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• infectious disease and the immune system

• Medicine

• Gastroenterology
• Infectious diseases
• Immunology

The activation of the host immune system following host penetration and invasion by a virus initiates a conflict that results in either viral clearance or viral persistence. Many of the correlates associated with viral evolution in the context of clearance or persistence are not fully elucidated. Our research is aimed at advancing our understanding of the molecular diversity of these viruses and how this impacts on disease outcome. Bacterial viruses impact on the microbiome diversity and this diversity changes between health and disease states. The predator prey relationship within the gut is modified by the immune system. However, there is considerable paucity of knowledge on how the immune system engages with these bacterial viruses and the impact this has on health and inflammatory disease states.
The research group currently explores these aspects of immunovirology in Hepatitis C infection and the immunovirology of the gut-microbiome and bacteriophage. The research group is located within the Department of Medicine, and the Alimentary Pharmabiotic Microbiome Institute, University College Cork, Ireland.

Liam Fanning, PhD. l.fanning@ucc.ie

APC Microbiome Institute, University College Cork, Ireland
Project Title: Phage immunity: A potential modifier of the microbiome in health and in inflammatory disease.
Supervisory team lead by Dr. Liam Fanning with Professors Colin Hill and Fergus Shanahan.
Description: The relative abundance and diversity of anti-bacterial antibodies differs between health and disease. Whether a parallel situation pertains to anti-phage antibodies is ill defined. The normative predator prey relationship between phage and bacteria influences bacterial richness, which influences microbiome health. The adaptive immune system is known to produce phage specific antibodies.**

Specifically the project will address the following knowledge gaps:
? Determine the prevalence of anti-phage antibodies in healthy controls and individuals with inflammatory disease
? Identify the spectrum of phage targeted by anti-phage antibodies
? Explore whether anti-phage activity, in particular as it relates to antibodies and antigen presentation, modulates the composition of the microbiome in health and disease
? The contribution of host derived anti-phage activity to inflammatory disease processes.

**Background reading:
1. Perez-Lopez A, Behnsen J, Nuccio SP, Raffatellu M. Nature reviews Immunology. 2016.
2. Brussow H. Virology. 2012;434(2):138-42.
3. Ando H, Lemire S, Pires Diana P, Lu Timothy K. Cell Systems.1(3):187-96.
4. O'Hara AM, Shanahan F. EMBO reports. 2006;7(7):688-93.
5. Moran C, Sheehan D, Shanahan F. 2015;31(2):130-6.
6. Sheehan D, Moran C, Shanahan F. 2015;50(5):495-507.
7. Macpherson A, Khoo UY, Forgacs I, Philpott-Howard J, Bjarnason I. Gut. 1996;38(3):365-75.
8. Barr JJ, Auro R, Furlan M, Whiteson KL, Erb ML, Pogliano J, et al. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(26):10771-6.
9. Barr JJ, Youle M, Rohwer F. Bacteriophage. 2013;3(3):e25857.
10. Hodyra-Stefaniak K, Miernikiewicz P, Drapala J, Drab M, Jonczyk-Matysiak E, Lecion D, et al. Scientific reports. 2015;5:14802.
11. Majewska J, Beta W, Lecion D, Hodyra-Stefaniak K, Klopot A, Kazmierczak Z, et al. Viruses. 2015;7(8):4783-99.