Ph.D.: University of Manchester, Manchester, UK. Microbiology, Molecular and Structural Biology.

Postdoctoral: University of California at Berkeley, Berkeley, Ca, USA. Microbiology and Systems Biology.

The research in our laboratory is focused on the studies of complex microbial communities associated with human gastrointestinal system. We use a variety of research techniques including ribosomal gene sequencing, metagenomics, phylogenetic microarrays, and fluorescent in situ hybridization to gain knowledge of community composition and function, its changes in disease, and its response to diet perturbations. We also associate microbial dynamics to changes in luminal and fecal metabolites in the same samples. We employ mathematical modeling to generate hypotheses of possible microbial and host-microbial interactions, that we then test in the in vitro human gut simulator system. We also study individual microbial species to gain insight into the specific roles these members play in our lives and how they interact with each other.

Specific ares of focus include:

• Role of gut microbes in human health and in gastrointestinal diseases such as IBS, metabolic syndrome, and obesity
• Human gut microbiota as a mediator of dietary effects on human physiology and immune system
• Degradation of dietary nutrients by gut microbial communities
• Network analysis of microbiota composition, functional capacity, and metabolite transformations

• Standard microbiology techniques
• Standard molecular biology methods
• Gene expression profiling with microarrays and qPCR
• Microbial community analysis by high-throughput sequencing, phylogenetic microarrays, and FISH
• Bioinformatics and computational biology
• Biostatistics and phylogenetic analysis

• Collaborative paper published:

S. Rajakaruna, B. Bandow, S. Pérez-Burillo, B. Navajas-Porras, J.Á. Rufián-Henares, D.R. Cool, K.-J. Cho, and O. Paliy. Human gut microbiota-fermented asparagus powder protects human epithelial cells from injury and inflammation (2025) Food Funct., 16(3): 1060-1071.

• Collaborative paper published:

B. Bandow, E.S. Shaaban, S. Rajakaruna, Z. Saleh, S.A. Abdelaziz, L. Hussein, O. Paliy. Diet Supplementation with Pomegranate Fruit Alters Distal Gut Microbiota of Healthy Female College Students (2025) Microorganisms, 13(2): 305.

• Collaborative paper published:

K.L. Sprague, S. Rajakaruna, B. Bandow, N. Burchat, M. Bottomley, H. Sampath, and O. Paliy. Gut Microbiota Fermentation of Digested Almond-Psyllium-Flax Seed-Based Artisan Bread Promotes Mediterranean Diet-Resembling Microbial Community (2024) Microorganisms, 12(6): 1189.

• Collaborative paper published:

S. Rajakaruna, S. Pérez-Burillo, J.Á. Rufián-Henares, and O. Paliy. Human gut microbiota fermentation of cooked eggplant, garlic, and onion supports distinct microbial communities (2024) Food Funct., 15(5): 2751-2759.

• Collaborative paper published:

A. Delgado-Osorio, B. Navajas-Porras, S. Pérez-Burillo, D. Hinojosa-Nogueira, Á. Toledano-Marín, S. Pastoriza de la Cueva, O. Paliy, and J.Á. Rufián-Henares. Cultivar and Harvest Time of Almonds Affect Their Antioxidant and Nutritional Profile through Gut Microbiota Modifications (2024) Antioxidants, 13(1): 84.

• Dr Paliy receives Fulbright Scholar award:

Dr Paliy has been selected as Fulbright Scholar for the 2022-2023. He will travel to Giza-Cairo in Egypt to work on a collaborative project with his colleague, Dr. Laila Hussein. Together they will investigate how supplementing diet of Egyptian teenagers with prebiotic fiber can improve children gut health and affect their intestinal microbes.

• Collaborative paper published:

S. Rajakaruna, S. Pérez-Burillo, D.L. Kramer, J.Á. Rufián-Henares, and O. Paliy. Dietary Melanoidins from Biscuits and Bread Crust Alter the Structure and Short-Chain Fatty Acid Production of Human Gut Microbiota (2022) Microorganisms, 10(7): 1268.

