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Figure 3 in Six new species of Aleuromarginatus Corbett, 1935 and Paramarginatus sarawakensis Dubey gen. and sp. nov. (Hemiptera: Aleyrodidae) from Southeast Asia

Figure 3. Aleuromarginatus frim Dubey sp. nov., holotype puparium, line drawings: (a) cephalothorax; (b) abdomen; (c) margin; (d) abdominal segments, setae; (e) vasiform orifice.

Figure 1 in Six new species of Aleuromarginatus Corbett, 1935 and Paramarginatus sarawakensis Dubey gen. and sp. nov. (Hemiptera: Aleyrodidae) from Southeast Asia

Figure 1. Aleuromarginatus asymmetricis Dubey sp. nov., holotype (a, c, d) and paratype (b) puparium, line drawings: (a) dorsal and ventral views; (b) abdominal depressions, setae; (c) posterior abdominal area, caudal setae; (d) legs and antenna.

Figure 2 in Six new species of Aleuromarginatus Corbett, 1935 and Paramarginatus sarawakensis Dubey gen. and sp. nov. (Hemiptera: Aleyrodidae) from Southeast Asia

Figure 2. Aleuromarginatus asymmetricis Dubey sp. nov., holotype (b, c, h) and paratype puparium (a, d–g) puparium: (a) dorsal view; (b) dorsal and ventral views; (c) margin, thoracic tracheal pore area; (d) cephalothorax; (e) abdominal segments, depressions, submedian setae; (f) posterior abdominal area, vasiform orifice; (g) caudal fold, ventral setae; (h) antenna, prothoracic leg.

Fig. 4 in Latilactobacillus fragifolii sp. nov., isolated from leaves of a strawberry plant (Fragaria x ananassa)

Fig. 4. Presence of known haem-dependent and manganese-dependent catalase encoding genes in five reference genomes of the genus Latilactobacillus and AMBP162T. Analysis was done by comparing the four known catalase genes from lactic acid bacteria against all predicted proteins from the six Latilactobacillus genomes using BLASTp.

Fig. 2 in Latilactobacillus fragifolii sp. nov., isolated from leaves of a strawberry plant (Fragaria x ananassa)

Fig. 2. Core genome phylogenetic tree of the genus Latilactobacillus. Genes were predicted with Prodigal version 2.6.3 [33] and core genes were determined, aligned and concatenated with SCARAP version 7cd24ba [16]. 662 strict core genes were found. Columns with one or more gaps were trimmed from the alignment with trimAl version 1.4.rev15 [34]. A maximum-likelihood phylogeny was inferred with IQ-Tree version 1.6.11 [31], using the LG+F+I+G4 amino acid substitution model. Bootstrap support was determined with the SH-aLRT test with 1000 replicates and the UFboot test with 1000 replicates. Branches with an SH-aLRT support of at least 80% and UFboot support of at least 95% were considered reliable and were indicated with a dark blue dot. The tree was visualized with ggtree version 3.0.2 [32].

Fig. 3 in Latilactobacillus fragifolii sp. nov., isolated from leaves of a strawberry plant (Fragaria x ananassa)

Fig. 3. Light microscope image at ×1000 magnification of Gram-stained cells of AMBP162T grown for 24 h at 30 °C in de Man–Rogosa–Sharpe broth, shaking at 200 r.p.m.

Fig. 2 in Turicibacter bilis sp. nov., a novel bacterium isolated from the chicken eggshell and swine ileum

Fig. 2. Whole genome sequence phylogeny of MMM721T, ISU324, PIG517 and all publicly available genomes on the PATRIC genome database as of November 2020. The tree is rooted by Eggerthia catenaformis OT569. Only bootstrap values>50% are noted for branch nodes. The PATRIC genome IDs are noted in parentheses after the strain name.

Fig. 1 in Turicibacter bilis sp. nov., a novel bacterium isolated from the chicken eggshell and swine ileum

Fig. 1. (a) Transmission electron microscope image of MMM721T cells. Bar, 1 Μm. (b) Scanning electron microscope image of MMM721T cells. Bar, 2 Μm. Cells were cultured in BHIGL for 24 h at 42 °C prior to fixation and visualization.

Fig. 2. A in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts

Fig. 2. A maximum-likelihood phylogenetic tree reconstructed using core genes (n=100) identified from whole-genome sequences, showing the evolutionary relationships among five novel Limosilactobacillus species, six L. reuteri subspecies and other recognized species in the genus Limosilactobacillus. GenBank or JGI accession numbers of these genomes are provided in parentheses. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. Strains of five novel Limosilactobacillus species are labelled by different colours; labels of six L. reuteri subspecies are colour representing vertebrate host origin: green for rodents, red for pigs, blue for humans and orange for poultry. The tree was drawn with iTOL [54].

Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts

Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S rRNA gene sequences. GenBank or JGI accession numbers of these genomes are provided in parentheses. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. Strains of five novel Limosilactobacillus species are labelled by different colours; labels of six L. reuteri subspecies are colour representing vertebrate host origin: green for rodents, red for pigs, blue for humans and orange for poultry. The tree was drawn with iTOL [54].

