title: A Genomic View of Lactobacilli and Pediococci Demonstrates that Phylogeny Matches Ecology and Physiology.
abstract: Lactobacilli are used widely in food, feed, and health applications. The taxonomy of the genus Lactobacillus, however, is confounded by the apparent lack of physiological markers for phylogenetic groups of lactobacilli and the unclear relationships between the diverse phylogenetic groups. This study used the core and pan-genomes of 174 type strains of Lactobacillus and Pediococcus to establish phylogenetic relationships and to identify metabolic properties differentiating phylogenetic groups. The core genome phylogenetic tree separated homofermentative lactobacilli and pediococci from heterofermentative lactobacilli. Aldolase and phosphofructokinase were generally present in homofermentative but not in heterofermentative lactobacilli; a two-domain alcohol dehydrogenase and mannitol dehydrogenase were present in most heterofermentative lactobacilli but absent in most homofermentative organisms. Other genes were predominantly present in homofermentative lactobacilli (pyruvate formate lyase) or heterofermentative lactobacilli (lactaldehyde dehydrogenase and glycerol dehydratase). Cluster analysis of the phylogenomic tree and the average nucleotide identity grouped the genus Lactobacillus sensu lato into 24 phylogenetic groups, including pediococci, with stable intra- and intergroup relationships. Individual groups may be differentiated by characteristic metabolic properties. The link between phylogeny and physiology that is proposed in this study facilitates future studies on the ecology, physiology, and industrial applications of lactobacilli.
authors.affiliation: Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Wuhan, China.
authors.forename: Jinshui
authors.initials: J
authors.lastname: Zheng
authors.affiliation: Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Wuhan, China.
authors.forename: Lifang
authors.initials: L
authors.lastname: Ruan
authors.affiliation: Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Wuhan, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Sun
authors.affiliation: University of Alberta, Department of Agricultural, Food and Nutritional Science, Edmonton, AB, Canada Hubei University of Technology, School of Food and Pharmaceutical Engineering, Wuhan, China mgaenzle@ualberta.ca.
authors.forename: Michael
authors.identifier: http://orcid.org/0000-0003-0972-928X
authors.initials: M
authors.lastname: Gänzle
mesh_terms: D004463:Ecology; D016680:Genome, Bacterial / Q000235:genetics*; D007778:Lactobacillus / Q000145:classification / Q000235:genetics*; D010376:Pediococcus / Q000145:classification / Q000235:genetics*; D010802:Phylogeny