Inimese mikrobiome

Inimese mikrobiome, inimestel ja inimestel elavate mikroorganismide (mikrobiota) täisarv ja täpsemalt mikroobsete genoomide kogum, mis aitavad kaasa inimese laiemale geneetilisele kujundile ehk metagenoomile. Inimese mikrobiomi moodustavad genoomid esindavad märkimisväärselt mitmekesist mikroorganismide hulka, mis hõlmab baktereid, arhaea (primitiivsed üherakulised organismid), seened ja isegi mõned algloomad ja mitteelustuvad viirused. Bakterid on vaieldamatult inimese mikrobiomi kõige arvukamad liikmed: ainuüksi bakteripopulatsiooni suurusjärgus on 75 triljonit - 200 triljonit organismi, samal ajal kui kogu inimkeha koosneb umbes 50 triljonist kuni 100 triljonini somaatilisest (keha) rakust. Suur mikroobide arvukus viitab sellele, et inimkeha on tegelikult “supraorganism,Inimese ja mikroobsete rakkude ja geenide kogum ning seega segu inimesest ja mikroobist.

Inimese mikrobiomi avastamine

Esimesed teaduslikud tõendid selle kohta, et mikroorganismid on osa normaalsest inimese süsteemist, ilmnesid 1880. aastate keskel, kui Austria lastearst Theodor Escherich täheldas tervete ja kõhulahtisuse käes kannatavate laste sooleflooras teatud tüüpi baktereid (hilisemat nimega Escherichia coli). Järgnevatel aastatel kirjeldasid teadlased mitmeid teisi inimkehast isoleeritud mikroorganisme, sealhulgas 1898. aastal liike Veillonella parvula, suu, seedetrakti, kuseteede ja ülemiste hingamisteede floora bakteriliige ning 1900. aastal bifidobakterite liikide soolefloora. Kogu 20. sajandi vältel eraldati ninakanalitest, suuõõntest, nahast, seedetraktist ja urogenitaaltraktist arvukalt teisi mikroorganisme, mida iseloomustati inimese mikrobiootana.Ehkki seda organismirühma on kontseptsioonist alates selle avastamisest mitmel viisil mõistetud, töötati inimese mikrobiomi kontseptsioon ja seeläbi selle intensiivne uurimine välja peamiselt 21. sajandi esimesel kümnendil.

Knowledge of the human microbiome expanded appreciably after 2007, the year the Human Microbiome Project (HMP)—a five-year-long international effort to characterize the microbial communities found in the human body and to identify each microorganism’s role in health and disease—was launched. The project capitalized on the decreasing cost of whole genome sequencing technology, which allows organisms to be identified from samples without the need for culturing them in the laboratory; the technology also facilitates the process of comparing DNA sequences of microorganisms isolated from different parts of the human body and from different people. In the first three years of the project, scientists discovered new members of the human microbiota and characterized nearly 200 different bacterial member species.

Microbial diversity

By some estimates, the human microbiota may consist of a total of 900 or 1,000 different species of microorganisms, making for an extraordinarily diverse collection of microbial genomes. This diversity manifests in differences in microbial composition not only from one human to the next but also between matching body parts, such as the right and left hands, of the same individual. For example, as one study has shown, a typical palm surface of the hand can harbour more than 150 different bacterial species, only 17 percent of which are common to both hands of the same person and only 13 percent of which are shared by different persons.

The human gut is another site characterized by a high degree of microbiome diversity and abundance. In a study of 124 European individuals, researchers isolated some 3.3 million microbial genes. Many of these genes represented frequently occurring bacterial gut species, at least 160 of which were believed to inhabit each person’s gut. The identification of such frequently occurring species in populations is fundamental to defining so-called common bacterial cores, which enable scientists to explore the interface of the human microbiome with factors such as diet, culture, and genotype (genetic makeup).

The role of the human microbiota

Most members of the human microbiota benefit humans by providing them with traits that they would not otherwise possess. Some microorganisms found in the human gut, for instance, obtain nutrients from ingested food in return for assisting with the breakdown of food or preventing the colonization of the gut by harmful bacteria. There are, however, many microorganisms in the human microbiota that are closely related to pathogenic (disease-causing) organisms or are themselves capable of becoming pathogenic. Examples include bacterial species of the genera Staphylococcus, Streptococcus, Enterococcus, Klebsiella, Enterobacter, and Neisseria.

Clostridium difficile infectionserves as a useful example for illustrating the significance of the relationship between the human microbiome and health and disease. C. difficile infection, which is characterized by severe recurrent diarrhea, abdominal cramping, and nausea, occurs most often in persons who receive a course of antibiotics while in a hospital. Antibiotics kill or inhibit the reproduction of pathogenic bacteria and in the process cause dramatic changes in normal human microbial communities, such that previously established colonies may be overtaken by colonies of different and potentially pathogenic species. In the case of C. difficile, researchers have discovered that infection can be treated effectively through fecal, or stool, transplantation, in which fecal material from a healthy person is transferred to the patient, thereby restoring populations of beneficial gut microbiota.

Scientists studying obesity have detected an increased abundance of Prevotella and Firmicutes bacteria and of methanogenic (methane-producing) archaea in obese individuals relative to normal-weight persons and persons who have undergone gastric bypass surgery. Scientists suspect that these microorganisms are more efficient at harvesting carbohydrates from food than are the types of microorganisms that dominate the gut flora of normal-weight individuals. The extra nutrients are then stored in the body as fat.

Ongoing study of the human microbiome is expected to continue to shed light on fundamental aspects of human physiology and particularly human nutrition. Improved understanding of nutritional requirements could lead to changes in dietary recommendations and in food production. In addition, information about the human microbiome could lead to the development of new diagnostic techniques and treatments for a variety of human diseases, as well as to the development of industrial products based on substances (e.g., enzymes) that are produced by members of the human microbiota.