Article

Pan-Genome and Comparative Genome Analyses of Propionibacterium acnes Reveal Its Genomic Diversity in the Healthy and Diseased Human Skin Microbiome

Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, California, USA.
mBio (Impact Factor: 6.79). 04/2013; 4(3). DOI: 10.1128/mBio.00003-13
Source: PubMed

ABSTRACT

Unlabelled:
Propionibacterium acnes constitutes a major part of the skin microbiome and contributes to human health. However, it has also been implicated as a pathogenic factor in several diseases, including acne, one of the most common skin diseases. Its pathogenic role, however, remains elusive. To better understand the genetic landscape and diversity of the organism and its role in human health and disease, we performed a comparative genome analysis of 82 P. acnes strains, 69 of which were sequenced by our group. This collection covers all known P. acnes lineages, including types IA, IB, II, and III. Our analysis demonstrated that although the P. acnes pan-genome is open, it is relatively small and expands slowly. The core regions, shared by all the sequenced genomes, accounted for 88% of the average genome. Comparative genome analysis showed that within each lineage, the strains isolated from the same individuals were more closely related than the ones isolated from different individuals, suggesting that clonal expansions occurred within each individual microbiome. We also identified the genetic elements specific to each lineage. Differences in harboring these elements may explain the phenotypic and functional differences of P. acnes in functioning as a commensal in healthy skin and as a pathogen in diseases. Our findings of the differences among P. acnes strains at the genome level underscore the importance of identifying the human microbiome variations at the strain level in understanding its association with diseases and provide insight into novel and personalized therapeutic approaches for P. acnes-related diseases.

Importance:
Propionibacterium acnes is a major human skin bacterium. It plays an important role in maintaining skin health. However, it has also been hypothesized to be a pathogenic factor in several diseases, including acne, a common skin disease affecting 85% of teenagers. To understand whether different strains have different virulent properties and thus play different roles in health and diseases, we compared the genomes of 82 P. acnes strains, most of which were isolated from acne or healthy skin. We identified lineage-specific genetic elements that may explain the phenotypic and functional differences of P. acnes as a commensal in health and as a pathogen in diseases. By analyzing a large number of sequenced strains, we provided an improved understanding of the genetic landscape and diversity of the organism at the strain level and at the molecular level that can be further applied in the development of new and personalized therapies.

    • "Certain strains are highly associated with the disease (Lomholt and Kilian, 2010; McDowell et al., 2012; Fitz-Gibbon et al., 2013; Tomida et al., 2013), while some strains are enriched in healthy skin (Fitz- Gibbon et al., 2013). "
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    ABSTRACT: The viral population, including bacteriophages, is an important component of the human microbiota, yet is poorly understood. We aim to determine whether bacteriophages modulate the composition of the bacterial populations, thus potentially playing a role in health or disease. We investigated the diversity and host interactions of the bacteriophages of Propionibacterium acnes, a major human skin commensal implicated in acne pathogenesis. By sequencing 48 P. acnes phages isolated from acne patients and healthy individuals and by analyzing the P. acnes phage populations in healthy skin metagenomes, we revealed that P. acnes phage populations in the skin microbial community are often dominated by one strain. We also found phage strains shared among both related and unrelated individuals, suggesting that a pool of common phages exists in the human population and that transmission of phages may occur between individuals. To better understand the bacterium-phage interactions in the skin microbiota, we determined the outcomes of 74 genetically defined Propionibacterium strains challenged by 15 sequenced phages. Depending on the Propionibacterium lineage, phage infection can result in lysis, pseudolysogeny, or resistance. In type II P. acnes strains, we found that encoding matching clustered regularly interspaced short palindromic repeat spacers is insufficient to confer phage resistance. Overall, our findings suggest that the prey-predator relationship between bacteria and phages may have a role in modulating the composition of the microbiota. Our study also suggests that the microbiome structure of an individual may be an important factor in the design of phage-based therapy.
    No preview · Article · Apr 2015 · The ISME Journal
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    • "A total of 12 of the 90 P. acnes genomes identified by the blastn search were not included in our phylogenetic analysis. Two were recently added to the P. acnes databases, i.e. the strains HL042PA3 [25] and DSM 1897. The following strains were previously identified as P. acnes by [19]: 409-HC1, 434-HC2, 5U42AFAA and CC003-HC2. "
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    ABSTRACT: The Gram-positive anaerobic bacterium Propionibacterium acnes is a prevalent member of the normal skin microbiota of human adults. In addition to its suspected role in acne vulgaris it is involved in a variety of opportunistic infections. Multi-locus sequence-typing (MLST) schemes identified distinct phylotypes associated with health and disease. Being based on 8 to 9 house-keeping genes these MLST schemes have a high discriminatory power, but their application is time- and cost-intensive. Here we describe a single-locus sequence typing (SLST) scheme for P. acnes. The target locus was identified with a genome mining approach that took advantage of the availability of representative genome sequences of all known phylotypes of P. acnes. We applied this SLST on a collection of 188 P. acnes strains and demonstrated a resolution comparable to that of existing MLST schemes. Phylogenetic analysis applied to the SLST locus resulted in clustering patterns identical to a reference tree based on core genome sequences. We further demonstrate that SLST can be applied to detect multiple phylotypes in complex microbial communities by a metagenomic pyrosequencing approach. The described SLST strategy may be applied to any bacterial species with a basically clonal population structure to achieve easy typing and mapping of multiple phylotypes in complex microbiotas. The P. acnes SLST database can be found at http://medbac.dk/slst/pacnes.
    Full-text · Article · Aug 2014 · PLoS ONE
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    ABSTRACT: The Journal of Investigative Dermatology publishes basic and clinical research in cutaneous biology and skin disease.
    Preview · Article · Jun 2013 · Journal of Investigative Dermatology
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