2009 – 2011 - Lomonosov Moscow State University (MSU) - Master's degree, Biotechnology
2009 – 2011 - Taras Shevchenko National University of Kyiv - Master's degree, Cytology, and histology
2005 – 2009 - Taras Shevchenko National University of Kyiv – Bachelor’s degree, Biology
Metagenome-assembled genomes from a population-based cohort uncover novel gut species and within-species diversity, revealing prevalent disease associations Kateryna Pantiukh, Kertu Liis Krigul, Oliver Aasmets, Elin Org Msystems, 2026 Metagenomic profiling has advanced the understanding of microbe-host interactions. However, widely used read-based approaches are limited by incomplete reference databases and the inability to resolve strain-level variation. Here, we present a scalable, genome-resolved framework that integrates population-specific metagenome-assembled genomes (MAGs) to discover novel species, within-species diversity, and disease associations. From 1,878 deeply sequenced samples in the Estonian Microbiome Cohort (EstMB-deep), we reconstructed 84,762 MAGs representing 2,257 species, including 353 (15.6%) previously uncharacterized species reaching up to 30% relative abundances in some individuals. We integrated these MAGs with the Unified Human Gastrointestinal Genome collection to create an expanded reference (GUTrep), enabling profiling of 2,509 EstMB individuals and testing associations with 33 prevalent diseases. Of the 25 diseases with significant associations, 8 involved newly identified species, underscoring the value of population-specific MAGs. To quantify within-species diversity, we developed the genome unit number (GUN), a novel MAG-based metric that informed within-species analyses. Based on normalized GUN, we prioritized Odoribacter splanchnicus, a prevalent species with the lowest within-species heterogeneity, yielding sufficient power for a within-species association study. We identified two dominant genome units, GU-N1 and GU-N2, with distinct gene repertoires and divergent disease associations. Notably, GU-N1 was negatively associated with gastritis, duodenitis, and hypertensive heart disease, associations undetected at the species level. Our study expands the human gut reference landscape, demonstrates the importance of population-specific MAGs for uncovering novel microbial diversity, and reveals new disease associations at the within-species level obscured at higher taxonomic levels, highlighting the need for genome-resolved approaches in microbiome research. IMPORTANCE Microbiome studies increasingly recognize that species-level profiles can mask critical within-species differences relevant to health and disease. However, our work shows that within-species diversity varies drastically across gut microbes, with some species exhibiting almost as many distinct within-species clusters as recovered genomes, making association studies at the within-species level essentially intractable. To address this, we introduce the genome unit number (GUN), a scalable metric for quantifying within-species structure. Using GUN, we demonstrate that only species with limited within-species diversity, such as Odoribacter splanchnicus , currently allow for robust within-species association testing. These findings emphasize the need to systematically evaluate species structure across the gut microbiome and call for the development of new computational and statistical approaches to enable meaningful within-species analyses in highly diverse species.
The Estonian Biobank’s journey from biobanking to personalized medicine Lili Milani, Maris Alver, Sven Laur, Sulev Reisberg, Toomas Haller, et al. Nature Communications, 2025 Large biobanks have set a new standard for research and innovation in human genomics and implementation of personalized medicine. The Estonian Biobank was founded a quarter of a century ago, and its biological specimens, clinical, health, omics, and lifestyle data have been included in over 800 publications to date. What makes the biobank unique internationally is its translational focus, with active efforts to conduct clinical studies based on genetic findings, and to explore the effects of return of results on participants. In this review, we provide an overview of the Estonian Biobank, highlight its strengths for studying the effects of genetic variation and quantitative phenotypes on health-related traits, development of methods and frameworks for bringing genomics into the clinic, and its role as a driving force for implementing personalized medicine on a national level and beyond.
A history of repeated antibiotic usage leads to microbiota-dependent mucus defects Kertu Liis Krigul, Rachel H. Feeney, Supapit Wongkuna, Oliver Aasmets, Sandra M. Holmberg, et al. Gut Microbes, 2024 Recent evidence indicates that repeated antibiotic usage lowers microbial diversity and lastingly changes the gut microbiota community. However, the physiological effects of repeated – but not recent – antibiotic usage on microbiota-mediated mucosal barrier function are largely unknown. By selecting human individuals from the deeply-phenotyped Estonian Microbiome Cohort (EstMB) we here utilised human-to-mouse faecal microbiota transplantation to explore long-term impacts of repeated antibiotic use on intestinal mucus function. While a healthy mucus layer protects the intestinal epithelium against infection and inflammation, using ex-vivo mucus function analyses of viable colonic tissue explants, we show that microbiota from humans with a history of repeated antibiotic use causes reduced mucus growth rate and increased mucus penetrability compared to healthy controls in the transplanted mice. Moreover, shotgun metagenomic sequencing identified a significantly altered microbiota composition in the antibiotic-shaped microbial community, with known mucus-utilising bacteria, including Akkermansia muciniphila and Bacteroides fragilis, dominating in the gut. The altered microbiota composition was further characterised by a distinct metabolite profile, which may be caused by differential mucus degradation capacity. Consequently, our findings suggest that long-term antibiotic use in humans results in an altered microbial community that has reduced capacity to maintain proper mucus function in the gut.
