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8 results for “Lactobacillaceae”
Fig. 2 in A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae
Fig. 2. Core genome phylogenetic tree of Lactobacillaceae. The phylogenomic analysis is based on the concatenated alignment of protein sequences for the 114 single-copy core genes. The maximum likelihood tree was inferred by RAxML as described previously [14] using the 244 Lactobacillus and Pediococcus species for which genome sequence data was available on the NCBI database on 19 August 2019. The tree was rooted via midpoint rooting. Bootstrap support values were calculated from 500 replicates, and only values above 90 % were labelled. Members of the same phylogenetic group that are the basis for the proposed taxonomy are indicated by the same colour for branches, and the type strain of each group is printed in bold. Outer rings provide information on genomic features and the inferred lifestyle of the species. The colour gradient in red represents the GC content of each genome sequence; higher GC contents are indicated by darker shading. The solid circles in brown represent genome sizes; the area of the circle correlates with the genome size. The second ring indicates the inferred natural habitats of the species as vertebrate host-adapted (red), insect-adapted (orange), nomadic (green), free-living (blue) or unassigned (white). This assignment of species to lifestyle was based on [17].
Fig. 6 in A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae
Fig. 6. Gene family presence/absence patterns in Lactobacillaceae and Leuconostocaceae. Each column represents a gene family presence/absence pattern in species of Lactobacillaceae and Leuconostoaceae, where presence is indicated with a dot. The absolute number of gene families that conform to each pattern is visualized in the marginal bar plot at the top. Separations between phylogroups are indicated with horizontal black lines. We defined genes that were present in all genomes of a clade and in none of the genomes outside of that clade as 'signature genes' (dark blue); other genes are shown in light blue. Only presence/absence patterns followed by four or more gene families are shown. Patterns of presence in a single species or all species are not shown. Unassigned species are clusters of closely related genomes which could not be assigned to a known species due to low whole-genome similarity to a type strain and/or low 16S rRNA similarity to a type strain.
Fig. 8 in A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae
Fig. 8. Heat map depicting the cAAI values of the 38 782 pairwise comparisons of all species in the families Leuconostocaceae and Lactobacillaceae for which genome sequence data was available in August 2019. The source file is provided as Table S3.
Fig. 5 in A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae
Fig. 5. Range of pairwise intra-genus cAAI values for all current and proposed genera in the families Lactobacillaceae and Leuconostocaceae. The dotted line designates the lowest cAAI value for current genera excluding Lactobacillus. Bars and symbols are coloured gray if the genus is exclusive, i.e. if the lowest intra-genus cAAI is higher than any inter-genus cAAI of species in that genus. Bars and symbols are coloured red and green, respectively, if the genus is non-exclusive, i.e. if the lowest intra-genus cAAI is lower than the highest inter-genus cAAI of species in that genus. Trivial values (100 % for self to self comparison) are shown only for genera that include one species. The data used for the graph is provided in Table S3. The y-axis label uses the proposed taxonomy as follows: Lentilactobacillus – L. buchneri group; Secundilactobacillus – L. collinoides group; Levilactobacillus – L. brevis group; Fructilactobacillus – L. fructivorans group; Acetilactobacillus, no prior designation; Apilactobacillus – L. kunkeei group; Limosilactobacillus – L. reuteri group; Paucilactobacillus – L. vaccinostercus group; Furfurilactobacillus – L. rossiae group; Lactiplantibacillus – L. plantarum group; Ligilactobacillus – part of L. salivarius group; Liquorilactobacillus - part of L. salivarius group; Dellaglioa – L. algidus; Loigolactobacillus – L. coryniformis group; Paralactobacillus – L. selangorensis; Latilactobacillus – L. sakei group; Lacticaseibacillus – L. casei group; Agrilactobacillus – L. composti; Schleiferilactobacillus – L. perolens group; Lapidilactobacillus – L. dextrinicus / convacus; Companilactobacillus – L. alimentarius group; Bombilactobacillus – L. mellifer/mellis group; Lactobacillus – L. delbrueckii group; Amylolactobacillus – L. amylophilus group; Holzapfelia – L. florum.
Fig. 4 in A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae
Fig. 4. Frequency distribution of pairwise cAAI in Lactobacillaceae and Leuconostocaceae. Inter-genus cAAI values are shown in descending order; Intra-genus cAAI values are shown in ascending order for the current taxonomy (dotted lines) and for the proposed taxonomy that divides the genus Lactobacillus in 25 genera (solid lines). Genera are colour coded; Lactobacillus; Pediococcus, Leuconostoc and Weissella. The number of pairwise cAAI values that is represented by the lines is indicated in the figure legend. Owing to the low number of values, intra-genus cAAI values for Fructobacillus, Oenococcus and Convivina are not shown. The data used for the graph is provided in Table S3.
Fig. 7 in A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae
Fig. 7. (a) Core genome phylogenetic tree with the type strains of 25 phylogenetic groups of the genus Lactobacillus, 31 type strains of other genera in the Lactobacillales and eight type strains from Bacillales as an outgroup. The phylogenomic analysis is based on the concatenated protein sequences of 170 single copy core genes. The maximum-likelihood tree was inferred by RAxML as described previously [5, 12]. Bootstrap support values were calculated from 500 replicates and only values of>80 % are labelled. Members of the same bacterial families are colour coded. (b) Overview tree of phylogroups of Lactobacillaceae and Leuconostocaceae. Subtree of the tree shown in Fig. S4; only the branches corresponding to type species of phylogroups of Lactobacillaceae or genera of Leuconostocaceae are shown.
Fig. 1 in A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae
Fig. 1. Cumulative number of species described in the genera Pediococcus and Lactobacillus until January 2020. The species description in January 2020 is included in the 2010–2019 count.
Fig. 3 in A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae
Fig. 3. Box plot of the intra-family and inter-family cAAI values in the families Leuconostocaceae and Lactobacillaceae. The reference line is drawn at a cAAI of 59 % in both panels.
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