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      Draft Genome Sequences of 26 Porphyromonas Strains Isolated from the Canine Oral Microbiome

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          Abstract

          We present the draft genome sequences for 26 strains of Porphyromonas ( P. canoris, P. gulae, P. cangingavalis, P. macacae, and 7 unidentified) and an unidentified member of the Porphyromonadaceae family. All of these strains were isolated from the canine oral cavity, from dogs with and without early periodontal disease.

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          An Integrated Pipeline for de Novo Assembly of Microbial Genomes

          Remarkable advances in DNA sequencing technology have created a need for de novo genome assembly methods tailored to work with the new sequencing data types. Many such methods have been published in recent years, but assembling raw sequence data to obtain a draft genome has remained a complex, multi-step process, involving several stages of sequence data cleaning, error correction, assembly, and quality control. Successful application of these steps usually requires intimate knowledge of a diverse set of algorithms and software. We present an assembly pipeline called A5 (Andrew And Aaron's Awesome Assembly pipeline) that simplifies the entire genome assembly process by automating these stages, by integrating several previously published algorithms with new algorithms for quality control and automated assembly parameter selection. We demonstrate that A5 can produce assemblies of quality comparable to a leading assembly algorithm, SOAPdenovo, without any prior knowledge of the particular genome being assembled and without the extensive parameter tuning required by the other assembly algorithm. In particular, the assemblies produced by A5 exhibit 50% or more reduction in broken protein coding sequences relative to SOAPdenovo assemblies. The A5 pipeline can also assemble Illumina sequence data from libraries constructed by the Nextera (transposon-catalyzed) protocol, which have markedly different characteristics to mechanically sheared libraries. Finally, A5 has modest compute requirements, and can assemble a typical bacterial genome on current desktop or laptop computer hardware in under two hours, depending on depth of coverage.
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            A Cross-Sectional Survey of Bacterial Species in Plaque from Client Owned Dogs with Healthy Gingiva, Gingivitis or Mild Periodontitis

            Periodontal disease is the most widespread oral disease in dogs which if left untreated results in significant pain to the pet and loss of dentition. The objective of this study was to identify bacterial species in canine plaque that are significantly associated with health, gingivitis and mild periodontitis (<25% attachment loss). In this survey subgingival plaque samples were collected from 223 dogs with healthy gingiva, gingivitis and mild periodontitis with 72 to 77 samples per health status. DNA was extracted from the plaque samples and subjected to PCR amplification of the V1-V3 region of the 16S rDNA. Pyrosequencing of the PCR amplicons identified a total of 274 operational taxonomic units after bioinformatic and statistical analysis. Porphyromonas was the most abundant genus in all disease stages, particularly in health along with Moraxella and Bergeyella. Peptostreptococcus, Actinomyces, and Peptostreptococcaceae were the most abundant genera in mild periodontitis. Logistic regression analysis identified species from each of these genera that were significantly associated with health, gingivitis or mild periodontitis. Principal component analysis showed distinct community profiles in health and disease. The species identified show some similarities with health and periodontal disease in humans but also major differences. In contrast to human, healthy canine plaque was found to be dominated by Gram negative bacterial species whereas Gram positive anaerobic species predominate in disease. The scale of this study surpasses previously published research and enhances our understanding of the bacterial species present in canine subgingival plaque and their associations with health and early periodontal disease.
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              Author and article information

              Journal
              Genome Announc
              Genome Announc
              ga
              ga
              GA
              Genome Announcements
              American Society for Microbiology (1752 N St., N.W., Washington, DC )
              2169-8287
              9 April 2015
              Mar-Apr 2015
              : 3
              : 2
              : e00187-15
              Affiliations
              [a ]University of California Davis Genome Center, Davis, California, USA
              [b ]The Waltham Centre for Pet Nutrition, Melton Mowbray, Leicestershire, United Kingdom
              [c ]Department of Evolution and Ecology and Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, USA
              [d ]ithree institute, University of Technology, Sydney, Australia
              Author notes
              Address correspondence to Jonathan A. Eisen, jaeisen@ 123456ucdavis.edu .
              Article
              genomeA00187-15
              10.1128/genomeA.00187-15
              4392144
              2818ff4c-8f45-4865-807c-3aa0868dbb97
              Copyright © 2015 Coil et al.

              This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

              History
              : 10 February 2015
              : 3 March 2015
              Page count
              Figures: 0, Tables: 1, Equations: 0, References: 4, Pages: 2, Words: 1335
              Categories
              Prokaryotes
              Custom metadata
              March/April 2015
              free

              Genetics
              Genetics

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