The use of whole genome amplification for genomic evaluation of bovine embryos K. S. Pantiukh, I. V. Rukin, S. V. Portnov, A. Khatib, S. V. Panteleev, et al. Vavilovskii Zhurnal Genetiki I Selektsii, 2019 The integration of high technologies into livestock production has been actively occurring in the last decade in the countries with a developed animal breeding. First of all, we are talking about reproductive technologies (IVF) and genomic technologies (general genomic evaluation of animal and genomic evaluation of breeding value). Combining reproductive and genomic technologies is a promising approach that allows receiving highquality breeding cattle in the shortest possible time. The basis of the proposed technology for accelerated reproduction of high-value breeding cattle is to obtain information about the genome of the embryo for genomic evaluation. The amount of genetic material that can be obtained for research is extremely limited, as it is necessary to preserve the viability of the embryo. The stage of the whole genome amplification was introduced to obtain a high quality of genetic material in a sufficient quantity. The main purpose of this work is to assess the possibility of using embryo biopsy specimens (bsp) for embryo genotyping using microarray chips and predicting the carrier status of lethal haplotypes at the embryo stage. We obtained 100 cattle embryos, of which 78 biopsy specimens were taken to analysis. For the biopsies obtained we performed the whole genome amplification. The quality and quantity of DNA for all the 78 samples after the whole genome amplification were satisfactory for further genotyping. The quality of the performed genotyping was satisfactory and allowed the assessment of lethal haplotype carriers (determining the sex of the animal and identification of the carrier status for sevenHolsteinlethal haplotypes). We tested 78 embryos. From the genotyping analysis, there was detected one carrier status for three lethal haplotypes, HH0 (Brachyspina), HH5, and HCD. The carrier status of HH0 and HH5 was confirmed by testing the casual mutation using PCR analysis. The carrier status for HCD has not been confirmed by casual mutation analysis. The situation in which an animal is an HCD carrier, but not the carrier of a casual mutation, can be explained. The putative ancestor of the haplotype is the bull HOCAN000000334489 WILLOWHOLME MARK ANTHONY (year of birth is 1975), but a casual mutation associated with this disease has arisen only in his descendant HOCAN000005457798 MAUGHLIN STORM (year of birth is 1991). The results obtained confirm the importance of testing the casual mutation in the animals that are carriers of lethal haplotypes according to the genotyping data.
Forecasting the Embryo productivity of donor cows on the basis of echographic characteristics of the ovaries A.V. Brigida, V.I. Sorokin, S.N. Kovalchuk, K.S. Pantiukh, I.V. Rukin, et al. Sel Skokhozyaistvennaya Biologiya, 2018 The main problem restricting the wide use of reproductive biotechnology in animal husbandry is insufficiently developed methods for selection of donor cows for embryo transfer. The objective reason is the variability of the ovarian response to gonadotropins injections. Until now, there is no reliable information about possibility of forecasting the embryo productivity of donor cows before gonadotropin stimulation, which affects substantively the economic feasibility of embryo transfer as a method of accelerated cattle reproduction. We have applied the post-pressing analysis of ovaries echograms for forecasting the embryo productivity of donor cows on the basis of comparisons of quantitative and qualitative indicators of ovaries after induced superovulation and its’ echographic characteristics. We carried out morphofunctional study of ovaries in donor cows (n = 30) on day 10 of estrous cycle, before artificial insemination (estrus) and on day 7 of the inducted estrous cycle, immediately before the extraction of embryos using data on post-pressing ovarian morphometry. Animals were divided