Microbiome Systems Biology

Our research is highly collaborative and explores the role of the microbiome in globally significant diseases for delivering novel patient-centric therapies. We are studying host-microbiome interactions in metabolic diseases, infection, cancer and critical care. In order to move from correlative to causative evidence between shifts in the microbiome and pathophysiology of diseases we design cross-sectional studies, prospective studies and randomized controlled intervention studies in disease subjects in combination with emerging new technologies, including transplantation of human fecal microbiota to germ free mice and evaluation of single species and microbial consortia in stem cell lines and artificial gut systems. We are also particularly interested on the dynamics between host and the associated microbes therefore we are working on algorithm development for generating probabilistic frameworks for learning persistence and colonization probabilities of microbiome therapeutics and microbial engineering. We also combine clinical data, host mutation patterns, microbiome, mycobiome and phageome data to create a comprehensive view of different diseases, identify subtypes and predict response treatment.


Amelia Barber
Jiarui Chen
Xiuqiang (Stephen) Chen
Sara Leal Siliceo
Howell Leung
Daniel Loos
Andrea Marfil Sánchez
Yueqiong (Bernard) Ni
Emmanouil Nychas
Bastian Seelbinder
Lin Lin Xu
Lu Zhang


Kang K, Imamovic L, Misiakou M, Sørensen MB, Heshiki Y, Ni Y, Zheng T, Li J, Ellabaan MMH, Colomer-Lluch M, Rode AA, Bytzer P, Panagiotou G#, Sommer MOA (corresponding author#) (2021) Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment. Gut Microbes 13(1), 1-19.
Marfil-Sánchez A*, Zhang L*, Alonso-Pernas P, Mirhakkak M, Mueller M, Seelbinder B, Ni Y, Santhanam R, Busch A, Beemelmanns C, Ermolaeva M, Bauer M#, Panagiotou G# (2021) An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness. Gut Microbes [Accepted]
Ni Y*, Lohinai Z*, Heshiki Y, Dome B, Moldvay J, Dulka E, Galffy G, Berta J, Weiss GJ, Sommer MOA, Panagiotou G# (2021) Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients. ISME J ,
Zhang J, Ni Y, Qian L, Fang Q, Zheng T, Zhang M, Gao Q, Zhang Y, Ni J, Hou X, Bao Y, Kovatcheva-Datchary P, Xu A, Li H, Panagiotou G#, Jia W (2021) Decreased abundance of Akkermansia muciniphila leads to the impairment of insulin secretion and glucose homeostasis in lean type 2 diabetes. Adv Sci (Weinh) 8(16), e2100536.
Haange SB, Jehmlich N, Krügel U, Hintschich C, Wehrmann D, Hankir M, Seyfried F, Froment J, Hübschmann T, Müller S, Wissenbach DK, Kang K, Buettner C, Panagiotou G, Noll M, Rolle-Kampczyk U, Fenske W, von Bergen M (2020) Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss. Microbiome 8(1), 13.
Heshiki Y, Vazquez-Uribe R, Li J, Ni Y, Quainoo S, Imamovic L, Li J, Sørensen M, Chow BKC, Weiss GJ, Xu A, Sommer MOA, Panagiotou G (2020) Predictable modulation of cancer treatment outcomes by the gut microbiota. Microbiome 8(1), 28.
Liu Y, Wang Y, Ni Y, Cheung CKY, Lam KSL, Wang Y, Xia Z, Ye D, Guo J, Tse MA, Panagiotou G**, Xu A**(corresponding authors**) (2020) Gut microbiome fermentation determines the efficacy of exercise for diabetes prevention. Cell Metab 31(1), 77-91.
Nie X, Chen J, Ma X, Ni Y, Shen Y, Yu H, Panagiotou G**, Bao Y** (corresponding authors**) (2020) A metagenome-wide association study of gut microbiome and visceral fat accumulation. Comput Struct Biotechnol J 18, 2596-2609.
Chen J*, McIlroy SE, Archana A, Baker DM, Panagiotou G** (2019) A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments. Microbiome 7(1), 104.
Li J, Rettedal EA, van der Helm E, Ellabaan M, Panagiotou G**, Sommer MOA**(corresponding authors**) (2019) Antibiotic treatment drives the diversification of the human gut resistome. Genom Proteom Bioinf 17(1), 39-51.