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Fig. 2 in Sphingobacterium prati sp. nov., isolated from agricultural soil and involved in lignocellulose deconstruction

Fig. 2. Maximim-likelihood phylogenetic tree based on the sequences of the concatenated rpoB–cpn60–16S rRNA genes showing the relationship of strain arapr2T with closely related Sphingobacterium species. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates were removed.

opennotspecifiedFeb 2022View details →

Fig. 1. 16S in Pseudochrobactrum algeriensis sp. nov., isolated from lymph nodes of Algerian cattle

Fig. 1. 16S rRNA gene minimum-likelihood phylogeny of a selected subset of Brucellaceae type strains. Bootstrap support over 1000 replications are indicated at each branching point. The tree is rooted according to a previously published Brucellaceae 16S rRNA topology conducted with several Rhizobiales outgroups [4].

opennotspecifiedJul 2020View details →

Fig. 1 in Fundicoccus ignavus gen. nov., sp. nov., a novel genus of the family Aerococcaceae isolated from bulk tank milk

Fig. 1. Maximum-likelihood tree based on the almost-complete 16S rRNA gene sequences of strains WS4937T, WS4759, WS5303 and type strains of all species of the family Aerococcaceae. Type strains of the type species are marked in bold. Sequences of the strains were retrieved from EzBioCloud. The tree was calculated using the Tamura–Nei model. Bootstrap values (>50%) based on 500 repetitions are shown at branch nodes. Analyses were performed using MEGA X. Lactococcus lactis subsp. lactis was used as an outgroup. Bar, 0.01 substitutions per nucleotide position.

Fig. 2 in RUMiNOCOCCUS BOViS sp. nov., a novel species of amylolytic RUMiNOCOCCUS isolated from the rumen of a dairy cow

Fig. 2. JE7A12T phylogenic tree by PhyloPhlan dendrogram; JE7A12 T and type strains of species of the genus Ruminococcus as well as type strains of other close phylogenetic neighbours. JE7A12T is indicated in green type, type strains of members of Ruminococcus group 1 are indicated in blue type. Branch length based on relative concatenated amino acid sequence similarity is appended to each branch. NCBI GenBank accession numbers are appended to each species label.

opennotspecifiedFeb 2022View details →

Fig. 2 in Pseudochrobactrum algeriensis sp. nov., isolated from lymph nodes of Algerian cattle

Fig. 2. Whole-genome maximum-likelihood phylogeny of a selected subset of Brucellaceae type strain genomes, based on the alignment of 854 core proteins. Bootstrap support over 100 replications are indicated at each branching point. The Pseudochrobactrum clade is boxed in pink. Pairwise gANI values are given as a heatmap, with values below the species threshold of 96.5 coloured as a white-to-blue gradient, and values above the threshold coloured as a blue-to-purple gradient.

Fig. 1 in Sphingobacterium prati sp. nov., isolated from agricultural soil and involved in lignocellulose deconstruction

Fig. 1. Phylogenetic tree of type strains closely related to strain arapr2T based on 16S rRNA gene sequences. The evolutionary history was inferred by MEGA 7.0 [32] using the the neighbour-joining method [33]. There were a total of 1315 positions in the final dataset. Bar, 0.02 substitutions per nucleotide position. The outgroup of the tree was Flavobacterium terrae R2A1-13T.

Fig. 1 in RUMiNOCOCCUS BOViS sp. nov., a novel species of amylolytic RUMiNOCOCCUS isolated from the rumen of a dairy cow

Fig. 1. JE7A12T 16S rRNA phylogenetic tree by MEGA X, dendrogram; JE7A12T and type strains of species of the genus Ruminococcus as well as type strains of closely related species. The tree was reconstructed using 16S rRNA type strain sequences from members of the order Clostridiales in the RDP database by the neighbor-joining method based on the comparison of 1500 nt sequences. JE7A12T node and label are in green type. Ruminococcus group 1 type strains are in blue type. Bootstrap values, resulting from 500 replications, are given at each branch point.

opennotspecifiedJul 2020View details →

Fig. 1 in Description of Luteithermobacter gelatinilyticus gen. nov., sp. nov., and Paremcibacter congregatus gen. nov., comb. nov. via reclassification of the genus Emcibacter

