Name of the project: Health programming, evolution of the infants’ microbiome

Name of the project: Health programming, evolution of the infants’ microbiome

IRN: AP09259975



The gut microbiota is known to be a dynamically changing ecosystem that plays a central role in human health and disease. It contributes to the proper functioning of the intestine, to the development and functioning of the immune system, and to protect the host organism from foreign pathogens through competitive antagonism. Responsible to produce short-chain fatty acids and secondary bile acids. Microbial colonization is a multifaceted process that depends on many factors. From the moment of birth, the intestines of the child are colonized by a wide group of microorganisms. Moreover, the method of birth provides a different signature of the microflora. The correct formation of the microbiome, according to our hypothesis, is a critical point in the formation of a healthy organism. In our work, we focus on the factors influencing the formation of resistome (acquisition of resistance genes) of microflora. The influence of the following factors on this process: the microbial flora of the intestines of mothers, the way of birth, nutrition and its frequency, the stress associated with vaccination according to the vaccination calendar, diseases, the introduction of antibiotics, complementary foods, etc. We hypothesize that the adherence of the Kazakh population to a diet based on red meat (horse meat, beef), flour products may affect the acquisition of a special microbial signature associated with antibiotic resistance.

The global goal of the project: Determination of the influence of environmental factors on sustainable changes in the intestinal microbiome of the infant.

The objectives of the first (2021) year of research are: Recruiting children for the study and starting the collection of stool samples and scrapings from the oral cavity. Working out the logistics of collecting biological material with clinical institutions. Preparation of electronic and paper questionnaire forms for participants to fill out. Bacterial DNA sequencing of the gut microbiome of infants and their mothers.

Expected and achieved results

The implementation of the project will allow: to identify the ways of formation of the intestinal metagenome and its influence on the delay in the growth and development of the child; to obtain new data on the contribution of nutrition, social pressure, environment to morbidity. The study will reveal the dominant factors influencing the formation of the "pathological microbiome" and leading to an unfavorable outcome. The main microbial and/or metagenomic biomarkers of child development will be identified. Prognostically significant results will be an improvement in the quality of life of people through the formation of recommendations on nutrition and methods for correcting the intestinal microbiome.

During the reporting period, we carried out work on recruiting newborn children and their mothers for the study. Inhabitants of Nur-Sultan city take part in the research. Collected data from the anamnesis from the first day of the child's life. During the reporting period, 101 participants were recruited. Recruiting newborns and their mothers for the study is ongoing. Collected data from the first day to six months of life. Also, data on the history of pregnancy, diseases during pregnancy, the severity of the course, complications in childbirth, the mode of birth, etc. are collected. The average height of the group of children at birth recruited during the reporting period is 54.26 cm, the average weight is 3602.26 g, the average gestation period is 279.15 days (39 weeks and 6 days). From birth to 1 month, more than 85% of children were exclusively breastfed, while only 81% of children were breastfed by 3 months of age. We have carried out and continue to work on collecting samples of feces and scrapings from the oral cavity in dynamics. So far, more than 260 samples have been collected. Total bacterial DNA was isolated from 255 to study the microbiome, metagenome, and resistome of newborns and their mothers. Samples were collected immediately after birth. Next, we collected feces and scrapings from the oral cavity after 1 month of life, 3 and 6 months of life of the same children. Also, samples were collected from mothers 1 month after delivery. This is necessary to compare the metagenome and resistome of the microflora of children and their mothers, to consider the possible transfer of certain taxa of microorganisms and their genes, as well as the transfer of antibiotic resistance genes. Since taxonomic composition alone is not enough to decipher the functions of the gut microbiome, sequencing to identify genes involved in metabolic pathways and mapping these short gene sequences will improve predictive functionality.


Research team

Full name

Participation in the project

Scientific / academic degree


Scopus Authors ID

Research ID

Kozhakhmetov Samat

Principal investigator

Ph.D., associate professor




Morenko Marina


Ph.D, D.M.Sc.




Chulenbaeva Laura






Schneider Ksenia






Meiramova Zarina


PhD doctoral student




Nurgaziev Madiyar


Master of Biology




Mukhanbetzhanov Nurislam


Master of Biology