into three groups (I, II и III, n = 10 for each group) with yellow body length of 2.5 cm, 1.5-2.5 cm and 1.5 cm, respectively. Echographic visualization of the ovaries was performed using endorectal ultrasonography. Polyovulatory response of ovaries was induced with FSHsuper (Russia) injected eight times, with 12 h interval, at decreasing doses. The embryos were recovered on day 7 after artificial insemination. Optimal criteria for predicting the polyovulatory response of ovaries and the quantity of embryos were determined on the basis of the ovarian morphometry. Statistically significant differences with the control were assessed by the Student’s t-test. It was found that the average areas of the ovaries on the echograms were 7.9±0.94, 5.7±0.78 and 3.5±0.06 cm2 for group I, group II and group III, respectively. The area of the yellow body in group I averaged 4.5±1.21 cm2, was 2.08 cm2 higher (P 0.05) than in group II, and exceeded the corresponding parameter in group III by 3.43 cm2 (P 0.05). A comparative evaluation of the ratio of the yellow body areas to the ovaries area of each animal and on average along the groups showed that in group I with the ratio of 57.1±3.01 % the number of yellow bodies was 11.6±1.26 and the average yield of the embryos was 9.3±1.23 per animal. In group II with the ratio of the areas of yellow bodies and ovaries of 42.1±2.9 % the number of yellow bodies before embryos recovery was 5.7±1.24, and 4.6±1.01 embryos were recovered per procedure. The lowest embryo recovery (less than one embryo per procedure) was observed in group III with the relative area of yellow bodies of 30.2±2.56 % and the average number of the yellow bodies of 1.8±0.18. Comparison of the size of the yellow bodies before the induction of polyovulation and data characterizing the efficiency of induction of superovulation and recovery of embryos showed that in animals with a ratio of the areas of the yellow body and ovary more than 50 %, high response can be obtained resulting in 11.6±1.26 yellow bodies and 9.3±1.23 embryos per extraction.
Report on noninvasive prenatal testing: Classical and alternative approaches. Kateryna S. Pantiukh, Nikolay N. Chekanov, Igor V. Zaigrin, Alexei M. Zotov, Alexander M. Mazur, et al. F1000research, 2016 Concerns of traditional prenatal aneuploidy testing methods, such as low accuracy of noninvasive and health risks associated with invasive procedures, were overcome with the introduction of novel noninvasive methods based on genetics (NIPT). These were rapidly adopted into clinical practice in many countries after a series of successful trials of various independent submethods. Here we present results of own NIPT trial carried out in Moscow, Russia. 1012 samples were subjected to the method aimed at measuring chromosome coverage by massive parallel sequencing. Two alternative approaches are ascertained: one based on maternal/fetal differential methylation and another based on allelic difference. While the former failed to provide stable results, the latter was found to be promising and worthy of conducting a large-scale trial. One critical point in any NIPT approach is the determination of fetal cell-free DNA fraction, which dictates the reliability of obtained results for a given sample. We show that two different chromosome Y representation measures—by real-time PCR and by whole-genome massive parallel sequencing—are practically interchangeable (r=0.94). We also propose a novel method based on maternal/fetal allelic difference which is applicable in pregnancies with fetuses of either sex. Even in its pilot form it correlates well with chromosome Y coverage estimates (r=0.74) and can be further improved by increasing the number of polymorphisms.
Metagenome-assembled genomes from a population-based cohort uncover novel gut species and within-species diversity, revealing prevalent disease associations K Pantiukh, KL Krigul, O Aasmets, E Org Msystems 11 (4), e00114-26 , 2026 2026
Human gut archaea collection from Estonian population K Pantiukh, E Org Scientific Data , 2026 2026
