Institute of Tropical Medicine Antwerp
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A genome-based species taxonomy of the Lactobacillus genus complex

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dc.contributor.author Wittouck, S. en_US
dc.contributor.author Wuyts, S. en_US
dc.contributor.author Meehan, C. J. en_US
dc.contributor.author van Noort, V. en_US
dc.contributor.author Lebeer, S. en_US
dc.date.accessioned 2020-08-25T09:38:54Z
dc.date.available 2020-08-25T09:38:54Z
dc.date.issued 2019 en_US
dc.identifier.issn 2379-5077 en_US
dc.identifier.doi http://dx.doi.org/10.1128/mSystems.00264-19 en_US
dc.identifier.other http://lib.itg.be/pdf/itg/2019/2019msyse0264.pdf en_US
dc.identifier.other 17 pp. en_US
dc.identifier.other 70 en_US
dc.identifier.other ITG-B3A; DBM; U-MYCOB; JIF; DOI; PDF; PMC; Abstract; ITMPUB; DSPACE68 en_US
dc.identifier.uri http://hdl.handle.net/10390/10972
dc.description.abstract There are more than 200 published species within the Lactobacillus genus complex (LGC), the majority of which have sequenced type strain genomes available. Although genome-based species delimitation cutoffs are accepted as the gold standard by the community, these are seldom actually checked for new or already published species. In addition, the availability of genome data is revealing inconsistencies in the species-level classification of many strains. We constructed a de novo species taxonomy for the LGC based on 2,459 publicly available genomes, using a 94% core nucleotide identity cutoff. We reconciled these de novo species with published species and subspecies names by (i) identifying genomes of type strains and (ii) comparing 16S rRNA genes of the genomes with 16S rRNA genes of type strains. We found that genomes within the LGC could be divided into 239 de novo species that were discontinuous and exclusive. Comparison of these de novo species to published species led to the identification of nine sets of published species that can be merged and one species that can be split. Further, we found at least eight de novo species that constitute new, unpublished species. Finally, we reclassified 74 genomes on the species level and identified for the first time the species of 98 genomes. Overall, the current state of LGC species taxonomy is largely consistent with genome-based species delimitation cutoffs. There are, however, exceptions that should be resolved to evolve toward a taxonomy where species share a consistent diversity in terms of sequence divergence. IMPORTANCE The Lactobacillus genus complex is a group of bacteria that constitutes an important source of strains with medical and food applications. The number of bacterial whole-genome sequences available for this taxon has been increasing rapidly in recent years. Despite this wealth of information, the species within this group are still largely defined by older techniques. Here, we constructed a completely new species-level taxonomy for the Lactobacillus genus complex based on approximately 2,500 whole-genome sequences. As a result of this effort, we found that many genomes are not classified to their correct species, and we were able to correct these. In addition, we found that some published species are abnormally large, while others are too small. Finally, we discovered at least eight completely novel species that have not been published before. Our work will help the field to evolve toward a more meaningful and complete taxonomy, based on whole-genome sequences. en_US
dc.language English en_US
dc.relation.uri http://www.ncbi.nlm.nih.gov/pubmed/31481601 en_US
dc.subject Lactobacillus en_US
dc.subject Bacteriology en_US
dc.subject Taxonomy en_US
dc.subject Genomics en_US
dc.title A genome-based species taxonomy of the Lactobacillus genus complex en_US
dc.type Article-E en_US
dc.citation.issue 5 en_US
dc.citation.jtitle mSystems en_US
dc.citation.volume 4 en_US
dc.citation.pages e00264-19 en_US
dc.citation.abbreviation mSystems en_US


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