University of Illinois Urbana-Champaign

Characterization of novel prophages in lysogenic murine isolate lactobacillus murinus EF-1

Fritz, Eric

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FRITZ-THESIS-2017.pdf

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https://hdl.handle.net/2142/99093

Description

Title
Characterization of novel prophages in lysogenic murine isolate lactobacillus murinus EF-1
Author(s)
Fritz, Eric
Issue Date
2017-07-19
Director of Research (if dissertation) or Advisor (if thesis)
Miller, Micheal J
Department of Study
Food Science & Human Nutrition
Discipline
Food Science & Human Nutrition
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
M.S.
Degree Level
Thesis
Date of Ingest
2018-03-02T19:59:35Z
Keyword(s)
  • Prophages
  • Lysogenic lactic acid bacteria (LAB)
  • Lactobacillus
Abstract
We sought to isolate and characterize prophage from an inducible lysogenic Lactobacilli host from a rat gastrointestinal tract. First we isolated a Lactobacillus murinus strain from a rat fecal sample. After initial antibiotic induction, high-throughput DNA sequencing and assembly identified the potential lysogenic bacterium as L. murinus EF-1. A 2.30 Mbp draft genome was generated with a 39.6% G+C content and 2196 identified coding regions. These metrics are similar to other Lactobacillus species. Bioinformatic analyses identified 3 intact prophages within the L. murinus EF-1 genome of 26.1, 25.4, and 49.6Kbp size. To confirm phage existence, the antibiotic induced lysate was subject to transmission electron microscopy. An identified Siphoviridae morphology was confirmed with an 80nm icosahedral head and 200nm noncontractile tail. High throughput induced viral DNA sequencing and mapping to EF-1 revealed 99.9% of 162.55k DNA reads mapped to presumed phage region 7.1. Further genetic analyses revealed a 39.1Kbp, 39.43% G + C content, circular inducible prophage whose genome encoded 58 putative coding regions, named phiEF-1.1. PhiEF-1.1 attachment sites were found inserted into a host arginine t-RNA. Additional putative protein characterization of phiEF-1.1 revealed coding regions to be divergent from 104 viral genomic coding regions through BLASTp amino acid sequence percent similarity. The low amino acid sequence identity of two murinus L. murinus GIT isolates strain’s to phiEF-1.1 suggests putative prophage coding regions are divergent. A low level of identity between phiEF-1.1 and other identified phage CDS found within strain EF-1 may be due to horizontal gene transfer or the presence of other prophages within EF-1. Together, this evidence provides the identification of a lysogenic L. murinus EF-1 and novel inducible prophage phiEF-1.1.
Graduation Semester
2017-08
Type of Resource
text
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http://hdl.handle.net/2142/99093
Copyright and License Information
Copyright 2017 Eric Fritz

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Graduate Dissertations and Theses at Illinois PRIMARY
Graduate Theses and Dissertations at Illinois
Dissertations and Theses - Food Science and Human Nutrition