A large-scale comparative metagenomic analysis of short-read sequencing platforms indicates high taxonomic concordance and functional analysis challenges K Zielińska, K Pantiukh, PP Łabaj, T Kosciolek, E Org bioRxiv, 2025.07. 06.662369 , 2025 2025 Citations: 2
Microbiome variations in osteoarthritis reflect aging and metabolic factors, not the disease K Bevc, L Malfertheiner, S Neuenschwander, VD Tran, M Pagni, ... bioRxiv, 2025.06. 24.661261 , 2025 2025
The Estonian Biobank’s journey from biobanking to personalized medicine L Milani, M Alver, S Laur, S Reisberg, T Haller, O Aasmets, E Abner, ... Nature communications 16 (1), 3270 , 2025 2025 Citations: 71
A history of repeated antibiotic usage leads to microbiota-dependent mucus defects KL Krigul, RH Feeney, S Wongkuna, O Aasmets, SM Holmberg, ... Gut Microbes 16 (1), 2377570 , 2024 2024 Citations: 26
From Biobanking to personalized medicine: The journey of the Estonian Biobank L Milani, M Alver, S Laur, S Reisberg, T Haller, O Aasmets, E Abner, ... medRxiv, 2024.09. 22.24313964 , 2024 2024 Citations: 26
METAGENOME-ASSEMBLED GENOMES FROM A POPULATION-BASED COHORT UNCOVER NOVEL GUT SPECIES AND STRAIN DIVERSITY, REVEALING PREVALENT DISEASE ASSOCIATIONS K Pantiukh, KL Krigul, O Aasmets, E Org bioRxiv, 2024.07. 06.602324 , 2024 2024
NO OBSERVABLE DIFFERENCES IN THE GUT MICROBIOME OF OSTEROARTHITIS PATIENTS K Bevc, L Malfertheiner, K Pantiukh, M Jaagura, A Havulinna, V Salomaa, ... Osteoarthritis and Cartilage 32, S60 , 2024 2024
Metagenome-assembled genomes of Estonian Microbiome cohort reveal novel species and their links with prevalent diseases K Pantiukh, O Aasmets, KL Krigul, E Org bioRxiv , 2024 2024 Citations: 3
The use of whole genome amplification for genomic evaluation of bovine embryos KS Pantiukh, IV Rukin, SM Portnov, A Khatib, SL Panteleev, AM Mazur Vavilov Journal of Genetics and Breeding 23 (4), 489-495 , 2019 2019 Citations: 5
Прогнозирование эмбриопродуктивности коров-доноров на основании эхографической характеристики яичников АВ Бригида, ВИ Сорокин, СН Ковальчук, КС Пантюх, ИВ Рукин, ... Сельскохозяйственная биология 53 (4), 753-761 , 2018 2018 Citations: 11
Profiling of microRNAs in wild type and early flowering transgenic Chrysanthemum morifolium by deep sequencing OA Shulga, AV Nedoluzhko, AV Shchennikova, NM Gruzdeva, ... Plant Cell, Tissue and Organ Culture (PCTOC) 128 (2), 283-301 , 2017 2017 Citations: 13
New approaches to prenatal screening for chromosomal abnormalities: Maternal blood DNA screening GT Sukhikh, DY Trofimov, IY Barkov, AE Donnikov, ES Shubina, ... Obstetrics and Gynecology 8, 72-8 , 2016 2016 Citations: 5
Report on noninvasive prenatal testing: classical and alternative approaches KS Pantiukh, NN Chekanov, IV Zaigrin, AM Zotov, AM Mazur, ... F1000Research 5, 722 , 2016 2016 Citations: 8
Новые подходы к проведению пренатального скрининга хромосомной патологии: ДНК-скрининг по крови матери Акушерство и гинекология 8 , 2016 2016 Citations: 22
Blood extracellular DNA sequencing-based noninvasive prenatal diagnosis of fetal aneuploidies in a pregnant woman KS Pantyukh, ES Shubina Obstetrics and gynecology 8, 5-11 , 2015 2015 Citations: 2
Неинвазивная пренатальная диагностика анеуплоидий плода, основанная на секвенировании внеклеточной ДНК крови беременной женщины КС Пантюх, ЕС Шубина Акушерство и гинекология, 5-11 , 2015 2015 Citations: 13
Development a new method for noninvasive prenatal detection of fetal aneuploidy: P2-23 K Pantiukh, A Shanko, E Khrameeva, N Mospan Prenatal Diagnosis 33, 79 , 2013 2013
Геномная селекция-будущее в разведении животных ИВ Рукин, ЕС Пантюх, ДС Груздев Зоотехния, 8-9 , 2013 2013 Citations: 48
MOST CITED SCHOLAR PUBLICATIONS
The Estonian Biobank’s journey from biobanking to personalized medicine L Milani, M Alver, S Laur, S Reisberg, T Haller, O Aasmets, E Abner, ... Nature communications 16 (1), 3270 , 2025 2025 Citations: 71
Геномная селекция-будущее в разведении животных ИВ Рукин, ЕС Пантюх, ДС Груздев Зоотехния, 8-9 , 2013 2013 Citations: 48