• Invited review published:

O. Paliy and S. Rajakaruna. Development of Microbiota - Is the Process Continuing Through Adolescence? (2022) in: Glibetic, M. (Ed.), Comprehensive Gut Microbiota, vol. 2. Elsevier, pp. 59–68.

• Dr Paliy receives Fulbright Specialist award:

Dr Paliy has been awarded the Fulbright Specialist status for the 2021-2025 period.

• Diggs Laboratory for Life Sciences

  

Our laboratory is situated on the 2nd floor of the newly constructed Diggs Laboratory for Life Science Research building. The building contains more spacious labs with large windows and has modern laboratory workbenches and office areas. It features open floor design for main laboratories, has wireless network hubs on all floors of the building, and is fitted with electronic temperature controls and light sensors.

• Paliy Lab: 265 Diggs

Our laboratory consists of three separate rooms and a common corridor space housing large equipment. Main laboratory has spaces for six researchers to carry out experimental work. Equipment situated in this room includes centrifuges, ABI qPCR machine, PCR thermocycler, laminar hood, incubator, UV-Vis spectrophotometer, vacuum evaporator, balances, etc.

• Anarobic culturing facility

  

The adjacent to main laboratory culturing room contains Coy dual anaerobic chamber system, dedicated CO₂ and low oxygen incubators, and class II laminar hood. Anaerboic polymer chamber allow us to culture obligate anaerobic microbes in oxygen-free conditions, whereas we can place different equipment pieces in the anaerobic vinyl chamber and carry out experiments with these anaerobes.

• Human gut simulator facility

A separate room houses in vitro simulator of human gut that we designed and built in our laboratory. Each gut simulator vessel simulates a separate region of the gut; three regions representing ascending, transverse, and descending colon are shown in the image. A mixture of N₂ and CO₂ gases is pumped periodically through each vessel to maintain anaerobic environment.

• Student office: 256 Diggs

A separate room in close proximity to the laboratory and to Dr. Paliy office serves as student office / computer room. The office has space for at least four students, additional desks are also positioned in the main laboratory. Student office houses three networked personal computers and a network printer. For sustenance during work, microwave and coffee machine are also strategically placed in the office.

• S. Rajakaruna, B. Bandow, S. Pérez-Burillo, B. Navajas-Porras, J.Á. Rufián-Henares, D.R. Cool, K.-J. Cho, and O. Paliy. Human gut microbiota-fermented asparagus powder protects human epithelial cells from injury and inflammation (2025) Food Funct., 16(3): 1060-1071. https://pubmed.ncbi.nlm.nih.gov/39821238/

• B. Bandow, E.S. Shaaban, S. Rajakaruna, Z. Saleh, S.A. Abdelaziz, L. Hussein, O. Paliy. Diet Supplementation with Pomegranate Fruit Alters Distal Gut Microbiota of Healthy Female College Students (2025) Microorganisms, 13(2): 305. https://pubmed.ncbi.nlm.nih.gov/40005672/

• K.L. Sprague, S. Rajakaruna, B. Bandow, N. Burchat, M. Bottomley, H. Sampath, and O. Paliy. Gut Microbiota Fermentation of Digested Almond-Psyllium-Flax Seed-Based Artisan Bread Promotes Mediterranean Diet-Resembling Microbial Community (2024) Microorganisms, 12(6): 1189. https://pubmed.ncbi.nlm.nih.gov/38930571/

• S. Rajakaruna, S. Pérez-Burillo, J.Á. Rufián-Henares, and O. Paliy. Human gut microbiota fermentation of cooked eggplant, garlic, and onion supports distinct microbial communities (2024) Food Funct., 15(5): 2751-2759. https://pubmed.ncbi.nlm.nih.gov/38380654/

