Evidence map›Paper›PMID 29490612›Full record

ArticleBMC microbiology2018

Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages.

Lucy Cheng, Laura J Marinelli, Noël Grosset, Sorel T Fitz-Gibbon, Charles A Bowman, Brian Q Dang, Daniel A Russell, Deborah Jacobs-Sera, Baochen Shi, Matteo Pellegrini and 4 more

Abstract read
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In one paragraph

Article in BMC microbiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

10 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Lucy ChengDivision of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095, CA, USA.
Laura J MarinelliDivision of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095, CA, USA. laurajmarinelli@gmail.com.
Noël GrossetEquipe Microbiologie de l'œuf et des Ovoproduits (MICOV), Agrocampus Ouest, INRA, (UMR1253) Science et Technologie du Lait et de l'Œuf, Rennes, France.
Sorel T Fitz-GibbonDepartment of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Charles A BowmanDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
Brian Q DangDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
Daniel A RussellDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
Deborah Jacobs-SeraDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
Baochen ShiDepartment of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Matteo PellegriniDepartment of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Jeff F MillerDepartment of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Michel GautierEquipe Microbiologie de l'œuf et des Ovoproduits (MICOV), Agrocampus Ouest, INRA, (UMR1253) Science et Technologie du Lait et de l'Œuf, Rennes, France.
Graham F HatfullDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
Robert L ModlinDivision of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095, CA, USA.

Funding

UCLA SPORE in Brain CancerP50CA211015 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Fausto Rodriguez · 2017 to 2026
$25.2M
Dynamics of viral host range evolutionR01GM116884 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI HATFULL, GRAHAM F. · 2015 to 2019
$2.0M
Effect of bacteriophages on cutaneous inflammation in acneK01AR066571 · NIAMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI MARINELLI, LAURA JANE · 2014 to 2017
$530k
Characterization of the Lysogenic Pathway in P. acnes BacteriophagesF32AR060655 · NIAMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI MARINELLI, LAURA JANE · 2011 to 2013
$129k
NCI NIH HHS P50 CA211015NIAMS NIH HHS F32 AR060655NIAMS NIH HHS F32-AR060655NIAMS NIH HHS K01 AR066571NIAMS NIH HHS K01-AR066571NIGMS NIH HHS R01 GM116884
6 · The paper itself

Abstract

backgroundA remarkable exception to the large genetic diversity often observed for bacteriophages infecting a specific bacterial host was found for the Cutibacterium acnes (formerly Propionibacterium acnes) phages, which are highly homogeneous. Phages infecting the related species, which is also a member of the Propionibacteriaceae family, Propionibacterium freudenreichii, a bacterium used in production of Swiss-type cheeses, have also been described and are common contaminants of the cheese manufacturing process. However, little is known about their genetic composition and diversity.

resultsWe obtained seven independently isolated bacteriophages that infect P. freudenreichii from Swiss-type cheese samples, and determined their complete genome sequences. These data revealed that all seven phage isolates are of similar genomic length and GC% content, but their genomes are highly diverse, including genes encoding the capsid, tape measure, and tail proteins. In contrast to C. acnes phages, all P. freudenreichii phage genomes encode a putative integrase protein, suggesting they are capable of lysogenic growth. This is supported by the finding of related prophages in some P. freudenreichii strains. The seven phages could further be distinguished as belonging to two distinct genomic types, or 'clusters', based on nucleotide sequences, and host range analyses conducted on a collection of P. freudenreichii strains show a higher degree of host specificity than is observed for the C. acnes phages.

conclusionsOverall, our data demonstrate P. freudenreichii bacteriophages are distinct from C. acnes phages, as evidenced by their higher genetic diversity, potential for lysogenic growth, and more restricted host ranges. This suggests substantial differences in the evolution of these related species from the Propionibacteriaceae family and their phages, which is potentially related to their distinct environmental niches.

Indexed as

Genome, ViralPhylogenyBacteriophagesBase CompositionBase SequenceCheeseChromosome MappingGenetic VariationGenomicsHost SpecificityLysogenyMolecular Sequence AnnotationProphagesPropionibacteriaceaePropionibacteriumPropionibacterium acnesBacteriophageCheese microbiotaCutibacterium acnesPhage genomicsPropionibacterium freudenreichii

Identifiers

PMID29490612
PMCPMC5831693

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.