A Genomic View of Lactobacilli and Pediococci Demonstrates that Phylogeny Matches Ecology and Physiology

Abstract

cLactobacilli 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 twodomain 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. Lactobacilli are significant members of animal and human microbiota and of the plant phyllosphere. Owing to their stable association with humans as well as raw material for food production, lactobacilli also occur in many or most food fermentations. Lactobacilli are at the interface of aerobic and anaerobic life. Many lactobacilli retain the conditional capacity for respiration (1), but their ecology and physiology are mainly related to the fermentative conversion of sugars to organic acids (2, 3). Lactobacilli employ the Embden-Meyerhof pathway (glycolysis) and/or the phosphoketolase pathway for conversion of hexoses (2). These pathways have a low energetic efficiency; lactobacilli compensate for this disadvantage by rapid depletion of carbon sources and by accumulation of organic acids to inhibit competitors. The evolution and ecology of lactobacilli are shaped by niche adaptation and reduction of genome size (4). Many species, e.g., Lactobacillus plantarum, maintain a genetic diversity that enables occupation of diverse ecological niches (5). Other species are highly specialized and reduce their genomes more extensively. Examples include the insect-associated Lactobacillus fructivorans (6); Lactobacillus iners, a species specialized for the female human urogenital tract (7); and Lactobacillus reuteri, a host-specific intestinal symbiont of vertebrate animals (8). Lactobacillus delbrueckii has undergone a very recent reduction of genome size to adapt to dairy fermentations ...

Structure-function relationships of bacterial and enzymatically produced reuterans and dextran in sourdough bread baking application

“…Likewise, beneficial effects of levan from Lactobacillus sanfranciscensis were obscured by increased acetate formation, which reduced bread volume (Kaditzky et al, 2007). Most heterofermentative lactobacilli preferentially metabolize fructose as electron acceptor, which results in the formation of mannitol and acetate (Korakli et al, 2001;Zheng et al, 2015). However, the absence of mannitol dehydrogenase in most strains of Weissella spp.…”

DFAST and DAGA: web-based integrated genome annotation tools and resources

“…Indeed, two pheS genes were found in the genome, each matching the deposited pheS gene sequences of L. kefiri and L. parakefiri. Our analysis suggests that its large genome size [18] and the similarity to L. kefiri [17] are attributable to the sequence contamination. Likewise, the genome of P. parvulus DSM 20332 T seems to be contaminated with another strain of P. acidilactici .…”

“…The genus Pediococcus is another member of Lactobacillaceae consisting of 11 species, and it is phylogenetically placed within the Lactobacillus cluster, near L. plantarum and L. brevis [15, 16]. In a recent study, the term Lactobacillus sensu lato was also proposed to refer to these genera [17]. In both genera, the number of new species described and genomes published have been growing with the improvement of isolation, cultivation, and identification methods as well as sequencing technology (Fig.…”

“…Nowadays, most type strains have been sequenced and become publicly available through large-scale sequencing projects, such as “Genome sequencing of JCM strains under the NBRP program” in Japan (BioProject ID: PRJDB547), “ Lactobacillus in severe early childhood caries” by Sanger Institute, UK (PRJEB3060), and “Genomic characterization of the genus Lactobacillus ” in China (PRJNA222257). The results of such projects have enabled genus-wide analyses covering almost 90% of the known species based on the genomic information [17, 18]. Our DAGA provides annotated genomes for the family Lactobacillaceae , which includes many species that have undergone reclassification and species difficult to distinguish by 16S rRNA gene sequences.…”

Gut Microbiota Dysbiosis and Role of Probiotics in Infant Colic

“…Pediococci are round-shaped bacteria belonging to the Lactobacillus group [48]. A probiotic formula including strains Pediococcus pentosaceus CECT 8330 and Bifidobacterium longum CECT 7894 showed a significant trend towards a greater reduction in daily crying time in just 14 days, in a pilot RCT comparing to placebo (p=0.083).…”