Gut microbiota


Normal human microflora (microbiota, normoflore, microbiome) has an ultimate biological meaning. There is a conception according to which gut microbiocenosis is a highly organized system, reacting to human organism dynamic state in different living conditions, health status and deceases with qualitative and quantitative changes.  Notably, priority in forming classical conceptions about microbiocenosis role, interactions between them and macroorganism belongs to Russian researchers (Mechnikov I.I., 1908; Ugolev A.M., 1972, 1985).

The overall number of microorganisms living in various human organism segments is more than 10 times higher than the number of its own cells and totals approximately 1014–1015. The greatest quantity of microorganisms falls on gastrointestinal tract, including oropharynx – 75-78%, all the rest populate genito-urinary tract (up to 2-3% in males and up to 9-12% in females) and skin.

Number of microorganism species found only in gut of healthy people exceeds 500. An overall gut microbiome weight is 1-3 kg. Number of bacteria differs in different parts of gut, the majority is found in large intestine (approximately 1010-1012 KOE/ml) and makes 35-50% of its contents.

In microbe communities, that form normal human microflora, between cells networks have been formed evolutionary, and they represent a system of trophic and energetic interactions inside gut microbiocenosis. Almost no available substrate is used in the interests of only a single microorganism species population. Gut microbiome, representing a complex of different microorganism species, has a great metabolic potential and is capable of implementing a number of biochemical processes like a huge biochemistry laboratory. In fact, nowadays a view on gut microbiome is formed in which it appears as a separate human organ. It does not contradict historically established definition of organ as a part of organism, evolutionary developed tissue complex united with common function, structural organization and development. So far, humans can be considered as “superorganisms”, whose metabolism is provided by well organized work of enzymes, coded by not only genome of Homo sapiens itself, but by symbiotic microorganisms’ genomes as well.

It is well known that traditional microbiological methods are not only unable to provide full qualitative and quantitative characteristics of microbiocenosis from human organism, but moreover they make impossible to analyze features of microorganisms’ population interactions, quorum sensing, etc.  However, based on knowledge about these features modern conceptions on human microecology should be created. Mainly, the problem consists in impossibility of cultivating more than 50% species from human normaflora. In case when it is possible, high cost of classic cultural and biochemistry methods used in biocenosis analysis greatly restricts their use in mass researches. In addition, these methods are almost always based on receive and study of pure cultures, which completely excludes possibility of getting information on biocenosis as a system.

New technologies, first of all molecular-genetic methods, created favorable prerequisites for appearance of basically new trends in studying microbe populations as well as features in between microorganism and microbiome-macroorganism interactions. Only due to creation and wide usage of efficient parallel sequencing methods a real opportunity to start metagenomic study appeared with necessary for systematic approach depth.  Usage of genetic platforms like GS FLX (Roсhe), HiSeq 2000 (Illumina), SOLiD™ 4 System (Applied Biosystems) allows to make full metagenomic study not only on 16S rRNA gene analysis but on results of full microorganism genes’, their plasmids and viruses sequencing. It significantly simplifies creation of an overall view of interactions between human organism and gut microbiocenosis because of possibility of reconstruction of metabolic pathways inside the studied system.