or pathogenic bacteria, but I had never heard of them being given a name collectively, and I had no idea that so much research had become focused upon them recently, particularly the bunch living in our guts (see Gut reaction – What is Your Gut? post).

And yet, after I’d read Tim Spector’s book1 and started raving about it to anyone who would listen (see About Us section), it seemed that everyone I spoke to was already familiar with the term. So if that is you, I apologise for going over well-trodden ground but on the other hand, there is some confusion out there, even amongst the science community about what the “correct terminology” actually ought to be. So perhaps this will help to clear it up…

When I did a quick search online for a definition, various things came up, but I have selected the Merriam-Webster online dictionary’s definition2 because it gave two meanings and I think it is important to highlight that there are indeed two subtly different but definitely distinct definitions that are both widely accepted and used. These are as follows:

  • a community of microorganisms (such as bacteria, fungi, and viruses) that inhabit a particular environment and especially the collection of microorganisms living in or on the human body;
  • the collective genomes of microorganisms inhabiting a particular environment and especially the human body.

So one meaning is the collection of “bugs” all living together in one place, and the other is the collection of all of the genetic material of those “bugs” living together in one place (see information about the Human Microbiome Project3 here).

Another term which is really important to mention here, as it is often used in scientific articles about collections of “bugs”, is microbiota. The definition of this, again from the Merriam-Webster dictionary, is:

  • the microscopic organisms of a particular environment.

Some people think that the term microbiota should always be used to describe the group of bugs whilst microbiome should be reserved for their genetic material,4 but there is evidence that the term microbiome has been around a lot longer than the concept of genome sequencing4 and, as I said previously, it appears to be widely used and accepted as a description for a community of microorganisms.

Anyway, I am going off on an interesting etymological tangent, but what has this all got to do with our health? Or cancer for that matter?

Well, the bottom line is that we are surrounded, covered and filled with a whole host of microorganisms, many of whom have evolved with us over thousands of years.5 The irony there, of course, is that we are the “hosts”. The “guests” lying within us come in various guises: they can either be commensals, pathogens or mutualistic symbiotes (what a mouthful!!! For further explanation see Glossary below). And it is the latter group that we are particularly interested in…

All sorts of figures have been quoted as being the total number of bacteria living in or on a human body, but a recent study estimated that there are around 3×1013 of them (yes, that’s 13 zeros! And as 12 zeros are considered to be 1 trillion, we are talking about a number of around 30 trillion, although the study estimates a range of around 4.4 trillion in a young infant to around 56 trillion in an obese adult).6,7

This approximates to a 1:1 ratio of bacteria to human cells or, in other words, suggests that we are in actual fact 50% human and 50% bacteria (I have to say, I’m not sure where the viruses and yeasts, etc. come into all of this).6,7 Certainly a rather weird concept!

The most up-to-date evidence so far seems to support the theory that the womb provides a sterile (no “bugs”) environment for a baby during pregnancy  and that the human body does not develop its microbiome until birth.6,8-16 After this, it is influenced by both genetic features of the host17 and environmental factors such as diet and antibiotic exposure.6,8-16

This means that everybody’s microbiome is likely to be different and scientists are working on data from the Human Microbiome Project 3 to see whether there is enough variation to be able to uniquely identify people in a population (like fingerprints) and if there is variation over time.6,18 Of course, if an individual’s microbiome has a significant impact on his or her health, the next question, is whether or not it can be manipulated to improve it… but that really is the million dollar question!!

For further insight into the relationship our personal microbiomes may have with our health, you might want to check out my next post: What has the gut microbiome got to do with health and disease?

 

Glossary and Useful links (also see Useful Resources page)

 Microbiome: see above

“Good bacteria”: bacteria which live on or in us and in some way benefit us (see mutualistic symbiotes below)

Commensals: organisms which live together in a relationship which involves one of the organisms (in this case the microorganism) benefiting from the other (in this case, the human), whilst the other (the human) is neither harmed, nor helped; compare with parasites, in which case one of the organisms in the relationship benefits at the expense of the other (the host); or mutualistic symbiotes where there is usually considered to be mutual benefit (living in symbiosis)

Pathogenic bacteria: bacteria which cause harm through infection

Microorganisms: a living thing that is so small cannot be seen with the naked eye

Bacteria: microorganisms that have certain defined characteristics, e.g. they are single-celled, they have cell walls, they don’t have a nucleus, etc.

Fungi: these may be microorganisms (such as yeasts) or macroorganims (such as mushrooms) and make up a whole Kingdom of their own in terms of taxonomy (the scientific classification of all living things), separate from Plants and Animals. They may be single or multi-celled and again have certain defined characteristics such as the presence of 2 substances in their cell walls called glucans (found in plant cell walls) and chitin (found in certain animal cell walls) which are not found combined in the cell wall of any other organisms (see https://en.wikipedia.org/wiki/Fungus).

Viruses: described as microorganisms but some debate as to whether they are actually “living” as they require a living host cell to be able to survive, grow and reproduce. Much smaller than bacteria, not even visible under a light microscope i.e. a “normal” microscope. Described by Google as being typically: “a nucleic acid molecule in a protein coat”.

