bioRxiv preprint doi: https://doi.org/10.1101/537084; this version posted January 31, 2019. The copyright holder for this preprint (which 1/31/2019was not certified by peer review) is the author/funder,paper who lgc has species granted taxonomy bioRxiv a license - Google to display Documenten the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. A genome-based species taxonomy of the Lactobacillus Genus Complex Stijn Wittouck1,2 , Sander Wuyts 1, Conor J Meehan3,4 , Vera van Noort2 , Sarah Lebeer1,* 1Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium 2Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium 3Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium 4BCCM/ITM Mycobacterial Culture Collection, Institute of Tropical Medicine, Antwerp, Belgium *Corresponding author;
[email protected] Abstract Background: There are over 200 published species within the Lactobacillus Genus Complex (LGC), the majority of which have sequenced type strain genomes available. Although gold standard, genome-based species delimitation cutoffs are accepted by the community, they are seldom checked against currently available genome data. In addition, there are many species-level misclassification issues within the LGC. We constructed a de novo species taxonomy for the LGC based on 2,459 publicly available, decent-quality genomes and using a 94% core nucleotide identity threshold. We reconciled thesede novo species with published species and subspecies names by (i) identifying genomes of type strains in our dataset and (ii) performing comparisons based on 16S rRNA sequence identity against type strains.