ORIGINAL ARTICLE Glutamine synthetase type I (glnAI) represents a rewarding molecular marker in the classification of bifidobacteria and related genera Jiří Killer 1,2 & Chahrazed Mekadim 1,2 & Věra Bunešová 2 & Jakub Mrázek 1 & Zuzana Hroncová 2 & Eva Vlková 2 Received: 18 January 2019 /Accepted: 29 April 2019 # Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i. 2019 Abstract The family Bifidobacteriaceae constitutes an important phylogenetic group that particularly includes bifidobacterial taxa dem- onstrating proven or debated positive effects on host health. The increasingly widespread application of probiotic cultures in the twenty-first century requires detailed classification to the level of particular strains. This study aimed to apply the glutamine synthetase class I (glnAI) gene region (717 bp representing approximately 50% of the entire gene sequence) using specific PCR primers for the classification, typing, and phylogenetic analysis of bifidobacteria and closely related scardovial genera. In the family Bifidobacteriaceae, this is the first report on the use of this gene for such purposes. To achieve high-value results, almost all valid Bifidobacteriaceae type strains (75) and 15 strains isolated from various environments were evaluated. The threshold value of the glnAI gene identity among Bifidobacterium species (86.9%) was comparable to that of other phylogenetic/ identification markers proposed for bifidobacteria and was much lower compared to the 16S rRNA gene. Further statistical and phylogenetic analyses suggest that the glnAI gene can be applied as a novel genetic marker in the classification, genotyping, and phylogenetic analysis of isolates belonging to the family Bifidobacteriaceae. Introduction Bifidobacteria, classified into the phylum Actinobacteria, rep- resent one of the major groups of probiotics that are well known for their proven or potential health–promoting effects. In general, these obligately anaerobic bacteria occupy the gas- trointestinal tract of mammals and social insects (Bunešová et al. 2014), and have also been detected in fishes and reptiles (Kopečný et al. 2010). Probiotic properties have been studied extensively in bifidobacteria of human origin and are associ- ated with reducing the risk of gastrointestinal infections, improving intestinal health by the regulation/modification of microbiota, improving cognitive functions by influencing the local and systemic antioxidant status or by immediate produc- tion of neurochemicals; stimulation/modulation and develop- ment of the immune system; synthesis of physiologically valuable compounds, enhancing the bioavailability of nutri- ents, reducing the symptoms of lactose intolerance, and posi- tively affecting the risk of certain other diseases (Nagpal et al. 2012). The ecology and significance of species classified into the scardovial genera with respect to host health have not been explored sufficiently, even though some of them are consid- ered as opportunistic pathogens (Sechovcová et al. 2017). Probiotics are available at pharmacies and sometimes at supermarkets in the form of freeze-dried tablets, primarily as dietary supplements and in supermarkets or retailers in the form of fermented milk, fruit, or vegetable drinks, and food. Novel probiotics containing different strains of bifidobacteria are emerging in the market annually. However, legislation associated with the accurate classsification of probiotic Bifidobacterium strains in many countries is unclear. Therefore, functional molecular-genetics techniques designed for identification and genotyping of bifidobacterial strains exhibiting the desired probiotic properties are actual (Hill et al. 2014). Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12223-019-00716-0) contains supplementary material, which is available to authorized users. * Jiří Killer Killer.Jiri@seznam.cz; killer@iapg.cas.cz 1 Institute of Animal Physiology and Genetics, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Krč, Czechia 2 Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00 Prague 6, Suchdol, Czechia Folia Microbiologica https://doi.org/10.1007/s12223-019-00716-0