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Taxonomy of Lactobacilli and Bifidobacteria

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Taxonomy of Lactobacilli and Bifidobacteria Curr. Issues Intestinal Microbiol. 8: 44–61. Online journal at www.ciim.net Taxonomy of Lactobacilli and Bifdobacteria Giovanna E. Felis and Franco Dellaglio*† of carbohydrates. The genus Bifdobacterium, even Dipartimento Scientifco e Tecnologico, Facoltà di Scienze if traditionally listed among LAB, is only poorly MM. FF. NN., Università degli Studi di Verona, Strada le phylogenetically related to genuine LAB and its species Grazie 15, 37134 Verona, Italy use a metabolic pathway for the degradation of hexoses different from those described for ‘genuine’ LAB. Abstract The interest in what lactobacilli and bifdobacteria are Genera Lactobacillus and Bifdobacterium include a able to do must consider the investigation of who they large number of species and strains exhibiting important are. properties in an applied context, especially in the area of Before reviewing the taxonomy of those two food and probiotics. An updated list of species belonging genera, some basic terms and concepts and preliminary to those two genera, their phylogenetic relationships and considerations concerning bacterial systematics need to other relevant taxonomic information are reviewed in this be introduced: they are required for readers who are not paper. familiar with taxonomy to gain a deep understanding of The conventional nature of taxonomy is explained the diffculties in obtaining a clear taxonomic scheme for and some basic concepts and terms will be presented for the bacteria under analysis. readers not familiar with this important and fast-evolving area, which importance is often underestimated. The Basic terms and concepts in bacterial taxonomy analysis of biodiversity and its cataloguing, i.e. taxonomy, Taxonomy or systematics may be defned as the process constitute the basis for applications and scientifc of cataloguing biodiversity, as it is the scientifc study communication: reliable identifcation and correct naming of the diversity of organisms with the ultimate goal of of bacterial strains are not only primary aims of taxonomic characterizing and arranging them in an orderly manner studies, but also fundamental elements in an applied (Schleifer and Ludwig, 1994). context, for the tracking of probiotic strains and a non Classifcation, identifcation and nomenclature are fraudulent labelling of fermented milks and pharmaceutical the three separate but related subdisciplines of taxonomy. products containing probiotic microorganisms. A number Classifcation is the process of clustering organisms into of resources freely available have been listed and their taxonomic groups (taxa) on the basis of similarities or use is suggested for people concerned with different relationships. Nomenclature is the assignment of names aspects of taxonomy. to the taxonomic groups according to international rules. Some perspectives in taxonomy have been outlined, Finally, identifcation is the process of determining the in particular considering the role of culture independent belonging of a new isolate to one of the established and analyses to reveal the still unknown and uncultured named taxa (Staley and Krieg, 1989). microorganisms. Finally, the impact of the availability Bacterial taxonomy is an area of growing interest: of whole-genome sequences in taxonomy is briefy it has implications for many basic scientifc and applied explained: they have already begun to give insights on felds and therefore, in some way, it underpins all bacterial evolution, which will surely have implications biological research (Tautz et al., 2003). It is considered on taxonomy, even if the analysis of data for lactic acid to have a ‘philosophical’ root, derived from human desire bacteria is still limited to few species. to recognize and understand the world, which requires a logical ordering of items (Rosselló-Mora, 2005). Moreover Introduction it has a strong practical motivation (Kandler, 1984): Species of the genera Lactobacillus and Bifdobacterium classifcation schemes, if reliable, could be predictive are some of the most important taxa involved in food and allow quick characterization of new isolates based microbiology and human nutrition, due to their role in on similarity with known taxa; identifcation procedures food and feed production and preservation, and also to allow confrmation of the