Find research datasets worth reusing

opennotspecifiedAug 2021View details →

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.

opennotspecifiedApr 2019View details →

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.

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.

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.

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.

Fig. 1 in DUganella laCTea sp. nov., DUganella gUangzHOUensis sp. nov., DUganella flavida sp. nov. and Massilia rivUli sp. nov., isolated from a subtropical stream in PR China and proposal to reclassify DUganella ginsengisOli as Massilia ginsengisOli comb. nov.

Fig. 1. Neighbour-joining tree based on the concatenated 92 core genes of strains FT50WT, FT80WT, FT92WT, FT94W, FT135WT and other related strains. Bar, 0.02 substitutions per nucleotide position. Bootstrap percentages>50% based on 1000 replications are shown at the branch points.

Fig. 1 in Oceanisphaera avium sp. nov., isolated from the gut of the cinereous vulture, Aegypius monachus

Fig. 1. Phylogenetic tree based on 16S rRNA gene sequences of strain AMac2203T and type strains of two closely related taxa. The neighbour-joining (NJ) algorithm was employed for reconstruction, and the maximum-parsimony (MP) and maximum-likelihood (ML) algorithms were used for additional analyses. Bootstrap values (>70 %) based on 1000 replicates are shown at the nodes (NJ/MP/ML, respectively). Filled diamonds indicate branches that are found in all trees, including those based on MP and ML. Enterobacter cloacae subsp. cloacae ATCC 13047T was established as an outgroup. Bar, 0.01 substitutions per nucleotide position.

opennotspecifiedApr 2019View details →

Fig. 2 in Wickerhamomyces menglaensis f.a., sp. nov., a yeast species isolated from rotten wood

Fig. 2. Photomicrographs of Wickerhamomyces menglaensis f.a., sp. nov. NYNU 1673. (a) Budding cells grown on YM broth for 3 days at 25 ǪC. (b) Pseudohyphae grown on YCBS agar for 13 days at 25 ǪC. Bar, 10 µm.

opennotspecifiedAug 2021View details →

Fig. 2 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. 2. Phylogenomic relationship based on concatenated alignment of amino acid sequences between strains A1T, B1T and H1T and other related taxa of the family Comamonadaceae. The tree was reconstructed using the maximum-likelihood method based on concatenated alignment of amino acid sequences of 30 conserved marker genes coded in the genomes. Bootstrap values are shown at branch points.

Fig. 1 in Pannonibacter carbonis sp. nov., isolated from coal mine water

Fig. 1. Phylogenetic tree showing the relationship of strains Q4.6T and Q2.11 with strains of closely related species within the genus Pannonibacter as inferred from 16S rRNA gene sequences. Data with gaps and ambiguous nucleotides were removed during alignment for reconstruction of the tree. The tree was generated using the NJ method in MEGA 7.0 based on a comparison of 1497 nt. Bootstrap values are expressed as percentages of 1000 replications. The GenBank/EMBL/DDBJ accession number of each sequence is shown in parentheses.

Fig. 3 in Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan

Fig. 3. Phylogenomic tree reconstructed on the TYGS (https://tygs.dsmz.de/). Tree inferred with FastME 2.1.6.1 [36] from genome BLAST distance phylogeny (GBDP) distances calculated from genome sequences. The branch lengths are scaled in terms of GBDP distance formula d5. The numbers above branches are GBDP pseudo-bootstrap support values>60% from 100 replications, with an average branch support of 84.6%. The tree was rooted at the midpoint [37]. Leaf labels with different colours indicate species and subspecies clusters.

Fig. 1. Neighbour-joining phylogenetic tree derived using 16S rRNA gene sequences, showing the relationships between strain HNM0687T in Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan

Fig. 1. Neighbour-joining phylogenetic tree derived using 16S rRNA gene sequences, showing the relationships between strain HNM0687T and other type strains of the genus Gordonia. Only values above 50% are shown. Asterisks represent clades that were also recovered by the maximum-likelihood and maximum-parsimony methods. Bar, one nucleotide substitution per 100 nucleotides.

Fig. 1 in Hymenobacter ginkgonis sp. nov., isolated from bark of Ginkgo biloba

Fig. 1. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showing the phylogenetic position of strain HMF4947T in the genus Hymenobacter. Bootstrap percentages (>70 %) from neighbour-joining (above nodes) analyses are shown. Filled and open circles indicate nodes recovered by all three treeing methods or by two treeing methods, respectively. Rhodocytophaga aerolata 5416 T-29T (EU004198) was used as an outgroup. Bar, 0.02 substitutions per nucleotide position.

Fig. 2 in Pseudonocardia lutea sp. nov., a novel actinobacterium isolated from soil in Chad

Fig. 2. Neighbour-joining tree showing the phylogenetic position of strain NEAU-G57T and related species based on 16S rRNA gene sequences. Asterisks denote branches that were also recovered using the maximum-likelihood method. Bootstrap values>50 % (based on 1000 replications) are shown at branch points. Bar, 0.01 substitutions per nucleotide position.

Fig. 1 in DraCOnibaCTerium mangrOVi sp. nov., isolated from mangrove sediment

Fig. 1. Phylogenetic relationship of strain GM2-18T and close relatives based on 16S rRNA gene sequences. The tree was reconstructed using the maximum-likelihood method. Bootstrapping was carried out with 1000 replicates. Branch node values below 50% are not shown. Lishizhenia tianjinensis CGMCC 1.7005T was selected as the outgroup. Bar, 0.02 nucleotide substitutions per position.

opennotspecifiedJul 2021View details →

Fig. 1 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. 1. (a) Sediments in the mangrove forest at KAUST bioturbated by Uca species crabs; crab barrows are indicated by yellow arrows. Leaves forming mangrove litter are also visible. Bar, 10 cm. (b) Aquarium filled with mangrove bioturbated sediments and FSW for the incubation of DCs; bar, 6 cm. (c) Aerial view of DCs placed on the surface of mangrove sediments and cover with FSW inside the aquarium; bar, 6 cm.

opennotspecifiedApr 2019View details →

Fig. 2. A in Dyella dinghuensis sp. nov. and Dyella choica sp. nov., isolated from forest soil

Fig. 2. A maximum-likelihood tree based on the concatenated sequences of the housekeeping genes atpD, gyrB and lepA, showing the relationship of strains DHOA06T and 4 M-K27T to other species in the genus Dyella. Filled circles at nodes indicate generic branches that were also recovered using neighbour-joining and maximum-parsimony algorithms. Bootstrap values are shown in percentages of 1000 replicates; only bootstrap values Ȅ50 % are indicated. Xanthomonas campestris ATCC 33913T was used as an outgroup. Bar, 0.02 substitutions per nucleotide position.