Science in Society Archive

The Forgotten Organ – The Human Microbiota

The symbiotic relationship between humans and the microbes living inside us is increasingly linked to health, disease and even behaviour Dr Eva Sirinathsinghji

The rapidly progressing study of the human microbiota is revealing that humans are not individual self-contained beings, but instead hugely complex super-organisms that blur the distinction between where ‘we’ end and ‘they’ begin.

The human microbiota consists of an estimated 100 trillion cells [1], at least 10 times the number of human cells, and new research is revealing how this symbiotic relationship determines human health and disease.  Colonising our outer surface and deeper layers of the skin, gastrointestinal tract, saliva, oral cavity and conjunctiva, the human microbiota affect many aspects of human physiology including immune cell development, digestion and extraction of nutrients, fat distribution, metabolism, angiogenesis, and even regulation of memory, mood, and well-being. Consequently, disturbances of the human microbiota are implicated in many disease states including chronic inflammation, bowel disease, metabolic disorders, cancers, depression and anxiety, autism and memory impairments. Further, many aspects of current lifestyle are thought to have resulted in changes in the human microbiota including improved sanitation, environmental toxins, food processing, diets, vaccinations, increased antibiotic use, decline in parasite infections,  caesarean sections, smaller family size, refrigeration, less crowded living conditions and sedentary habits.

Two huge collaborative efforts in this rapidly expanding field include the International Human Microbiome Consortium [2] and the US National Institute of Health’s Human Microbiome Project (HMP) [3], the latter a 5 year project concluding in 2013 aimed at characterising the microbiotic communities residing in different parts of the body. Modern deep sequencing and metabonomic technologies - the study of the genetic material taken directly from its natural environment - have been employed to identify species previously unknown because they could not be cultured in the laboratory. The enormous data-gathering by the HMP has already yielded 190 papers involving the development of a reference set of microbial genomes and computational tools for analyzing new data sets, the establishment of a resource repository, and the exploration of relationship between microbiota and disease.

The new projects build on much older wisdom of the benefits of probiotics to digestion and overall health. Most, if not all cultures seem to have examples of probiotic foods in their traditional cuisine, including foods such buttermilk, sauerkraut, kefir, fermented soya (miso), fermented millet, fermented sorghum, pulque (fermented probiotic beverage from Mexico), that were consumed to maintain good health. Indeed one of the common probiotics researched today is the fungus Saccharomyces boulardii, which grows on the outside of lychee skins. It was first isolated when scientists noted people consuming the skin to protect themselves from cholera. It is also used to treat Candida infections [4].

We shall be featuring a series of reports on the human microbiota and health, the first of which dealing with our mind, mood and behaviour. 

Article first published 20/11/13


  1. Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 2006, 124, 837-848
  2. The International Human Microbiome Consortium,, accessed 1st November 2013
  3. The Human Microbiome Project., accessed 1st November 2013
  4. Saccharomyces boulardii

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Malcolm Rands Comment left 21st November 2013 08:08:51
thanks for starting this discussion. I predict this topic will be mainstream in the near future and will have profound impacts on how we look at health and well being

Douglas Hinds Comment left 21st November 2013 08:08:42
1.- Since Eukaryotes (including humans) resulted from a consortium of Prokaryotes, we all evolved from the same origin anyway (so much for h. sapiens' sense of exceptionalism); 2.- Aleksandrovich Krasil'nikov (also known as Nikolai Krasilnikov), claimed in his work: SOIL MICROORGANISMS AND HIGHER PLANTS (Published by the Academy of Sciences of the USSR Moscow 1958 and for THE NATIONAL SCIENCE FOUNDATION, WASHINGTON, D.C. and THE DEPARTMENT OF AGRICULTURE, USA by THE ISRAEL PROGRAM FOR SCIENTIFIC TRANSLATIONS 1961) found currently at: The plants themselves determine the nature of the symbiotic soil microorganisms they share their biome with: "Investigations show that the vegetative cover is a powerful factor in the life of microorganisms. The peculiarities of the plant species leave their imprint on the quantitative and qualitative composition of the microflora biocoenoses of soils. Plants create and form microbial societies, which effect the microbial population of the entire root system and harvest remains. During their life, plants excrete through their roots various organic and mineral substances which attract microorganisms. During the growth cycle of the plant, roots constantly form and shed root hairs, lose necrotic epidermal cells, etc. All these elements are then taken up by the microbes and become the source of their nourishment". We had best learn more about the myriad organisms we share an environment with, in order to be able to work with rather than against the remainder of the other's compatible and complementary creatures.

Lurnr Comment left 9th December 2013 18:06:02
Um, no, your thinly veiled pantheistic paradigm notwithstanding, we are a WHOLE lot more than the sum total of our cells and microbiota: we have souls. They don't.