UCLA UCLA Electronic Theses and Dissertations Title Genomic and metagenomic studies of the gut and skin microbiome with probiotic applications Permalink https://escholarship.org/uc/item/79x5d64c Author Liu, Jared Publication Date 2016 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA Los Angeles Genomic and metagenomic studies of the gut and skin microbiome with probiotic applications A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Molecular and Medical Pharmacology by Jared Liu 2016 © Copyright by Jared Liu 2016 ABSTRACT OF THE DISSERTATION Genomic and metagenomic studies of the gut and skin microbiome with probiotic applications by Jared Liu Doctor of Philosophy in Molecular and Medical Pharmacology University of California, Los Angeles, 2016 Professor Huiying Li, Chair Growing knowledge of the human microbiome has increased interest in probiotics, which can affect both the host and the microbiota. Genomic and metagenomic analyses can elucidate these effects and thereby provide important considerations for probiotic therapy. This dissertation describes genomic and metagenomic studies of two potential probiotic microorganisms, the gut bacterium Lactobacillus johnsonii and the bacteriophage of the skin commensal Propionibacterium acnes. Studies in an Atm-deficient mouse model of ataxia telangiectasia revealed that lymphoma latency, lifespan, and systemic genotoxicity are associated with the abundances of specific intestinal microbes, such as L. johnsonii. We isolated a strain of this species, 456, and observed that systemic genotoxicity and inflammation were reduced when 456 was inoculated into these mice. Strain 456 also reduced genotoxicity in wild-type mice but exacerbated genotoxicity induced by whole-body proton irradiation. Genome comparison of strain 456 with 8 other sequenced L. johnsonii strains revealed that 456 was genetically distant from other mouse ii isolates. Analysis of non-core genomic regions additionally revealed potential host-attachment proteins specific to the genome of 456. I next investigated the diversity and host interactions of phages that infect P. acnes, a commensal bacterium implicated in acne pathogenesis and several other diseases. Genome comparison of P. acnes phages isolated from acne patients and healthy individuals revealed that populations of these viruses are often dominated by one strain and that phage strains could be shared among both related and unrelated individuals. Phage infection can result in lysis, pseudolysogeny, or resistance depending on the P. acnes lineage. Metagenomic analysis further revealed that phage populations are prevalent at varying abundance across individuals, are highly personal, and show limited genetic change over time within individual strains. P. acnes phages may potentially be transmitted between related individuals. Based on these studies, the effectiveness of L. johnsonii probiotics may depend on strain genetics as well as the conditions under which they are applied. Effective phage therapy for P. acnes-associated diseases may depend on the structure and dynamics of an individual’s P. acnes and phage populations. These considerations merit further investigation in the context of these microbes as well as other probiotics. iii The dissertation of Jared Liu is approved. Jing Huang Jonathan Braun Ren Sun Robert Schiestl Huiying Li, Committee Chair University of California, Los Angeles 2016 iv TABLE OF CONTENTS ABSTRACT OF THE DISSERTATION ................................................................................... ii Acknowledgements ................................................................................................................... vii Vita .............................................................................................................................................. x Chapter 1: Introduction ............................................................................................................... 1 Chapter 2: Intestinal Bacteria Modify Lymphoma Incidence and Latency by Affecting Systemic Inflammatory State, Oxidative Stress, and Leukocyte Genotoxicity ....................... 5 Abstract ....................................................................................................................................... 6 Introduction ................................................................................................................................. 6 Materials and Methods ................................................................................................................ 7 Results ......................................................................................................................................... 8 Discussion ................................................................................................................................. 13 Chapter 3: Gut microflora and probiotic treatment affect radiation-induced genotoxicity 17 Abstract ..................................................................................................................................... 18 Introduction ............................................................................................................................... 18 Methods ..................................................................................................................................... 19 Results ....................................................................................................................................... 22 Discussion ................................................................................................................................. 25 Chapter 4: Genome sequencing and comparative analysis of Lactobacillus johnsonii 456 . 27 Abstract ..................................................................................................................................... 28 Introduction ............................................................................................................................... 28 Methods ..................................................................................................................................... 29 Results ....................................................................................................................................... 30 Discussion ................................................................................................................................. 37 Chapter 5: The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin ............................................................................................................................. 39 Abstract ..................................................................................................................................... 40 Introduction ............................................................................................................................... 40 Materials and Methods .............................................................................................................. 41 Results ....................................................................................................................................... 43 Discussion ................................................................................................................................. 50 v References ................................................................................................................................. 53 Chapter 6: Metagenomic analysis of Propionibacterium acnes bacteriophage populations in the human skin microbiome ....................................................................................................... 56 Abstract ..................................................................................................................................... 57 Introduction ............................................................................................................................... 57 Methods ..................................................................................................................................... 58 Results ....................................................................................................................................... 63 Discussion ................................................................................................................................. 73 Chapter 7: Conclusions .............................................................................................................. 75 Divergent modulation of systemic genotoxicity by L. johnsonii and the gut microbiota: treatment context may matter .................................................................................................... 76 Comparative genome analysis can provide insights into probiotic function ............................ 76 Diversity and host interactions of P. acnes bacteriophages: microbiome structure may also matter ......................................................................................................................................... 77 Phage dynamics: temporal stability and transmissibility of probiotic treatment ...................... 77 Appendix .....................................................................................................................................