The Human Microbiome

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Chapter: Pharmaceutical Microbiology : Principles Of Microbial Pathogenicity And Epidemiology

Even though some parts of the human body are free from microorganisms (axenic state), the body harbours millions of mutualistic and commensal symbionts. Each of us unwittingly carries a population of bacterial cells on our skin and in our mouth and digestive tract that outnumbers cells carrying our own genome by approximately ten to one.


THE HUMAN MICROBIOME

 

Even though some parts of the human body are free from microorganisms (axenic state), the body harbours millions of mutualistic and commensal symbionts. Each of us unwittingly carries a population of bacterial cells on our skin and in our mouth and digestive tract that outnumbers cells carrying our own genome by approximately ten to one. Mutualistic relationships occur when both organisms (microbial and host cell) benefit from the interactions, whereas commensalism is a state in which one member of the relationship benefits without significantly affecting the other. Microorganisms that colonize body surfaces (internal and external) without normally causing disease constitute the microbiome. The microbiome comprises a number of distinct microbiotas which are characteristic of the region of the body colonized.

 

The microbiome is present throughout life and may comprise predominantly bacteria, with some fungi and protozoa, the majority of which are commensal. The microbiome begins to develop when the amniotic membrane surrounding the unborn child ruptures, allowing contact with vaginal, faecal and skin associated microorganisms from the mother during childbirth. Microorganisms enter the infant’s mouth and nose during passage through the birth canal, colonization of the upper respiratory tract occurs with the first breath of air, and the beginning of the colon microbiota occurs during feeding. The development of the resident microbiota is therefore initiated during the first few months of life. By comparison, transient microbiotas remain in the body for only a few hours, days or months. They are found in the same locations as the resident flora, but cannot persist because of their inability to compete with the microbiome, to resist elimination by the body’s defence mechanisms or to tolerate the chemical and physical changes encountered.


Changes in relative abundance of normal microbiota, for whatever reason (e.g. major changes to diet, antibiotic treatment, hormonal changes, chemo or radiotherapy), may allow one or more members of the microbiome to become opportunistic pathogens. For example, reductions in numbers of protective lactobacilli within the vagina brought about through antibiotic use can allow Candida albicans, a minority member of the normal microbiota, to grow more prolifically, resulting in an opportunistic vaginal yeast infection such as vaginal candidiasis. Following appropriate treatment, the normal flora is typically re-established in adults. In some areas of the body, such as the gastrointestinal tract, it is claimed that the recolonization by desired species can be encouraged by administration of probiotics. These are live cultures of intestinal bacteria that are marketed as conferring a health benefit and preventing digestive problems. Prebiotics, (normally fibre like carbohydrates) that represent preferred or selective growth substrates for probiotic bacteria already present within the digestive tract are also of demonstrable benefit.

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