Using Matrix-Assisted Laser Desorption/Ionization Time of Flight Spectra To Elucidate Species Boundaries by Matching to Translated DNA Databases

A method has been established to map a bacterial colony
to the
ever-expanding database of publicly available bacterial genomes by
means of matrix-assisted laser desorption/ionization (MALDI) spectra.
To accomplish this, spectra are mapped to the predicted masses of
∼65 families of mostly ribosomal proteins. Each of the ∼40 000
bacterial strains in the database receives scores, together with tables
listing identified protein sequences and how the highest ranking strains
are related to one another. The approach was first confirmed with
16 distinct species of bacteria from the Vibrionales whose genome had been sequenced. Identifications of a few species
of bacteria from environmental samples from compost, lakes, and streams
in Massachusetts are also reported. Most of these organisms map to
known species in the Gammaproteobacteria and Firmicutes. The clades of bacteria deducible from shared
ribosomal protein sequences do not always correspond well to named
bacterial species. Instead, the identifications made by this methodology
indicate groupings of organisms that can readily be distinguished
by MALDI-TOF and indicate which polymorphisms in highly conserved
proteins demarcate the groupings. Successful identifications highlight
organism interrelationships that can be deduced from the available
genomes, sorting together genomes into new proposed clades typically
consistent with relationships deduced from DNA sequence analysis.
In contrast, if for a high-quality spectrum from a fresh colony, no
group of related organisms receives high scores, one might infer that
no closely related genome has yet been deposited into the database.