For a biologist the discovery of a new species is a significant achievement. This is probably easier for a microbiologist than many other biologists, but is still a satisfying achievement. The identification and characterization of Streptococcus bovimastitidis resulted from a discussion at the World Buiatrics Conference in Cairns when we agreed to perform whole genome sequencing on a collection of Strep. uberis isolates gathered during two clinical mastitis trials in New Zealand.
While reviewing the species identification data on the collection it was clear that one of the isolates had failed to be identified as Strep. uberis, or any other species in the reference library. A quick look at the assembled sequence data showed that there hadn’t been any problem with the sequencing itself which eliminated the most likely cause. This piqued our curiosity and so began the search to identify this anomaly.
The Kraken software used for the initial species identification compares the sequence data of the whole genome with a library of previously sequenced bacteria. While many bacterial species have been genome sequenced there are a considerable number that have not, so the next step was to look at the 16S ribosomal RNA sequence (16S rRNA) which encodes a part of a subunit of a prokaryotic ribosome. This gene has been found to evolve extremely slowly, is easily sequenced, and is
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