Fig. 1. Phylogenetic tree based on nearly complete 16S rRNA gene sequences (1321 bp), showing the relationship between strain MEBiC09520T and the nearest members of the class Alphaproteobacteria. The tree is based on the Juke and Cantor distance model and the neighbour-joining method with 1000 bootstraps. The maximum-likelihood and maximum-parsimony algorithms with bootstrapping were also used. The sequences of Caulobacter vibrioides DSM 9893T (AJ227754) and Erythrobacter litoralis HTCC2594 (CP000157) were used as an outgroup. Nodes recovered by three treeing methods at>70% are indicated by stars, recovered by three methods but at <70% by open circles and recovered by two methods by closed circles.

opennotspecifiedJul 2020View details →

Fig. 2 in Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan

Fig. 2. Neighbour-joining phylogenetic tree derived using gyrB sequences, showing the relationships between strain HNM0687T and other type strains of genus Gordonia. Only values above 50% were shown. Asterisks represent clades that were also recovered by the maximum-likelihood and maximum-parsimony methods. Bar, five nucleotide substitutions per 100 nucleotides.

Fig. 1. A 16S in Dyella dinghuensis sp. nov. and Dyella choica sp. nov., isolated from forest soil

Fig. 1. A 16S rRNA gene sequence-based maximum-likelihood tree showing phylogenetic relationships of strains DHOA06T and 4 M- K27T. Filled circles at nodes indicate generic branches that were also recovered using neighbour-joining and maximum-parsimony algorithms. Xanthomonas campestris ATCC 33913T was used as an outgroup. Bootstrap values are shown in percentages of 1000 replicates; only bootstrap values Ȅ50 % are indicated. Bar, 0.01 substitutions per nucleotide position.

Fig. 1 in Wickerhamomyces menglaensis f.a., sp. nov., a yeast species isolated from rotten wood

Fig. 1. Phylogenetic tree derived from the neighbour-joining analysys based on sequences of the D1/D2 domains of the LSU rRNA gene, showing the placement of Wickerhamomyces menglaensis f.a., sp. nov. in the Wickerhamomyces clade. Saccharomyces cerevisiae NRRL Y-12632 was used as an outgroup. Sequences were retrieved from the GenBank and CBS (*) databases. Bootstrap values of above 50 % are given at nodes based on 1000 replications. Bar, 0.02 substitutions per site.

Fig. 2 in Pseudomonas capsici sp. nov., a plant-pathogenic bacterium isolated from pepper leaf in Georgia, USA

Fig. 2. Phylogenomic relationships between Pseudomonas capsici sp. nov. strains and closely related Pseudomonas species listed in Table 1. The tree was generated with FastME 2.1.6.1 [22] from GBDP distances calculated from genome sequences on the TYGS [19]. The branch lengths are scaled in terms of GBDP distance formula d5. The numbers at nodes are genome BLAST distance phylogeny approach pseudo-bootstrap support values (>60%) from 100 replications, with an average branch support of 94.9%. The tree was rooted at the midpoint [29]. GenBank accession numbers are shown within parentheses, with T indicating type strains.

opennotspecifiedJul 2021View details →

Fig. 2 in MaNgROVIVIRga CUNICULI gen. nov., sp. nov., a moderately halophilic bacterium isolated from bioturbated Red Sea mangrove sediment, and proposal of the novel family MaNgROVIVIRgaCeae fam. nov.

Fig. 2. (a) Maximum-likelihood phylogenetic tree based on the 16S rRNA gene sequences presenting the position of Mangrovivirga cuniculi R1DC9T (MT146883). Only bootstrap values (expressed as percentages of 1000 replications) exceeding 50% are shown at branching points. Psychroflexus torquis ATCC 700755T (GenBank accession no. U85881) was used as an outgroup. Bar, 0.040 substitutions per nucleotide position. Filled circles indicate branches that were also recovered using the neighbour-joining method. (b) Maximumlikelihood phylogenetic tree highlighting the position of R1DC9T relative to the other type strains within the order Cytophagales, including members of the families Marivirgaceae, Roseivirgaceae, Reichenbachiellaceae, Fulvivirgaceae, Cesiribacteraceae and Flammeovirgaceae. The phylogenetic tree was built using 120 concatenated single-copy genes obtained using GTDB-Tk software [34]. Bootstrap values greater than 50% based on 1000 replications are indicated at branching nodes. Bar, 0.2 substitutions per nucleotide position.

