A Genome-Based Species Taxonomy of the <italic toggle="yes">Lactobacillus</italic> Genus Complex

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 checke...

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Autores principales:	Stijn Wittouck, Sander Wuyts, Conor J. Meehan, Vera van Noort, Sarah Lebeer
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	genomics Lactobacillus taxonomy species delimitation core genome Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/2334d91035184b6284730d6372a62515
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spelling	oai:doaj.org-article:2334d91035184b6284730d6372a625152021-12-02T18:15:44ZA Genome-Based Species Taxonomy of the <italic toggle="yes">Lactobacillus</italic> Genus Complex10.1128/mSystems.00264-192379-5077https://doaj.org/article/2334d91035184b6284730d6372a625152019-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00264-19https://doaj.org/toc/2379-5077ABSTRACT 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 Further, we found at least eight de novo species that constitute new, unpublished species.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 ∼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.Stijn WittouckSander WuytsConor J. MeehanVera van NoortSarah LebeerAmerican Society for MicrobiologyarticlegenomicsLactobacillustaxonomyspecies delimitationcore genomeMicrobiologyQR1-502ENmSystems, Vol 4, Iss 5 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	genomics Lactobacillus taxonomy species delimitation core genome Microbiology QR1-502
spellingShingle	genomics Lactobacillus taxonomy species delimitation core genome Microbiology QR1-502 Stijn Wittouck Sander Wuyts Conor J. Meehan Vera van Noort Sarah Lebeer A Genome-Based Species Taxonomy of the <italic toggle="yes">Lactobacillus</italic> Genus Complex
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 ∼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.
format	article
author	Stijn Wittouck Sander Wuyts Conor J. Meehan Vera van Noort Sarah Lebeer
author_facet	Stijn Wittouck Sander Wuyts Conor J. Meehan Vera van Noort Sarah Lebeer
author_sort	Stijn Wittouck
title	A Genome-Based Species Taxonomy of the <italic toggle="yes">Lactobacillus</italic> Genus Complex
title_short	A Genome-Based Species Taxonomy of the <italic toggle="yes">Lactobacillus</italic> Genus Complex
title_full	A Genome-Based Species Taxonomy of the <italic toggle="yes">Lactobacillus</italic> Genus Complex
title_fullStr	A Genome-Based Species Taxonomy of the <italic toggle="yes">Lactobacillus</italic> Genus Complex
title_full_unstemmed	A Genome-Based Species Taxonomy of the <italic toggle="yes">Lactobacillus</italic> Genus Complex
title_sort	genome-based species taxonomy of the <italic toggle="yes">lactobacillus</italic> genus complex
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/2334d91035184b6284730d6372a62515
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A Genome-Based Species Taxonomy of the <italic toggle="yes">Lactobacillus</italic> Genus Complex

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