Microbiota and archaea

Human microbiota or....
          ....a new look on ourselves

For more than a century, microbes, these bugs invisible to our eyes without microscopes, were known from the majority of us only through a deforming lens: evil pathogens that we had to fight, responsible for the worst epidemics. However, they contain valuable auxiliaries for the development of humanity: thus, the "yeast" to which we still owe the bread or beer, is certainly one of the first species domesticated by humans (at least as soon as possibly the Neolithic). 

Microbes also live in close relationship with humans (and animals in general). They have co-evolved with us, participate in our biology and therefore form part of what constitutes us. We can thus speak of a real conceptual revolution of our perception of what is biologically a human. Over the course of history, our knowledge has led us to reconsider our place in the universe, often by coming up against dogmas of all kinds (and still today!): 

Thus, the Man and his planet are not at the center of the universe and Man is a product of evolution that shares the same biological ancestor with other primates as with ... yeast or bacteria. We now discover that his own body is home to billions of microbes (the human microbiome), commensals and symbiotics participating in his own physiology and the proper functioning of the body. Man is in fact a meta-organism, made up of these own cells and microbes, in slightly larger quantities than "genetically" human cells. Scientists no longer hesitate to speak now of a human organ that has been forgotten until now, about the human intestinal microbiota.

Thus, the human being, supposedly sterile at birth, is gradually colonized by microbes of all kinds forming a microbiota. "Microbiota" is the right name to describe this set of microbes, what was previously called "flora" .... Justified term when we believed the biological world shared between animals and plants (see here). This term and this classification are no longer necessary. 

These microbes colonize all parts of man in direct relation to the external environment, in other words, many of the epithelia of coating of our organism. For example, the skin, the lungs, ... harbor microbes.

The most colonized area remains the human digestive tract ... and in particular the small intestine and the colon. The latter forms one of the densest microbiomes of the planet.

The microbiota evolves during lifespan.

This image is from our work with Paul. W. O'Toole (article by Burkhardt Flemer and coll. published in 2017.) It shows the differences of fecal microbiota in laboratory rats at different stages of their lives. Find more information here (in English)

Archaeome, archaea in these microbiota:

Microbes and human microbiota may not be seen as made up only of bacteria. Two other domains of the living (eukaryotes and archaea) as well as viruses are also part of microbiomes. These lasts certainly have a regulatory role in the constitution and the activity of these microbiota which is currently poorly known. In fact, archaea are known since more or less time as natural members of the human intestinal microbiota (and many other animals). It is particularly true for methanogenic Archaea (see here the next chapter) to which our works are more specifically dedicated (reviewed here ). However, the currently used technical tools (analysis of microbiomes by sequencing the 16s marker amplicon) may hide their presence if these tools are not specifically sought, as well as bioinformatics analysis tools and associated databases.

A number of us had a hunch that the diversity of archaea in these microbiota were dumped. These Archaea are the archaeome, in other words the archaeal component of the microbiome. Since 2003, a part of our work is dedicated to the diversity and functionnality of methanogens within the gut microbiote and its relationship with human / human health. Our work (2008 and  2010) revealed the presence of several new species of methanogens in the intestinal tract the man, in fact belonging to a new lineage, forming a new order among the taxonomic rank.

However, no comprehensive method of research of the Archaea was currently used for the sets of human microbiomes. The work of Christine Moissl-Eichinger et al. in the Medical University of Graz, Austria now give first tools that can reveal archeal diversity with a higher precision : this diversity seems to be much more important than imagined initially... The image is retrieved from the American scientific magazine Science (November 24, 2017: Science journalist Elizabeth Pennisi reports about the works of C. Moissl-Eichinger just published in mBio (Koskinen et al, 2017). According to our opinion and that of Uri Gophna (University of Tel Aviv) and Mark Pimentel (Los Angeles), rapid advances are to be expected on the basis of tools described in the mBio paper: indeed, first data present a large archaeal diversity with many archaea still completely unknown: important biological functions are suspected both inside of the microbiota iand with the human host. This particularly applies to Thaumarchaea on the skin as well as some methanogens in the digestive tract. An adverse role of some of these archaea is sometimes suspected eg in the colon:  Mark Pimentel for example suspects Methanobrevibacter smithii to be involved in deleterious effects in human. However, if correlations are indeed highlighted between intestinal transit times / constipation and prevalence of this archeon, a cause-effect relationship has not been proven. Indeed, our (in vitro) works rather suggest that higher prevalence of this archaeon is a consequence rather than a direct cause of slowed transit time (for example, see our work 2017 in J. Neurogastroenterol. Motil.). It is quite possible that these 2 visions are not opposed, and may reflect 2 different stages in implantation and over-development of this archaeon. Whatever, this remains to be determined.