• A. Delgado-Osorio, B. Navajas-Porras, S. Pérez-Burillo, D. Hinojosa-Nogueira, Á. Toledano-Marín, S. Pastoriza de la Cueva, O. Paliy, and J.Á. Rufián-Henares. Cultivar and Harvest Time of Almonds Affect Their Antioxidant and Nutritional Profile through Gut Microbiota Modifications (2024) Antioxidants, 13(1): 84. https://pubmed.ncbi.nlm.nih.gov/38247508/

• L.M. Ketelboeter, A. Gordon, S.U. Welmillage, V. S. Sreevidya, O. Paliy and P. Gyaneshwar. Transcriptomic and physiological responses of Rhizobium sp. IRBG74 to Sesbania cannabina and Rice (Oryza sativa L) rhizosphere (2023) Plant Soil, 483(1-2): 515-532. https://link.springer.com/article/10.1007/s11104-022-05761-2

• S. Rajakaruna, S. Pérez-Burillo, D.L. Kramer, J.Á. Rufián-Henares, and O. Paliy. Dietary Melanoidins from Biscuits and Bread Crust Alter the Structure and Short-Chain Fatty Acid Production of Human Gut Microbiota (2022) Microorganisms, 10(7): 1268. https://pubmed.ncbi.nlm.nih.gov/35888986/

• S. Perez-Burillo, S. Rajakaruna, and O. Paliy. Growth of Bifidobacterium species is inhibited by free fatty acids and bile salts but not by glycerides (2022) AIMS Microbiol., 8(1): 53–60. https://aimspress.com/article/doi/10.3934/microbiol.2022005

• O. Paliy and S. Rajakaruna. Development of Microbiota - Is the Process Continuing Through Adolescence? (2022) in: Glibetic, M. (Ed.), Comprehensive Gut Microbiota, vol. 2. Elsevier, pp. 59–68. https://www.sciencedirect.com/science/article/pii/B978012819265800022X

• S. Pérez-Burillo, S. Rajakaruna, O. Paliy, S. Pastoriza, J.Á. Rufián-Henares. Bioactivity of food melanoidins is mediated by gut microbiota (2020) Food Chem. 316: 126309. https://www.ncbi.nlm.nih.gov/pubmed/32059165

• M.P. Craig, S. Rajakaruna, O. Paliy, M. Sajjad, S. Madhavan, N. Reddy, J. Zhang, M. Bottomley, S. Agrawal, M.P. Kadakia. Differential MicroRNA Signatures in the Pathogenesis of Barrett’s Esophagus (2020) Clin. Transl. Gastroenterol. 11(1): e00125. https://www.ncbi.nlm.nih.gov/pubmed/31934893

• R.T. Agans, A. Gordon, S. Hussain, O. Paliy. Titanium dioxide nanoparticles elicit lower direct inhibitory effect on human gut microbiota than silver nanoparticles (2019) Toxicol. Sci., 172(2): 411-416. https://www.ncbi.nlm.nih.gov/pubmed/31550005. This article was chosen for Tox Spotlight section.

• S. Rajakaruna, D.A. Freedman, A.R. Sehgal, X. Bui, and O. Paliy. Diet quality and body mass indices show opposite associations with distal gut microbiota in a low-income cohort (2019) J. Food Sci. Technol., 4(7): 846-851. https://www.siftdesk.org/article-details/Diet-quality-and-body-mass-indi...

