Abstracts

Oral Presentation Abstracts
all of them belonged to B. melitensis biovar
2 str. 63/9. A neighbor-joining tree analysis
identified one of the isolates as an outlier. Furthermore,
variations (SNPs and indels) were
spread all over the genome; but 138 SNPs
were common among the 14 isolates, supporting
the same ancestral origin. In addition,
SNPs (2 - 478) unique to each isolate were
also identified, which divided the B. melitensis
biovar 2 into two major variant groups. In
conclusion, this study suggest that biovar 2 is
the most prevalent biovar of B. melitensis in
Kuwait. Furthermore, at least two major variant
groups exist within biovar 2. Supported
by Kuwait University Research Sector grant
SRUL02/13.
n S6:4
MICROBIAL GENOMIC TAXONOMY AT
GENBANK
S. Federhen;
NCBI, Bethesda, MD.
Incorrectly identified genomes at GenBank
are a problem for users of the data. Some
genomes are submitted with incorrect species
identifications. Others were correctly identified
when they were submitted but should now
be updated based on a subsequent taxonomic
publication, for example the description of a
new species. GenBank has traditionally relied
on the submitters to provide the correct
taxonomic identifications for their sequence
submissions. Two developments have combined
to change this situation in the domain
of microbial genomes. First, the curation of
type material in the NCBI taxonomy database
allows us to flag sequences from type in the
nucleotide and genome domains of Entrez.
Second, current sequencing technology makes
it fast and easy to generate microbial genomes.
It has been clear for some time that the current
paradigm of species delimitation by 16S rRNA
sequence and DNA-DNA hybridization (DDH)
would eventually be replaced with a model
based on whole genome analysis. We present
a proposal to find and correct misidentified
genomes based on average nucleotide identity
(ANI) from type and proxytype. Sequences
from type are reliably identified (by definition)
once we have verified that they are free from
contamination and are actually from the strain
with which they are annotated. All other identifications
are a matter of opinion, and will be
subject to verification. We have genomes from
type (both finished and WGS) for 4000 species,
including 3500 bacteria. This represents
25% of bacterial species with validly published
names. The other 75% of bacterial species
will generally have an assortment of short sequences
from type in GenBank - at least a 16S
sequence, but often more. These sequences are
used to probe our existing genomes and predict
where the genome from type will appear once
we do get one. In many cases we can designate
a proxy for the missing type from among
the genomes that we do have - we call these
‘proxytype’ genomes. Taken together, these
genomes from type and proxytype represent a
scaffold of reliably identified sequences that
we can use in conjunction with some simple
genome-wide comparison measures to validate
the identifications in our other genomes.
Once we have identified genomes that need
taxonomic updates, we plan to correct the entries,
add a structured comment detailing the
evidence for the update, and notify the submitters
of the change. This represents a significant
change in policy for GenBank - a new genomic
paradigm for validating taxonomic identifications,
some new types of analysis, as well as
a shift in the boundary for database-driven
source feature updates. We convened a workshop
to present the proposal, with representation
from a broad spectrum of the bacterial
taxonomic community (GenBank genomic
taxonomy workshop, 12-13 May 2015). This
group unanimously endorsed our genomic approach
to validating taxonomic identifications
in genomes at GenBank.
ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic
Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens
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