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

Fritz, Eric

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

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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