We are not alone! 

New findings regarding the human microbiome

Puran Falaturi

Bacteria, viruses, fungi and mites reside in droves on the bodies of complex multi-celled organisms. The totality of all the foreign microorganisms found in the body space of an organism is referred to as the microbiome. There are ten times as many foreign microorganisms present in and on the human body than cells that belong to the body itself; the majority of these foreign cells are found in the gastrointestinal tract. To put it extremely, we are bacteria walking on two legs.

A genuine breakthrough in the research of these microorganisms could be achieved through the development of genome sequencing. In keeping with the phenomenon of the Great Plate Count Anomaly, only one in a hundred of the species visible under the microscope can be bred in the laboratory, identified and more closely analyzed (2). With genome sequence analysis it is now possible to register the multitude of microorganisms that do not reproduce under laboratory conditions and which previously could not be identified.

Following on the heels of the Human Genome Project, the Human Microbiome Project was initiated in 2007. The ongoing research of the foreign cell masses in our own bodies is good for lots of surprises. And it is a crucial aspect of really understanding the basal physiological processes in the human body.
 

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The "Who's Who" of skin flora

Where are different skin flora organisms typically found on the skin? The illustration presented here is based on a 2009 publication by Grice EA, et al. It shows the most common sites of skin infections and the pathogens (phyla) responsible for these infections.

Bacteria and mites (Demodex) are mostly found on the epidermis. Mites are particularly fond of the area of the face as well as the hair follicles. Viruses and fungi penetrate more deeply into the dermis. They are found along the hair shaft and follicles and also in the sweat glands and sebaceous glands.

The bacteria – both cocci and rod-shaped bacteria – form entire colonies which communicate among themselves and with other microorganisms (6). Malassezia species live in hypha structures or singly on the surface of the skin. Viruses are found independently as well as within bacteria.

Particularly large numbers of microorganisms are present in warm moist milieus such as intertriginous areas, nasal cavities or the navel (predominantly staphylococci or corynebacteria as well as Bacteroides species and Clostridium species).

At body sites where there is large amount of sebaceous matter – for example the glabella, the nasal folds or the back of the head – the skin flora composition is somewhat different (predominantly corynebacteria, propionibacteria, Malassezia species) as opposed to drier areas such as the outer side of the arms (predominantly coagulase negative staphylococci).

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It is a known fact that the bacteria present in the gastrointestinal tract have an essential role in basic metabolic processes and that the immune system of the skin is dependent on the interaction of bacteria and the body's own immune system (1). Most of these microorganisms are apathogenic species which live with us on either a commensal or a symbiotic basis.

A superficial life

The skin flora make up a good share of the human microbiome. Its composition depends on the one hand on endogenous factors and on the other hand on exogenous environmentally based factors. Genotype (susceptibility), gender, age, life style, immunological characteristics, underlying diseases and the exact localization on the body all play a role in determining the composition of the skin flora, as do climate and geographical location.

A distinction is made between resident and transient microorganisms in this population. The transient microorganisms can also be present for longer periods and thus don't necessarily cause infections.

It is very helpful to consider the normal flora of the human body when dealing with infections that occur via dermal entry portals, particularly in connection with nosocomial infections.
 

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Who belongs to whom?

Potentially pathogenic human skin flora types are shown in the illustration with their taxonomic classification:

Actinobacteria (gram-positive) (phylum)
Micrococci/micrococcaceae (family): Genus: Micrococcus
Additional genera of other families: Corynebacteria, propionibacteria, myxobacteria

Firmicutes (gram-positive) (phylum)
Clostridium (Class) (Genus: Clostridium);
Bacilli (Class) (Genera: Streptococci, Staphylococci, Bacillus, Listeria);
Mollicutes (Class) (Genus: Mycolplasmas))

Proteobacteria (phylum) (gram-negative)
Enterobacteriales (order) (Enterobacteria (family) (Genera: Escherichia, Proteus, Klebsiella, Erwina, Serratia, Yersinia, Salmonella);
Legionellales (order) (families: 1. Legionellaceae, 2. Coxiellaceae (genera: Coxiella, Rickettsiella));
Pasteurellaceae (order) (genera: Haemophilus, Actinobacillus);
Pseudomonales (order) (families: 1.) Moraxellaceae (genera: Acinetobacter, Moraxella), 2.) Pseudomonadaceae (genus: Pseudomonas)

Bacteroidetes (phylum): Bacteroidales (family), Bacteroides (genus), Species: Bacteroides fragilis, Bacteroides thetaiotamicron

Cyanobacteria (phylum)(gram-negative)

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Even though the skin represents an immunological barrier to the outside world, certain microorganisms located there that are normally harmless can be responsible for infections if they advance into atypical localizations or if they are present in immunocompromised patients. One example of this is catheter-associated sepsis.

Coagulase negative staphylococci are the most common pathogens causing catheter-associated infections together with Staphylokokkus aureus (temporarily resident flora), enterococci, gram-negative rod bacteria (such as Escherichia coli) and Candida species. In immunosuppressed patients, atypical myxobacteria or anaerobes are more and more frequently the cause of catheter-associated sepsis. Cumulatively, staphylococci and propionibacteria make up the largest portion of the dermal microbiome.

Sources:

1. Grice EA, Segre JA, "The skin microbiome", Nat Rev Microbiol. Author manuscript; available in PMC 2013 Jan 3, Published in final edited form as: Nat Rev Microbiol. 2011 Apr; 9(4): 244–253
   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535073/
2. Hugenholtz P, Genome. "Exploring prokaryotic diversity in the genomic era", Biol. 2002; 3(2): reviews0003.1–reviews0003.8., Published online 2002 Jan 29
3. Human Genome Project (HGP)
   http://web.ornl.gov/sci/techresources/Human_Genome/index.shtml
4. Human Microbiome Project (HMP)
   http://hmpdacc.org/
5. Universitätsklinikum Ulm - Medizinische Mikrobiologie und Hygiene
   http://www.uniklinik-ulm.de/struktur/institute/medizinische-mikrobiologie-und-hygiene/home/diagnostik/leistungen/leistungsverzeichnis-infektionskrankheiten/fremdkoerper-assoziierte-infektionen.html
6. Grice EA, et al., "A comprehensive analysis of skin microbiota across 20 sites. Topographical and temporal diversity of the human skin microbiome", Science, 2009; 324:1190–1192. [PubMed: 19478181]
   https://www.sciencemag.org/content/324/5931/1190.abstract
7. "How bacteria talk", Bonnie Bassler, TED 2009
   https://www.ted.com/talks/bonnie_bassler_on_how_bacteria_communicate?language=en