identity of strains used, for the probiotic properties exhibited by some strains. These instance, in patented industrial processes; fnally, correct traits are of increasing importance and receive attention nomenclature allows not only scientifc communication from the consumer and market. but also unequivocal labelling of products containing The genus Lactobacillus belongs to the Lactic Acid microorganisms, providing customer and producer Bacteria (LAB), a defnition which groups Gram-positive, satisfaction. catalase-negative bacterial species able to produce Taxa in the classifcation system are arranged in a lactic acid as main end-product of the fermentation hierarchical way. At present, two prokaryotic domains are recognized: Archaea and Bacteria. Domains are divided into phyla and the levels below the phylum are classes, *For correspondence: [email protected] orders (or subdivisions, depending on the group), families, †Present address: NIZO food research, Kluyver Centre genera and species. Different taxonomic levels are for Genomics of Industrial Fermentation, PO Box 20, characterized by different suffxes in the taxon names. 6710 BA Ede, The Netherlands. © Horizon Scientifc Press. Offprints from www.ciim.net Further Reading Caister Academic Press is a leading academic publisher of advanced texts in microbiology, molecular biology and medical research. Full details of all our publications at caister.com • MALDI-TOF Mass Spectrometry in Microbiology Edited by: M Kostrzewa, S Schubert (2016) www.caister.com/malditof • Aspergillus and Penicillium in the Post-genomic Era Edited by: RP Vries, IB Gelber, MR Andersen (2016) www.caister.com/aspergillus2 • The Bacteriocins: Current Knowledge and Future Prospects Edited by: RL Dorit, SM Roy, MA Riley (2016) www.caister.com/bacteriocins • Omics in Plant Disease Resistance Edited by: V Bhadauria (2016) www.caister.com/opdr • Acidophiles: Life in Extremely Acidic Environments Edited by: R Quatrini, DB Johnson (2016) www.caister.com/acidophiles • Climate Change and Microbial Ecology: Current Research and Future Trends Edited by: J Marxsen (2016) www.caister.com/climate • Biofilms in Bioremediation: Current Research and Emerging Technologies • Flow Cytometry in Microbiology: Technology and Applications Edited by: G Lear (2016) www.caister.com/biorem Edited by: MG Wilkinson (2015) www.caister.com/flow • Microalgae: Current Research and Applications • Probiotics and Prebiotics: Current Research and Future Trends Edited by: MN Tsaloglou (2016) www.caister.com/microalgae Edited by: K Venema, AP Carmo (2015) www.caister.com/probiotics • Gas Plasma Sterilization in Microbiology: Theory, Applications, Pitfalls and New Perspectives • Epigenetics: Current Research and Emerging Trends Edited by: H Shintani, A Sakudo (2016) Edited by: BP Chadwick (2015) www.caister.com/gasplasma www.caister.com/epigenetics2015 • Virus Evolution: Current Research and Future Directions • Corynebacterium glutamicum: From Systems Biology to Biotechnological Applications Edited by: SC Weaver, M Denison, M Roossinck, et al. 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(2015) • Alphaviruses: Current Biology www.caister.com/bacteria-plant Edited by: S Mahalingam, L Herrero, B Herring (2016) www.caister.com/alpha • Aeromonas Edited by: J Graf (2015) • Thermophilic Microorganisms www.caister.com/aeromonas Edited by: F Li (2015) www.caister.com/thermophile • Antibiotics: Current Innovations and Future Trends Edited by: S Sánchez, AL Demain (2015) www.caister.com/antibiotics • Leishmania: Current Biology and Control Edited by: S Adak, R Datta (2015) www.caister.com/leish2 • Acanthamoeba: Biology and Pathogenesis (2nd edition) Author: NA Khan (2015) www.caister.com/acanthamoeba2 • Microarrays: Current Technology, Innovations and Applications Edited by: Z He (2014) www.caister.com/microarrays2 • Metagenomics of the Microbial Nitrogen Cycle: Theory, Methods and Applications Edited by: D Marco (2014) www.caister.com/n2 Order from caister.com/order Taxonomy of Lactobacilli and Bifdobacteria 45 As microorganisms have too simple a structure and performed and properties attributed, they are, frst of all, too few informative characters compared with higher characteristics of the strain under study. organisms (e.g. morphology), progress in bacterial The phylogenetic approach has revolutionized taxonomy has always been dependent on advances in bacterial systematics. Relatedness among organisms
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