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Volume 18, Number 3—March 2012


A Systematic Approach for Discovering Novel, Clinically Relevant Bacteria

Robert Schlaberg1Comments to Author , Keith E. Simmon1, and Mark A. Fisher
Author affiliations: University of Utah School of Medicine, Salt Lake City, Utah, USA (R. Schlaberg, M.A. Fisher); ARUP Laboratories, Salt Lake City (R. Schlaberg, K.E. Simmon, M.A. Fisher)

Main Article

Table 2

Tentative novel taxa represented by >5 clinical isolates*†

Family Identity, % Initial cluster size Reviewed cluster size Gram stain morphology Result
Micrococcaceae 98.5 15 0 GPR Rothia aeria, short reference sequence
Actinomycetaceae 98.7 12 11 GPR 1 strain with >1% dissimilarity
Thermoactinomycetaceae 91.8 12 12 GPR Belong to Kroppenstedtia eburnea gen. nov., sp. nov.
Moraxellaceae 96.4 11 11 GNR Most similar to Acinetobacter ursingii
Corynebacteriaceae 98.1 10 10 GPR Most similar to Corynebacterium. mucifaciens
Corynebacteriaceae 98.6 10 5 GPR Most similar to C. jeikeium, 5 isolates are C. jeikeium
Enterobacteriaceae 98.9 10 10 GNR Most similar to Enterobacter cloacae
Streptomycetaceae 98.5 9 0 GPR Streptomyces thermoviolaceus subsp. thermoviolaceus
Nocardiaceae 98.9 9 9 GPR Most similar to Nocardia vermiculata
Cardiobacteriaceae 98.9 8 0 GNR Belong to Cardiobacterium hominis, poor reference sequence
Flavobacteriaceae 86.5 7 7 GNR Most similar to Chryseobacterium daecheongense
Actinomycetaceae 96.9 7 7 GPR Most similar to Actinomyces odontolyticus
Actinomycetaceae 98.5 6 6 GPR Most similar to Actinomyces meyeri
Thermoactinomycetaceae 90.8 5 5 GPR Most similar to Laceyella putida
Actinomycetaceae 95.0 5 3+2 GPR 2 separate taxa
Streptococcaceae 96.7 5 5 GPC Most similar to Streptococcus oralis
Enterobacteriaceae 97.3 5 5 GNR Most similar to Dickeya dieffenbachiae
Actinomycetaceae 97.8 5 3+2 GPR 2 separate taxa
Streptococcaceae 97.9 5 5 GPC Most similar to Streptococcus mitis

*GPR, gram-positive rods; GNR, gram-negative rods; GPC, gram-positive cocci.
†initial and reviewed clusters sizes indicate number of isolates in each cluster before and after manual review, outcome of manual review, and most similar valid species names are listed. Manual review was performed for all clusters with at least 5 isolates. Sequences were aligned with type strain sequences, and manual BLAST (23) analysis was performed to calculate pairwise sequence identities.

Main Article

1These authors contributed equally to this article.