• S. Pérez-Burillo, T. Mehta, S. Pastoriza, D.L. Kramer, O. Paliy, J.Á. Rufián-Henares. Potential probiotic salami with dietary fiber modulates antioxidant capacity, short chain fatty acid production and gut microbiota community structure (2019) Food Sci. Technol. 105: 355-362. https://www.sciencedirect.com/science/article/pii/S002364381930088X

• S. Pérez-Burillo, T. Mehta, A. Esteban-Muñoz, S. Pastoriza, O. Paliy, J.Á. Rufián-Henares. Effect of in vitro digestion-fermentation on green and roasted coffee bioactivity: The role of the gut microbiota (2019) Food Chem. 279: 252-259. https://www.ncbi.nlm.nih.gov/pubmed/30611488

• R. Agans, A. Gordon, D.L. Kramer, S. Pérez-Burillo, J.A. Rufián-Henares, and O. Paliy. Dietary fatty acids sustain the growth of the human gut microbiota (2018) Appl. Environ. Microbiol. 84(21): e01525-18. https://www.ncbi.nlm.nih.gov/pubmed/30242004 This article was highlighted in AEM and Wright State BSoM press-releases.

• E. Labib, M. Blaut, L. Hussein, M. Gouda, D.L. Kramer, O. Paliy, B. Ganesh, P. Schumann, R. Pukall, A. Woting, M.T. Fouad. Molecular diversity of gut microbiota and short chain fatty acids in egyptian adults following dietary intervention with fermented sobya (2018) J. Food Microbiol. Saf. Hyg. 3 (2): 1000139. https://www.longdom.org/open-access/molecular-diversity-of-gut-microbiot...

• E. Kim, M. Lambert, G. Fallata, J. Rowe, T. Martin, A. Satoskar, N. Reo, O. Paliy, E. Cormet-Boyaka, and P.N. Boyaka. Intestinal epithelial cells regulate gut CCL11 responses and severity of allergy (2018) Front. Immunol. 9: 1692. https://www.ncbi.nlm.nih.gov/pubmed/30123215

• S. Sakaram, M. Craig, N. Hill, A. Aljagthmi, C. Garrido, O. Paliy, M. Bottomley, M.L. Raymer, and M. Kadakia. Identification of novel ΔNp63α-regulated miRNAs using an optimized small RNA-Seq analysis pipeline (2018) Sci. Rep. 8: 10069. http://www.ncbi.nlm.nih.gov/pubmed/29968742

• M.C. Jugan, A.J. Rudinsky, A. Gordon, D.L. Kramer, J.B. Daniels, O. Paliy, P. Boyaka, and C. Gilor. Effects of oral Akkermansia muciniphila supplementation in healthy dogs following antimicrobial administration (2018) Am. J. Vet. Res. 79(8): 884-892. https://www.ncbi.nlm.nih.gov/pubmed/30058857

• V. Shankar, R. Agans, and O. Paliy. Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities (2017) Sci. Rep. 7(1): 6481. http://www.ncbi.nlm.nih.gov/pubmed/28743891

• V. Shankar, M. Gouda, J. Moncivaiz, A. Gordon, N.V. Reo, L. Hussein, and O. Paliy. Differences in gut metabolites and microbial composition and functions between Egyptian and US teenagers are consistent with consumed diets (2017) mSystems 2(1): e00169-16. http://www.ncbi.nlm.nih.gov/pubmed/28191503

• O. Paliy and V. Shankar. Application of multivariate statistical techniques in microbial ecology (2016) Mol. Ecol. 25(5): 1032-57. http://www.ncbi.nlm.nih.gov/pubmed/26786791

• V. Shankar, N.V. Reo, and O. Paliy. Simultaneous fecal microbial and metabolite profiling enables accurate classification of pediatric irritable bowel syndrome (2015) Microbiome 3: 73. http://www.ncbi.nlm.nih.gov/pubmed/26653757

• V. Shankar, D. Homer, L. Rigsbee, H.J. Khamis, S. Michail, M. Raymer, N.V. Reo, and O. Paliy. The networks of human gut microbe-metabolite associations are different between health and irritable bowel syndrome (2015) ISME J., 9(8): 1899-903. http://www.ncbi.nlm.nih.gov/pubmed/25635640

• S. Michail, M. Lin, M.R. Frey, R. Fanter, O. Paliy, B. Hilbush, and N.V. Reo. Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease (2015) FEMS Microbiol. Ecol., 91(2): 1-9. http://www.ncbi.nlm.nih.gov/pubmed/25764541

• O. Paliy and V. Shankar. Applications of phylogenetic microarrays to profiling of human microbiomes (2014) in Microarrays: Current Technology, Innovations and Applications, Caister Academic Press, Norfolk, UK.

