Microbiome

According to current knowledge, the term “microbiome” was first used in 1952 by J. L. Mohr. He used it to refer to the totality of microorganisms within a specific habitat. However, this early usage went largely unnoticed. The ecological definition commonly used today can be traced back to the research group led by John M. Whipps (Whipps JM et al. 1988). In 1988, the authors defined the microbiome as: a characteristic microbial community within a sufficiently well-defined habitat with specific physicochemical properties—including its entire “theater of activity” (Berg G et al. 2020).

The geneticist and Nobel laureate Joshua Lederberg, who is often cited as the primary author of the term “microbiome,” did not, in fact, coin the term originally. In 2001, he adapted and popularized the term “microbiome” to refer to the totality of commensal, symbiotic, and pathogenic microorganisms that colonize the human body as a shared ecological habitat (Lederberg J, McCray AT 2001).

A term referring to the totality of all microorganisms (bacteria, viruses, fungi, protozoa) colonizing the human body—the microbiota—along with its structural elements, metabolites, and signaling molecules.

The microbiome colonizes all of our points of contact with the environment. This primarily affects the gut and skin, as well as the so-called “semi-mucous membranes,” such as the oral and genital mucosa.

See also: gut microbiome, skin microbiome,oral microbiome, urogenital microbiome,vaginal microbiome, mycobiome, virome.

In total, the human microbiota consists of 10 to 100 trillion microorganisms—ten times more than the number of human cells. In terms of genes, these microorganisms in the human body possess 3.3 million genes—150 times more than the number of human genes (25,500).

The microorganisms that humans harbor outnumber human cells by a factor of 10. The biodiversity of a habitat is reflected by alpha diversity. Alpha diversity describes the number of species present in a habitat or biotope.   

The term “microbiome” was coined based on the term “genome.”  

The term “microbiota” (plural of “microbiome”) refers to individual (organ-specific) colonizations. The goal of future research will be to investigate the effects of diseases on the microbiome. Furthermore, researchers are interested in the extent to which changes in the gut microbiome influence sensitization to food allergens.  

The composition of the microbiome is influenced by the mode of delivery (vaginal birth vs. cesarean section), becomes diverse during childhood, stabilizes in adulthood, and declines again in old age. The microbiome consists mainly of four bacterial phyla, the so-called phylogenetic core:

• Firmicutes,
• Bacteroides,
• Proteobacteria
• Actinobacteria.

In patients with IBD (inflammatory bowel disease), there is a quantitative and qualitative change in the microbiome:

• Bacterial diversity decreases.
• The composition becomes unstable.
• There is an increase in Enterobacteria and unusual bacterial strains.

The North American“Human Microbiome Project (HMP)” was launched in 2007. In Europe, the “Metagenomics of the Human Intestinal Tract (MetaHIT)” program was initiated in 2008.  

In analogy to the term microbiome, the term"mycobiome" was coined to describe the entirety of all commensal or pathogenic fungi that colonize humans or other living organisms.

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