Three bench-top high-throughput sequencing instruments are now available. The 454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies) are laser-printer sized and offer modest set-up and running costs. Each instrument can generate a draft bacterial genome sequence in days, making them attractive for use in the identification and characterization of pathogens in the clinical setting. We compared the performance of these instruments by sequencing isolates of Escherichia coli O104:H4 from the German outbreak of 2011. We compared performance of the platforms, analysing throughput, read length, read error profile and rate, de novo assembly quality and completeness. MiSeq had the highest throughput and lowest error rate. The 454 Junior generated the longest reads and best assemblies. The Ion Torrent PGM produced intermediate throughput with the shortest reads. The Ion Torrent PGM and 454 GS Junior both suffer from errors in homopolymers

A total of 31 strains of Prevotella intermedia were subjected to DNA-DNA hybridization and were characterized by performing physiological tests and by performing a multilocus enzyme analysis, using malate dehydrogenase and glutamate dehydrogenase. All of the strains assigned to P. intermedia fermented glucose and sucrose, hydrolyzed starch but not esculin, and produced indole, acetic, isobutyric, isovaleric, and succinic acids as metabolic end products. The results of DNA reassociation experiments performed with the reference probe permitted separation of the strains into two well-defined homology groups. In addition, strains with DNAs that hybridized with DNA from strain ATCC 25611T ( ' I ' = type strain) had high levels of peptidase activity and cleaved lipid substrates (4-methylumbelliferyl laurate and 4-methylumbellifelyl elaidate). Multilocus enzyme electrophoresis revealed two electromorphic profiles, one characteristic of strain ATCC 25611T and the other characteristic of strain ATCC 335aT. We propose that a new species, Prevotella nigrescens, should be created for the genetically distinct group of strains that hybridized with strain ATCC 33563T. Strain ATCC 33563 is designated the type strain of P. nigrescens.The "black-pigmented bacteroides" have undergone major taxonomic revisions at both the generic and species levels within the last decade (for a review, see reference 14).

No abstract

The occurrence and surface properties of Prevotella intermedia and P. nigrescens in healthy sites and in periodontic and endodontic infections were studied among 73 strains, tentatively identified as P. intermedia. Fifteen strains were from necrotic root canal infections, 41 were from periodontal samples, and 17 isolates were obtained from healthy gingival sites. Identification of isolates as either P. intermedia or P. nigrescens was based on differences in malate and glutamate dehydrogenase electrophoretic mobilities which allowed unambiguous separation of P. intermedia and P. nigrescens. The majority of strains from periodontal samples were P. intermedia (29 of 41 strains). In endodontic samples only 4 out of 15 isolates were P. intermedia, while all except 1 of 17 strains from healthy gingival sites were identified as P. nigrescens. SDS‐PAGE of whole cell proteins revealed 31 and 38 kDa proteins in P. nigrescens which were not detected in P. intermedia. Surface biotinylation of cells, followed by Western blotting and detection by alkaline phosphatase conjugated extravidin, showed strong staining of the 31 kDa protein in P. nigrescens indicating that this protein is located on the surface of the cell. Corresponding staining was not seen in P. intermedia. Fimbria‐like projections were observed using electron microscopy of negatively‐stained cells of P. nigrescens. The results show that P. intermedia and P. nigrescens may have different site specificities and surface properties and thus emphasize the need for accurate identification of these two species for the evaluation of their role in the pathogenesis of oral infections. J Periodontol 1994;65:56–61.