• V. Shankar, M.J. Hamilton, A. Khoruts, A. Kilburn, T. Unno, O. Paliy, and M.J. Sadowsky. Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation (2014) Microbiome, 2: 13. http://www.ncbi.nlm.nih.gov/pubmed/24855561

• O. Paliy, V. Shankar, and M. Sagova-Mareckova. Phylogenetic microarrays (2014) in Bioinformatics and Data Analysis in Microbiology, Caister Academic Press, Norfolk, UK.

• O. Paliy, C.J. Piyathilake, A. Kozyrskyj, G. Celep, F. Marotta, R. Rastmanesh. Excess body weight during pregnancy and offspring obesity: Potential mechanisms (2014) Nutrition, 30: 245-251. http://www.ncbi.nlm.nih.gov/pubmed/24103493

• O. Paliy. The golden age of molecular ecology (2013) J. Phylogen. & Evolution. Biol., 1(3): e105.

• V. Shankar, R. Agans, B. Holmes, M. Raymer, and O. Paliy. Do gut microbial communities differ in pediatric IBS and health? (2013) Gut Microbes, 4(4): 347–352. http://www.ncbi.nlm.nih.gov/pubmed/23674073

• B. Withman, T.S. Gunasekera, P. Beesetty, R. Agans, and O. Paliy. Transcriptional responses of uropathogenic Escherichia coli to increased environmental osmolality caused by salt or urea (2013) Infect. Immun., 81(1): 80-89. http://www.ncbi.nlm.nih.gov/pubmed/23090957

• L. Rigsbee, R. Agans, V. Shankar, H. Kenche, H. Khamis, S. Michail, and O. Paliy. Quantitative profiling of gut microbiota of children with diarrhea-predominant irritable bowel syndrome (2012) Am. J. Gastroenterol., 107: 1740-51. http://www.ncbi.nlm.nih.gov/pubmed/22986438

• O. Paliy and R. Agans. Application of phylogenetic microarrays to interrogation of human microbiota (2012) FEMS Microbiol. Ecol., 79(1): 2-11. http://www.ncbi.nlm.nih.gov/pubmed/22092522

• O. Paliy and B. Foy. Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays (2011) Bioinformatics, 27(15): 2134-40. http://www.ncbi.nlm.nih.gov/pubmed/21653518

• R. Agans, L. Rigsbee, H. Kenche, S. Michail, H. Khamis, and O. Paliy. Distal gut microbiota of adolescent children is different from that of adults (2011) FEMS Microbiol. Ecol., 77(2): 404-12. http://www.ncbi.nlm.nih.gov/pubmed/21539582

• M. Sugawara, G.R. Shah, M.J. Sadowsky, O. Paliy, J. Speck, A.W. Vail, and P. Gyaneshwar. Expression and functional roles of Bradyrhizobium japonicum genes involved in the utilization of inorganic and organic sulfur compounds in free-living and symbiotic conditions (2011) Mol. Plant Microbe Interact. 24(4), 451-7. http://www.ncbi.nlm.nih.gov/pubmed/21190435

• L. Rigsbee, R. Agans, B. Foy, and O. Paliy. Optimizing the analysis of human intestinal microbiota with phylogenetic microarray (2011) FEMS Microbiol. Ecol., 75, 332-42. http://www.ncbi.nlm.nih.gov/pubmed/21155851

• O. Paliy, H. Kenche, F. Abernathy, and S. Michail. High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray (2009) Appl. Environ. Microbiol. 75(11), 3572-9. http://www.ncbi.nlm.nih.gov/pubmed/19363078