Just one microbiota?

Many micro-ecosystems are yet to be explored

Let’s have a look at the beginning of this story, the discovery of the lactic acid bacteria benefits, till the complexity of the microbial ecosystems already discovered.

A bit of history
The study of the gut microbiota dates back to the early 20th century. While Pasteur became interested in pathogenic bacteria, one of his students, Metchnikoff, decided a few years later to study the particular characteristics of “good” bacteria in our intestines. He proposed the theory that the consumption of fermented milk by the particularly long-lived shepherds of Bulgaria stimulated the growth in the intestines of lactic acid bacteria, the so-called probiotics.

Gut microbiota
It is now well known that in our gut reside most of the bacteria that live in symbiosis with the human body, along with fungi, yeasts and viruses, totaling about 100 trillion microorganisms. Bacteria belonging to the phyla Firmicutes and Bacteroidetes account for about 90% of the gut microbiota; the remaining part consists of Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia1.

Oral cavity
Beyond the gut microbiota, bacteria also colonize, to a lesser extent, other anatomical sites. The mouth, for example, is the second most colonized site after the gut. The 12 phlya present are Firmicutes, Fusobacteria, Proteobacteria, Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Spirochaetes, Synergistetes, SR1, Saccharibacteria, and Gracilibacteria. The oral microbiota is subject to change over time due to exposure to the external environment and daily food intake2.

Urogenital tract
The vaginal microbiota is characterized by the abundance of Lactobacilli, which ensure the maintenance of a low pH and the production of anti-microbial compounds. It can be classified into 5 community state types (CSTs) dominated by L. crispatus, L. gasseri, L. iners, obligate anaerobic bacteria, and L. jensenii, respectively3.

It’s the most important interface with the environment. On its surface, the most commonly encountered phyla are Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria, with the latter more represented than the intestine. Staphylococcus epidermidis and other coagulase-negative staphylococci were among the first colonizers to be studied. Fungi called Malassezia are often isolated from the sebaceous areas of the skin4.

There are also resident bacterial communities in the eye, ear, lung and other tissues about which we have limited information at present and for which extensive investigations are required.

Despite emerging evidence in the scientific literature, we still have much to discover about the commensal bacteria that colonize our bodies in terms of species and functions.


1Thursby E., Juge N. Introduction to the human gut microbiota. Biochem. J. 2017;474:1823–1836. doi: 10.1042/BCJ20160510.

2Deo PN, Deshmukh R. Oral microbiome: Unveiling the fundamentals. J Oral Maxillofac Pathol. 2019;23(1):122-128. doi:10.4103/jomfp.JOMFP_304_18

3Chen X, Lu Y, Chen T, Li R. The Female Vaginal Microbiome in Health and Bacterial Vaginosis. Front Cell Infect Microbiol. 2021;11:631972. Published 2021 Apr 7. doi:10.3389/fcimb.2021.631972

4Grice EA, Segre JA. The skin microbiome [published correction appears in Nat Rev Microbiol. 2011 Aug;9(8):626]. Nat Rev Microbiol. 2011;9(4):244-253. doi:10.1038/nrmicro2537

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