Abstract
BackgroundLactic acid bacteria (LAB) are important in the food industry for the production of fermented food products and in human health as commensals in the gut. However, the phylogenetic relationships among LAB species remain under intensive debate owing to disagreements among different data sets.ResultsWe performed a phylogenetic analysis of LAB species based on 232 genes from 28 LAB genome sequences. Regardless of the tree-building methods used, combined analyses yielded an identical, well-resolved tree topology with strong supports for all nodes. The LAB species examined were divided into two groups. Group 1 included families Enterococcaceae and Streptococcaceae. Group 2 included families Lactobacillaceae and Leuconostocaceae. Within Group 2, the LAB species were divided into two clades. One clade comprised of the acidophilus complex of genus Lactobacillus and two other species, Lb. sakei and Lb. casei. In the acidophilus complex, Lb. delbrueckii separated first, while Lb. acidophilus/Lb. helveticus and Lb. gasseri/Lb. johnsonii were clustered into a sister group. The other clade within Group 2 consisted of the salivarius subgroup, including five species, Lb. salivarius, Lb. plantarum, Lb. brevis, Lb. reuteri, Lb. fermentum, and the genera Pediococcus, Oenococcus, and Leuconostoc. In this clade, Lb. salivarius was positioned most basally, followed by two clusters, one corresponding to Lb. plantarum/Lb. brevis pair and Pediococcus, and the other including Oenococcus/Leuconostoc pair and Lb. reuteri/Lb. fermentum pair. In addition, phylogenetic utility of the 232 genes was analyzed to identify those that may be more useful than others. The genes identified as useful were related to translation and ribosomal structure and biogenesis (TRSB), and a three-gene set comprising genes encoding ultra-violet resistance protein B (uvrB), DNA polymerase III (polC) and penicillin binding protein 2B (pbpB).ConclusionsOur phylogenomic analyses provide important insights into the evolution and diversification of LAB species, and also revealed the phylogenetic utility of several genes. We infer that the occurrence of multiple, independent adaptation events in LAB species, have resulted in their occupation of various habitats. Further analyses of more genes from additional, representative LAB species are needed to reveal the molecular mechanisms underlying adaptation of LAB species to various environmental niches.
Highlights
Lactic acid bacteria (LAB) are important in the food industry for the production of fermented food products and in human health as commensals in the gut
A recent study using 141 core proteins from 17 LAB species suggested that Lb. delbrueckii diverged earliest within the acidophilus complex, while Lb. acidophilus/Lb. helveticus and Lb. gasseri/Lb. johnsonii clustered into a sister group [8]
The strategy of developing potential orthologous gene sets for LAB phylogenomic studies was different from those used in previous LAB analyses
Summary
Lactic acid bacteria (LAB) are important in the food industry for the production of fermented food products and in human health as commensals in the gut. A recent study using 141 core proteins from 17 LAB species suggested that Lb. delbrueckii diverged earliest within the acidophilus complex, while Lb. acidophilus/Lb. helveticus and Lb. gasseri/Lb. johnsonii clustered into a sister group [8]. An analysis of 141 core proteins suggested that the Lb. sakei/Lb. casei clade is more related to acidophilus complex, while the other Lactobacillus species and Pediococcus, Oenococcus, as well as Leuconostoc group together, in which Oenococcus/Leuconostoc diverged earliest, followed by Lb. salivarius, Pediococcus, Lb. reuteri, and lastly the species most recently diverged, Lb. plantarum and Lb. brevis [8]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
