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Fragment of the aspartyl-tRNA synthetase applicable as a shared classification and phylogenetic marker in particular representatives of the order Lactobacillales

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Abstract

The order Lactobacillales represents a morphologically, metabolically, and physiologically diverse group of bacteria. Lactic acid bacteria represent the core of this phylogenetic group. They are a part of epiphytic microflora, fermented dairy, meat, fruit and vegetable products, and the digestive tract of humans and animals. Despite the fact that these bacteria form a phenotypically and genotypically heterogeneous group, their phylogenetic relationship enables to propose a common genetic marker usable in classification, typing, and phylogeny. By creation of consensus sequence based on available genomic sequences of some representatives of order Lactobacillales, a specific primer-pair binding variable region of aspS gene (length of 615 nts) encoding the aspartyl-tRNA synthetase was designed. This gene has not yet been used in classification and phylogeny of the order Lactobacillales, although it meets the requirements of molecular markers (distribution and single copy in bacterial genomes, functional constancy and genetic stability, sequence variability among taxonomic units, irreplaceable role in proteosynthesis). Primers were applied on 54 type and wild Lactobacillales strains. Obtained sequences allowed to provide alignments for purpose of phylogenetic tree reconstructions that uncovered particular phylogenetic clusters of vagococci/enterococci, obligately homofermentative and heterofermentative lactobacilli. Although a relatively short fragment of the aspS gene (approximately 33% of the complete gene sequence) was evaluated, much higher sequence variability (61.8% of pairwise identity) among strains examined compared with 16S rRNA gene (90.7%, length of 1318 nt) provides a relatively simple and effective tool for classification and typing of selected representatives of the order Lactobacillales.

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Funding

This study was funded by the Project Excellence (No. CZ.02.1.01/0.0/0.0/15_003/0000460), the Czech Health Research Council (Project No. 16-27449A), and the Institution research project No. RO 0318 of the Food Research Institute Prague (Ministry of Agriculture of the Czech Republic).

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Authors and Affiliations

  1. Institute of Animal Physiology and Genetics, v.v.i., of the Czech Academy of Sciences, Vídeňská 1083, Prague 4 – Krč, 142 20, Czechia

    Chahrazed Mekadim, Jiří Killer & Jakub Mrázek

  2. Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czechia

    Chahrazed Mekadim, Jiří Killer & Radko Pechar

  3. Food Research Institute Prague, Radiová 1285/7, Prague 10 – Hostivař, 102 00, Czechia

    Radko Pechar

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  1. Chahrazed Mekadim
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  2. Jiří Killer
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  3. Radko Pechar
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  4. Jakub Mrázek
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Correspondence to Jiří Killer.

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Mekadim, C., Killer, J., Pechar, R. et al. Fragment of the aspartyl-tRNA synthetase applicable as a shared classification and phylogenetic marker in particular representatives of the order Lactobacillales. Folia Microbiol 64, 113–120 (2019). https://doi.org/10.1007/s12223-018-0638-8

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  • DOI: https://doi.org/10.1007/s12223-018-0638-8

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