Fig. 3 in Lactobacillus suantsaii sp. nov., isolated from suan-tsai, a traditional Taiwanese fermented mustard green

Fig. 3. Phylogenomic tree of Lactobacillus suantsaii sp. nov. L88T with strains of closely related species. The tree was reconstructed by the maximum-likelihood method on the basis of a comparison of 660 core genes. Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293T was used as an outgroup. Bar, 10 % sequence divergence.

Fig. 1 in Bosea psychrotolerans sp. nov., a psychrotrophic alphaproteobacterium isolated from Lake Michigan water

Fig. 1. Neighbour-joining tree based on 16S rRNA gene sequences showing relationships among strains 1131T, 13 and 1175 and members of the genus Bosea. Numbers at nodes represent the percentages of bootstrap support based on neighbour-joining analyses of 1000 resampled datasets. Values less than 70 % were not reported. Filled circles indicate that the corresponding nodes (groupings) were also recovered in the maximum-likelihood tree. Bradyrhizobium japonicum USDA 6T (AP012206) was used as the outgroup. Bar, 0.002 nucleotide substitutions per position.

Fig. 1 in Paracoccus onubensis sp. nov., a novel alphaproteobacterium isolated from the wall of a show cave

Fig. 1. Maximum-likelihood phylogenetic tree based on 16S rRNA gene sequences showing the relationship of strain 1011MAR3C25T with other species of the genus Paracococcus. Bootstrap values (>50%) are expressed as percentages of 1680 replicates. There were a total of 1418 positions in the final dataset. The 16S rRNA gene sequence of Rhodobacter capsulatus ATCC 11166T (D16428) was used as an outgroup. Bar, 0.02 substitutions per nucleotide position.

Fig. 1 in Halococcoides cellulosivorans gen. nov., sp. nov., an extremely halophilic cellulose-utilizing haloarchaeon from hypersaline lakes

Fig. 1. Morphology of strain HArcel1T growing at 4 M total NaCl and 37 ǪC. (a) Colonies on amorphous cellulose plates forming large hydrolysis zones; (b) phase contrast microphotograph of cells grown with amorphous cellulose in liquid culture; (c) phase contrast microphotograph of cells forming biofilm on a cellulose fibre; (d) electron microscopy of thin sections of cells grown with amorphous cellulose. CW, cell wall; CM, cytoplasmic membrane; N, nucleoid.

Fig. 2 in Bosea psychrotolerans sp. nov., a psychrotrophic alphaproteobacterium isolated from Lake Michigan water

Fig. 2. Phylogenetic tree based on the concatenated sequences (1933 bp) of five housekeeping gene fragments (rpoB, gyrB, atpD, dnaK and recA) of Bosea species with validly published names and strains 1131T, 1175 and 13. Numbers at nodes are given in percentages and represent the levels of bootstrap support based on neighbour-joining analyses of 1000 resampled datasets. Values <70 % are not reported. Filled circles indicate that the corresponding nodes (groupings) were also recovered in the maximum-likelihood tree. Bradyrhizobium japonicum USDA 6T (AP012206) was used as the outgroup. Bar, 0.01 nucleotide substitutions per position. Sequence accession numbers for all strains are reported in Table S2.

Fig. 1 in Saccharopolyspora rhizosphaerae sp. nov., an actinomycete isolated from rhizosphere soil in Thailand

Fig. 1. Neighbour-joining phylogenetic tree based on the 16S rRNA gene sequences, showing the genetic relatedness between strain H219T and other type strains in the genus Saccharopolyspora. Streptosporangium roseum DSM 43021T (NR074558) was used as the outgroup. Bootstrap values above 50 % or higher (percentages of 1000 replications) are shown. Bar, 0.01 substitutions per nucleotide position. Filled circles indicate branches that are also recovered in the maximum-parsimony and the maximum-likelihood trees (see Figs S3 and S4).

Fig. 3 in Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov., Serpentinimonas barnesii sp. nov. and Serpentinimonas maccroryi sp. nov., hyperalkaliphilic and facultative autotrophic bacteria isolated from terrestrial serpentinizing springs

Fig. 3. Microscopic observation of strain A1T. (a) Phase contrast microscopy image of strain A1T grown on acetate and oxygen. The three strains are visually indistinguishable. (b) SEM image of strain A1T on carbon filter paper. Morphologies are indistinguishable for the three strains. (c) TEM image of strain A1T grown on acetate with oxygen.