Genome: the complete set of genetic material in an organism (all the genes needed to make that organism function and all the things needed to help make those genes work, plus a lot of extra bits we’re not really sure of yet…)

Microbiota: the microscopic organisms of a particular environment (Merriam-Webster online dictionary)

 

References

  1. The Diet Myth – The Real Science Behind What We Eat: book by Tim Spector, Professor of Genetic Epidemiology at King’s College London and author; see http://www.tim-spector.co.uk/
  2. Merriam-Webster Online Dictionary: https://www.merriam-webster.com/dictionary/microbiome
  3. Human Microbiome Project: https://www.genome.gov/27549400/the-human-microbiome-project-extending-the-definition-of-what-constitutes-a-human/
  4. Microbiome terminology: http://www.microbe.net/2015/04/08/what-does-the-term-microbiome-mean-and-where-did-it-come-from-a-bit-of-a-surprise/
  5. Seksik P,Landman C. “Understanding Microbiome Data: A Primer for Clinicians.” Digestive Diseases. 2015 Sep 14;33 Suppl 1:11-16. [Epub ahead of print] https://www.ncbi.nlm.nih.gov/pubmed/26366561
  6. Microbiome and Cancer: Cancer Quest is a cancer education and outreach programme at Emory University, Atlanta, USA.  They aim to provide reliable information about cancer biology and treatment and have a useful page about the relevance of the human microbiome at https://www.cancerquest.org/cancer-biology/microbiome?gclid=CjwKEAjwppPKBRCGwrSpqK7Y5jcSJACHYbWY32C4KJY9zWIadThmrYqqT6Rm9bCzvC_FgWO8RCRQYhoCmYrw_wcB
  7. Sender R, Fuchs S, Milo R. “Revised Estimates for the Number of Human and Bacteria Cells in the Body.” PLOS Biology. 2016 Aug 19;14(8):e1002533. https://www.ncbi.nlm.nih.gov/pubmed/27541692 (NB: PLOS Biology is a peer-reviewed open-access journal)(Reference from: cancerquest.org)
  8. Perez-Muñoz ME, Arrieta MC, Ramer-Tait AE, Walter J. “A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome.” Microbiome. 2017 Apr 28;5(1):48. doi: 10.1186/s40168-017-0268-4. Review. PMID: 28454555 https://www.ncbi.nlm.nih.gov/pubmed/28454555 (free full text available on PubMed)
  9. Cho I, Blaser MJ. “The Human Microbiome: at the interface of health and disease.” Nature reviews. Genetics. 2012 Mar 13; 13(4): 260-270. https://www.ncbi.nlm.nih.gov/pubmed/22411464 (free full text available on PubMed)(Reference from: cancerquest.org)
  10. Ursell LK, Metcalf JL, Parfrey LW, Knight R. “Defining the Human Microbiome.” Nutrition reviews. 2012 Aug; 70(Suppl 1): S38-S44. https://www.ncbi.nlm.nih.gov/pubmed/22861806 (free full text available on PubMed)(Reference from: cancerquest.org)
  11. Haque SZ,Haque M. “The ecological community of commensal, symbiotic, and pathogenic gastrointestinal microorganisms – an appraisal.” Clinical and Experimental Gastroenterology. 2017 May 5;10:91-103. doi: 10.2147/CEG.S126243. eCollection 2017. https://www.dovepress.com/the-ecological-community-of-commensal-symbiotic-and-pathogenic-gastroi-peer-reviewed-article-CEG (free full text available on Dovepress)
  12. Gritz EC, Bhandari V. “The human neonatal gut microbiome: a brief review.”Frontiers in Pediatrics. 2015;3:17. (Reference from “A critical assessment of the “sterile womb” and “in utero colonization” theories”)
  13. Grönlund MM, Lehtonen OP, Eerola E, Kero P. “Fecal microflora in healthy infants born by different methods of delivery: permanent changes in intestinal flora after cesarean delivery.”Journal of Pediatric Gastroenteroly and Nutrition. 1999;28(1):19–25. (Reference from “A critical assessment of the “sterile womb” and “in utero colonization” theories”)
  14. Pandey PK, Verma P, Kumar H, Bavdekar A, Patole MS, Shouche YS. “Comparative analysis of fecal microflora of healthy full-term Indian infants born with different methods of delivery (vaginal vs cesarean): Acinetobacter sp. prevalence in vaginally born infants.”Journal of Biosciences. 2012;37(6):989–998. (Reference from “A critical assessment of the “sterile womb” and “in utero colonization” theories”)
  15. Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J. “The placenta harbors a unique microbiome.”Science Translational Medicine. 2014;6(237):237ra65. (Reference from “A critical assessment of the “sterile womb” and “in utero colonization” theories”)
  16. Adlerberth I, Wold AE. “Establishment of the gut microbiota in Western infants.”Acta Paediatrica. 2009;98:229–238. (Reference from “A critical assessment of the “sterile womb” and “in utero colonization” theories”)
  17. Blekhman R,Goodrich JK, Huang K, Sun Q, Bukowski R, Bell JT, Spector TD, Keinan A, Ley RE, Gevers D, Clark AG. “Host genetic variation impacts microbiome composition across human body sites.” Genome Biology. 2015 Sep 15;16:191. doi: 10.1186/s13059-015-0759-1. https://www.ncbi.nlm.nih.gov/pubmed/26374288 (free full text available on PubMed)
  18. Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJ, Huttenhower C. “Identifying personal microbiomes using metagenomic codes.” Proceedings of the National Academy of Sciences of the USA. 2015 Jun 2;112(22):E2930-8. https://www.ncbi.nlm.nih.gov/pubmed/25964341 (free full text available on PubMed)(Reference from: cancerquest.org)
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