Evolution of the Bacterial Species Lactobacillus delbrueckii: A Partial Genomic Study with Reflections on Prokaryotic Species Concept

Germond, Jacques-Edouard; Lapierre, Luciane; Delley, Michèle; Mollet, Beat; Felis, Giovanna E.; Dellaglio, Franco

doi:10.1093/molbev/msg012

Cited by 75Probiotics and Fermented FoodsBacterial Genetics and BiotechnologyGenomics and Phylogenetic Studies

Evolution of the Bacterial Species Lactobacillus delbrueckii: A Partial Genomic Study with Reflections on Prokaryotic Species Concept

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Germond, Jacques-Edouard, Lapierre, Luciane, Delley, Michèle, Mollet, Beat, Felis, Giovanna E., Dellaglio, Franco·2003·Molecular Biology and Evolution

DOI 10.1093/molbev/msg012

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Abstract

The species Lactobacillus delbrueckii consists at present of three subspecies, delbrueckii, lactis and bulgaricus, showing a high level of DNA-DNA hybridization similarity but presenting markedly different traits related to distinct ecological adaptation. The internal genetic heterogeneity of the bacterial species L. delbrueckii was analyzed. Phenotypic and several genetic traits were investigated for 61 strains belonging to this species. These included 16S rDNA sequence mutations, expression of beta-galactosidase and of the cell wall-anchored protease, the characterization of the lactose operon locus and of the sequence of lacR gene, galactose metabolism, and the distribution of insertion sequences. The high genetic heterogeneity of taxa was confirmed by every trait investigated: the lac operon was completely deleted in the subsp. delbrueckii, different mutation events in the repressor gene of the operon led to a constitutive expression of lacZ in the subsp. bulgaricus. Structural differences in the same genetic locus were probably due to the presence of different IS elements in the flanking regions. The different expression of the cell wall-anchored protease, constitutive in the subsp. bulgaricus, inducible in the subsp. lactis, and absent in the subsp. delbrueckii was also a consequence of mutations at the gene level. The galT gene for galactose metabolism was found only in the subsp. lactis, while no specific amplification product was detected in the other two subspecies. All these data, together with the absence of a specific IS element, ISL6, from the major number of strains belonging to the subsp. bulgaricus, confirmed a deep internal heterogeneity among the three subspecies. Moreover, this evidence and the directional mutations found in the 16S rDNA sequences suggested that, of the three subspecies, L. delbrueckii subsp. lactis is the taxon closer to the ancestor. Limitations of the current prokaryotic species definition were also discussed, based on presented evidences. Our results indicate the need for an accurate investigation of internal heterogeneity of bacterial species. This study has consequences on the prokaryotic species concept, since genomic flexibility of prokaryotes collides with a stable classification, necessary from a scientific and applied point of view.

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In two proteinase-deficient strains of L. delbrueckii subsp. delbrueckii, several copies of the KSDX repeat have been shown to be duplicated or deleted.
“In the two proteinase-deficient strains of L. delbrueckii subsp. delbrueckii (ATCC 9649 and NCFB701744), several copies of this repeat have been shown to be duplicated or deleted (12).”
From Determination of the Domain of the Lactobacillus delbrueckii subsp. bulgaricus Cell Surface Proteinase PrtB Involved in Attachment to the Cell Wall after Heterologous Expression of the prtB Gene in Lactococcus lactis (2003) · cites this paper as [12]
The ‘Expression of the Cell Wall-Anchored Protease’ section identifies ATCC 9649 and NCFB 701744 as protease-deficient and reports insertions or deletions in a region composed of four-amino-acid repeats. Our copy does not identify those repeats as KSDX, so the specific repeat named in the claim is not verified. (LLM, conf=0.82)
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Authors: Germond, J.-E., Lapierre, L., Delley, M., Mollet, B., Felis, G. E., & Dellaglio, F.
Affiliations: Nestec (Switzerland) (CH)
University of Verona (IT)
ORCID: Felis, Giovanna E.
Venue: Molecular Biology and Evolution
Publisher: Oxford University Press (OUP)
Published: 2003-01
Volume: 20
Issue: 1
Pages: 93-104
ISSN: 0737-4038 (ISSN-L)
1537-1719
DOI: 10.1093/molbev/msg012
OpenAlex: W1985995960
Cited by: 73
References: 41
Citations by year: 2026: 2 · 2025: 3 · 2024: 3 · 2023: 2 · 2022: 4 · 2021: 1 · 2020: 4 · 2019: 1 · 2018: 2 · 2017: 1 · 2016: 3 · 2015: 1 · 2014: 4 · 2013: 4 · 2012: 4
FWCI: 6.62
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: Molecular Biology and Evolution (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: Lactobacillus delbrueckii, Lactobacillus delbrueckii subsp. delbrueckii, Lactobacillus delbrueckii subsp. lactis, Lactobacillus bulgaricus, bacterial species concept, lac operon, beta-galactosidase expression, galactose metabolism, GALT gene, insertion sequences, bacterial taxonomy
MeSH terms: Amino Acid Sequence, Bacterial Proteins, Base Sequence, Biological Evolution, Galactose, Lactobacillus, Molecular Sequence Data, Phylogeny, Promoter Regions, Genetic, Genome, Bacterial, Sequence Analysis, DNA

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Evolution of the Bacterial Species Lactobacillus delbrueckii: A Partial Genomic Study with Reflections on Prokaryotic Species Concept

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