A history of repeated antibiotic usage leads to microbiota-dependent mucus defects KL Krigul, RH Feeney, S Wongkuna, O Aasmets, SM Holmberg, ... Gut Microbes 16 (1), 2377570 , 2024 2024 Citations: 26
From Biobanking to personalized medicine: The journey of the Estonian Biobank L Milani, M Alver, S Laur, S Reisberg, T Haller, O Aasmets, E Abner, ... medRxiv, 2024.09. 22.24313964 , 2024 2024 Citations: 26
Новые подходы к проведению пренатального скрининга хромосомной патологии: ДНК-скрининг по крови матери Акушерство и гинекология 8 , 2016 2016 Citations: 22
Profiling of microRNAs in wild type and early flowering transgenic Chrysanthemum morifolium by deep sequencing OA Shulga, AV Nedoluzhko, AV Shchennikova, NM Gruzdeva, ... Plant Cell, Tissue and Organ Culture (PCTOC) 128 (2), 283-301 , 2017 2017 Citations: 13
Неинвазивная пренатальная диагностика анеуплоидий плода, основанная на секвенировании внеклеточной ДНК крови беременной женщины КС Пантюх, ЕС Шубина Акушерство и гинекология, 5-11 , 2015 2015 Citations: 13
Прогнозирование эмбриопродуктивности коров-доноров на основании эхографической характеристики яичников АВ Бригида, ВИ Сорокин, СН Ковальчук, КС Пантюх, ИВ Рукин, ... Сельскохозяйственная биология 53 (4), 753-761 , 2018 2018 Citations: 11
Report on noninvasive prenatal testing: classical and alternative approaches KS Pantiukh, NN Chekanov, IV Zaigrin, AM Zotov, AM Mazur, ... F1000Research 5, 722 , 2016 2016 Citations: 8
The use of whole genome amplification for genomic evaluation of bovine embryos KS Pantiukh, IV Rukin, SM Portnov, A Khatib, SL Panteleev, AM Mazur Vavilov Journal of Genetics and Breeding 23 (4), 489-495 , 2019 2019 Citations: 5
New approaches to prenatal screening for chromosomal abnormalities: Maternal blood DNA screening GT Sukhikh, DY Trofimov, IY Barkov, AE Donnikov, ES Shubina, ... Obstetrics and Gynecology 8, 72-8 , 2016 2016 Citations: 5
Metagenome-assembled genomes of Estonian Microbiome cohort reveal novel species and their links with prevalent diseases K Pantiukh, O Aasmets, KL Krigul, E Org bioRxiv , 2024 2024 Citations: 3
A large-scale comparative metagenomic analysis of short-read sequencing platforms indicates high taxonomic concordance and functional analysis challenges K Zielińska, K Pantiukh, PP Łabaj, T Kosciolek, E Org bioRxiv, 2025.07. 06.662369 , 2025 2025 Citations: 2
Blood extracellular DNA sequencing-based noninvasive prenatal diagnosis of fetal aneuploidies in a pregnant woman KS Pantyukh, ES Shubina Obstetrics and gynecology 8, 5-11 , 2015 2015 Citations: 2
Metagenome-assembled genomes from a population-based cohort uncover novel gut species and within-species diversity, revealing prevalent disease associations K Pantiukh, KL Krigul, O Aasmets, E Org Msystems 11 (4), e00114-26 , 2026 2026
Human gut archaea collection from Estonian population K Pantiukh, E Org Scientific Data , 2026 2026
Microbiome variations in osteoarthritis reflect aging and metabolic factors, not the disease K Bevc, L Malfertheiner, S Neuenschwander, VD Tran, M Pagni, ... bioRxiv, 2025.06. 24.661261 , 2025 2025
METAGENOME-ASSEMBLED GENOMES FROM A POPULATION-BASED COHORT UNCOVER NOVEL GUT SPECIES AND STRAIN DIVERSITY, REVEALING PREVALENT DISEASE ASSOCIATIONS K Pantiukh, KL Krigul, O Aasmets, E Org bioRxiv, 2024.07. 06.602324 , 2024 2024
NO OBSERVABLE DIFFERENCES IN THE GUT MICROBIOME OF OSTEROARTHITIS PATIENTS K Bevc, L Malfertheiner, K Pantiukh, M Jaagura, A Havulinna, V Salomaa, ... Osteoarthritis and Cartilage 32, S60 , 2024 2024
Development a new method for noninvasive prenatal detection of fetal aneuploidy: P2-23 K Pantiukh, A Shanko, E Khrameeva, N Mospan Prenatal Diagnosis 33, 79 , 2013 2013
Publications
Pantiukh KS, Chekanov NN, Zaigrin IV, Zotov AM, Mazur AM, Prokhortchouk EB. Report on noninvasive prenatal testing: classical and alternative approaches. F1000Res. 2016 Apr 22;5:722.
Pantiukh K., Shanko A., Khrameeva E., Mospan N. Development a new method for noninvasive prenatal detection of fetal aneuploidy// Prenat Diagn 2013; 33(Suppl. 1): P-53.
Patent 2585519 (27.05.2016) A method for selecting target DNA regions
