Microbiome

Joshua Lederberg

Term for the totality of all microorganisms colonizing the human organism (bacteria, viruses, fungi, protozoa). The microbiome colonizes all our points of contact with the environment. This mainly concerns the intestines and skin as well as the so-called semi-mucous membranes such as the oral mucosa and genital mucosa.

The microbiome comprises about 2% of our body weight. The microorganisms that humans harbor exceed the number of human cells by a factor of 10. The biodiversity of a habitat is reflected by the alpha diversity. Alpha diversity describes the number of species present in a habitat or biotope.

This term microbiome was coined in reference to the term "genome".

Microbiota (plural of microbiome) refers to individual (organ-related) colonizations. The aim of future research will be to examine the effects of diseases on the microbiome. Furthermore, we are interested in the extent to which changes in the intestinal microbiome influence sensitization to food allergens.

The composition of the microbiome is influenced by the mode of birth (vaginal birth vs. caesarean section), acquires diversity in childhood, stabilizes in adulthood and decreases again in old age. The microbiome consists mainly of four bacterial strains, the so-called phylogenetic core:

• Firmicutes,
• Bacteroides,
• Proteobacteria
• Actinobacteria.

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

• The 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.

1. ADF/ECARF Award (2016) Communication from ECARF. Allergology 39: 345
2. Arifuzzaman M et al. (2019) MRGPR-mediated activation of local mast cells clears cutaneous bacterial infection and protects against reinfection. Sci Adv 5:eaav0216.
3. Chiang CC et al (2019) Neutrophils in psoriasis. Front Immunol. 10:2376
4. Dong X et al. (2022) Keratinocyte-derived defensins activate neutrophil-specific receptors Mrgpra2a/b to prevent skin dysbiosis and bacterial infection. Immunity 55:1645-1662.e7.
5. Gerdol M et al. (2020).Functional insights From the evolutionary diversification of big defensins. Front Immunol 11:758
6. Grice EA et al (2011) The skin microbiome. Nat Rev Microbiol 9:244-253
7. Kabashima K et al. (2019) The immunological anatomy of the skin. Nat Rev Immunol 19:19-30
8. Kahlerta, C et al.(2014) Microbiome - the discovery of an organ. Switzerland Med Forum 14:342-344
9. Matsumoto M et al. (2021) Interaction between Staphylococcus Agr virulence and neutrophils regulates pathogen expansion in the skin. Cell Host Microbe 29:930-940.
10. Tseng PY et al. (2022) Specific β-defensins stimulate pruritus through activation of sensory neurons J. Invest Dermatol 142:594-602.