Find research datasets worth reusing

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. 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. 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.

Fig. 1 in Pseudomonas capsici sp. nov., a plant-pathogenic bacterium isolated from pepper leaf in Georgia, USA

Fig. 1. Phylogenetic relationships based on partial gene sequences of 16S rRNA between Pseudomonas capsici sp. nov. strains and closely related Pseudomonas species listed in Table 1. The 16S rRNA gene sequences (1266 nucleotides) were aligned using MAFFT (version 7.294b) [10]. The alignment was used to construct a phylogenetic tree using the PHYML package with the maximum-likelihood method and with the best substitution model estimated by jmodelTest version 2.1.10 [12]. The clade including Pseudomonas viciae, Pseudomonas brassicacearum and Pseudomonas mediterranea was used for outgroup rooting. Numbers at nodes represent bootstrap values from 1000 replicates. Bar, 1 nt substitution per 100 nt. GenBank accession numbers are shown within parentheses along with the strain, with T indicating type strains.

opennotspecifiedAug 2018View details →

Fig. 1 in Brevibacterium hankyongi sp. nov., isolated from compost

Fig. 1. Phylogenetic relationship between strain BS05T and other related species of the genus Brevibacterium. The tree was reconstructed using the maximum-likelihood method based on 16S rRNA gene sequences. Bootstrap values (expressed as percentages of 1000 replications) greater than 50 % are shown at branch points. Filled circles indicate that the corresponding nodes were also recovered in the tree generated with maximum-parsimony and neighbour-joining algorithms. Spelaeicoccus albus D3-40T (HF570029) was used as an outgroup. Bar, 0.005 substitutions per nucleotide position.

Fig. 1 in Lactobacillus suantsaii sp. nov., isolated from suan-tsai, a traditional Taiwanese fermented mustard green

Fig. 1. Phylogenetic tree based on 16S rRNA gene sequences showing the relationship 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 approximately 1419 bp, and Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293T was used as an outgroup. Bootstrap values (>60 %) based on 1000 replicates are shown at branch nodes. Bar, 2 % sequence divergence.

opennotspecifiedMay 2018View details →

Fig. 1 in Hymenobacter aquatilis sp. nov., isolated from a mesotrophic artificial lake

Fig. 1. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showing the phylogenetic position of strain HMF3095T in the genus Hymenobacter. Bootstrap percentages (>70 %) from neighbour-joining (below nodes) analyses are shown. Filled and open circles indicate nodes recovered by all three treeing methods or with two treeing methods, respectively. Adhaeribacter aerophilus 6424 S-25T was used as an outgroup. Bar, 0.01 substitutions per nucleotide position.

opennotspecifiedJul 2020View details →

Fig. 4 in Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan

Fig. 4. Scanning electron microscopy image of strain HNM0687T grown on ISP2 agar at 28 °C for 7 days.

opennotspecifiedMay 2018View details →

Fig. 1 in Roseovarius ramblicola sp. nov., a moderately halophilic bacterium isolated from saline soil in Spain

Fig. 1. Maximum-likelihood phylogenetic tree based on nearly complete 16S rRNA gene sequences showing the relationships between strain D15T, type species of the genus Roseovarius and the closest related species in the family Rhodobacteraceae. Filled circles indicate nodes that were also recovered in the maximum-parsimony and neighbour-joining trees based on the same sequences. Numbers at nodes are levels of bootstrap support (percentages) based on analyses of 1000 re-sampled datasets; only values above 50 % are shown. Bar, 0.05 nt changes per position. The GenBank/EMBL/DDBJ accession number of each sequence is shown in parentheses.

opennotspecifiedMar 2017View details →

Fig. 1. Neighbour-joining phylogenetic tree reconstructed using the 16S in Lysobacter humi sp. nov., isolated from soil

Fig. 1. Neighbour-joining phylogenetic tree reconstructed using the 16S rRNA gene sequences of strains FJY8T and related taxa. Numbers at branch nodes present bootstrap values (>50 %) obtained as percentages of 1000 replicates. Filled circles indicate the corresponding nodes recovered by using the maximum-parsimony algorithm. Bar, 0.02 substitutions per nucleotide position.