TY - JOUR
T1 - Genomic and Ecogenomic Characterization of Proteus mirabilis Bacteriophages
AU - Jones, Brian
AU - Nzakizwanayo, Jonathan
N1 - Funding Information:
This research was sponsored by the Genomic Science Program, U.S. Department of Energy, Office of Science – Biological and Environmental Research as part of the Plant Microbe Interfaces Scientific Focus Area (http://pmi.ornl.gov). Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725. GB and GMNB were supported through the Michigan State University AgBioResearch project MICL02416 and USDA NIFA project MICL08541. GB and GMNB also acknowledge NSF grant DEB-1441728 and the DOE Office of Science Great Lakes BioEnergy Research Center BER DE-SC0018409.
Funding Information:
The authors would like to thank Lee Gunter, Jud Isebrands, Zachary Moore, Paul Bloese and Bernard McMahon for supplying Populus cuttings, and Natalie Vande Pol for bioinformatic assistance. The authors of the manuscript are employed by Oak Ridge National Laboratory, which is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725.
Publisher Copyright:
Copyright © 2019 Bonito, Benucci, Hameed, Weighill, Jones, Chen, Jacobson, Schadt and Vilgalys.
PY - 2019/8/6
Y1 - 2019/8/6
N2 -
Proteus mirabilis often complicates the care of catheterized patients through the formation of crystalline biofilms which block urine flow. Bacteriophage therapy has been highlighted as a promising approach to control this problem, but relatively few phages infecting
P. mirabilis have been characterized. Here we characterize five phages capable of infecting
P. mirabilis, including those shown to reduce biofilm formation, and provide insights regarding the wider ecological and evolutionary relationships of these phages. Transmission electron microscopy (TEM) imaging of phages vB_PmiP_RS1pmA, vB_PmiP_RS1pmB, vB_PmiP_RS3pmA, and vB_PmiP_RS8pmA showed that all share morphologies characteristic of the
Podoviridae family. The genome sequences of vB_PmiP_RS1pmA, vB_PmiP_RS1pmB, and vB_PmiP_RS3pmA showed these are species of the same phage differing only by point mutations, and are closely related to vB_PmiP_RS8pmA. Podophages characterized in this study were also found to share similarity in genome architecture and composition to other previously described
P. mirabilis podophages (PM16 and PM75). In contrast, vB_PimP_RS51pmB showed morphology characteristic of the
Myoviridae family, with no notable similarity to other phage genomes examined. Ecogenomic profiling of all phages revealed no association with human urinary tract viromes, but sequences similar to vB_PimP_RS51pmB were found within human gut, and human oral microbiomes. Investigation of wider host-phage evolutionary relationships through tetranucleotide profiling of phage genomes and bacterial chromosomes, indicated vB_PimP_RS51pmB has a relatively recent association with
Morganella morganii and other non-
Proteus members of the
Morganellaceae family. Subsequent host range assays confirmed vB_PimP_RS51pmB can infect
M. morganii.
AB -
Proteus mirabilis often complicates the care of catheterized patients through the formation of crystalline biofilms which block urine flow. Bacteriophage therapy has been highlighted as a promising approach to control this problem, but relatively few phages infecting
P. mirabilis have been characterized. Here we characterize five phages capable of infecting
P. mirabilis, including those shown to reduce biofilm formation, and provide insights regarding the wider ecological and evolutionary relationships of these phages. Transmission electron microscopy (TEM) imaging of phages vB_PmiP_RS1pmA, vB_PmiP_RS1pmB, vB_PmiP_RS3pmA, and vB_PmiP_RS8pmA showed that all share morphologies characteristic of the
Podoviridae family. The genome sequences of vB_PmiP_RS1pmA, vB_PmiP_RS1pmB, and vB_PmiP_RS3pmA showed these are species of the same phage differing only by point mutations, and are closely related to vB_PmiP_RS8pmA. Podophages characterized in this study were also found to share similarity in genome architecture and composition to other previously described
P. mirabilis podophages (PM16 and PM75). In contrast, vB_PimP_RS51pmB showed morphology characteristic of the
Myoviridae family, with no notable similarity to other phage genomes examined. Ecogenomic profiling of all phages revealed no association with human urinary tract viromes, but sequences similar to vB_PimP_RS51pmB were found within human gut, and human oral microbiomes. Investigation of wider host-phage evolutionary relationships through tetranucleotide profiling of phage genomes and bacterial chromosomes, indicated vB_PimP_RS51pmB has a relatively recent association with
Morganella morganii and other non-
Proteus members of the
Morganellaceae family. Subsequent host range assays confirmed vB_PimP_RS51pmB can infect
M. morganii.
KW - Arbuscular mycorrhizal fungi
KW - Bacterial communities
KW - Endophytes
KW - Fungal communities
KW - Microbiome
KW - NGS sequencing
KW - Populus deltoides
KW - Rhizosphere
UR - http://www.scopus.com/inward/record.url?scp=85065142958&partnerID=8YFLogxK
U2 - 10.3389/fmicb.2019.01783
DO - 10.3389/fmicb.2019.01783
M3 - Article
C2 - 31447809
SN - 1664-302x
VL - 10
SP - 1
EP - 14
JO - Frontiers in Microbiology
JF - Frontiers in Microbiology
M1 - 1783
ER -