Fig. 3. A in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts

Fig. 3. A maximum-likelihood phylogenetic tree reconstructed using core genes (n=100) identified from whole-genome sequences, showing the evolutionary relationships among six L. reuteri subspecies. The tree was reconstructed using 33 L. reuteri genomes available in public databases (n=6 for L. reuteri subsp. kinnaridis, n=2 for L. reuteri subsp. porcinus, n=5 for L. reuteri subsp. murium, n=10 for L. reuteri subsp. reuteri, n=5 for L. reuteri subsp. suis and n=5 for L. reuteri subsp. rodentium) and L. balticus BG-AF3-AT was used as an outgroup. Further information on the involved genome sequences is listed in Table S1. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. The tree was drawn with iTOL [54].

Fig. 2 in PareUZebyella sediminis gen. nov., sp. nov., a novel marine bacterium in the family FlaVObaCTeriaCeae, isolated from a tidal flat sediment

Fig. 2. Phylogenomic tree constructed based on up-to-date bacterial 92 core genes of strain S2-4-21T and strain MT2-5-19 with closely related type strains in the family Flavobacteriaceae Cryomorpha ignava QSSC 1-22T was selected as the outgroup. Bar, 0.05 represented the amino acid substitution per position. The node values showed the gene support index (gsi).

Fig. 2 in Salinadaptatus halalkaliphilus gen. nov., sp. nov., a haloalkaliphilic archaeon isolated from salt pond in Inner Mongolia Autonomous Region, China

Fig. 2. Maximum likelihood phylogenetic tree based on rpoB' gene sequences. Bootstrap values (%) were based on 1000 replicates and shown with more than 70% bootstrap support. The sequence of Methanospirillum hungatei JF-1T was used as an outgroup. GenBank accession numbers were shown in parentheses. Bar, 0.1 substitutions per nucleotide position.

Fig. 1 in PareUZebyella sediminis gen. nov., sp. nov., a novel marine bacterium in the family FlaVObaCTeriaCeae, isolated from a tidal flat sediment

Fig. 1. Neighbour-joining phylogenetic tree constructed based on 16S rRNA gene sequences showing the relationships of strain S2- 4-21T and strain MT2-5-19 with closely related type strains in the family Flavobacteriaceae. Bootstrapping was carried out with 1000 replicates. Branch node values below 50% are not shown. Black circle at the node represent the congruent topology compared to maximum-likelihood phylogenetic tree. Cryomorpha ignava ACAM 647T was selected as the outgroup. Bar, 0.02 represented the nucleotide substitution per position.

Fig. 1 in Salinadaptatus halalkaliphilus gen. nov., sp. nov., a haloalkaliphilic archaeon isolated from salt pond in Inner Mongolia Autonomous Region, China

Fig. 1. Maximum likelihood phylogenetic tree based on 16S rRNA gene sequences. Bootstrap values (%) were based on 1000 replicates and shown with more than 70% bootstrap support. The sequence of Methanospirillum hungatei JF-1T was used as an outgroup. GenBank accession numbers were shown in parentheses. Bar, 0.05 substitutions per nucleotide position.

Fig. 2. Phylogenomic tree showing the relationship between strain CTD02-10-2T in Chryseoglobus indicus sp. nov., isolated from deep sea water

Fig. 2. Phylogenomic tree showing the relationship between strain CTD02-10-2T and closely related species. The phylogenetic relationship of the related genomes was determined using UBCG pipeline3 tool with GTR + CAT model based on concatenated alignment of 92 core genes. Genome sequences for each of the type strains are available from the NCBI databases, with the GenBank accession numbers shown in parentheses. Tropheryma whipplei Neuro14T (CAUR000000000) was used as an outgroup. Bootstrap values (expressed as percentages of 1000 replications) over 70% are shown at branching nodes. Bar, 0.05 substitutions per nucleotide position.

Fig. 1 in Arachidicoccus soli sp. nov., a bacterium isolated from soil

Fig. 1. Neighbour-joining tree based on a comparative analysis of 16S rRNA gene sequences, showing the phylogenetic relationships of strain KIS59-12T and other type strains in the family Chitinophagaceae. Filled circles indicate that the corresponding nodes were also recovered in trees generated with maximum-parsimony and maximum-likelihood algorithms. Percentage bootstrap values (from 1000 replications) greater than 70% are shown at nodes. Bar, 0.02 substitutions per nucleotide position. Saprospira grandis LewinT was used as an outgroup.

Fig. 3 in Streptomyces gossypiisoli sp. nov., isolated from cotton soil in Xinjiang, PR China

Fig. 3. Neighbour-joining phylogenetic tree based on concatenated partial sequences of the housekeeping genes atpD, gyrB, recA, rpoB and trpB. The relationships between strain TRM 44567T and the type strains of phylogenetically closely related species of the genus Streptomyces were analysed. *, Branches that were also found using the maximum-likelihood method; +, branches that were also found using the maximum-parsimony method; *+, branches that were found using all three methods. Numbers at nodes are percentage bootstrap values based on 1000 replicates; only values>50% are given. Bar, 0.0100 substitutions per nucleotide position.

Fig. 4 in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts

Fig. 4. Pairwise average nucleotide identity values (ANI; %) of genome sequences belonging to the same or different L. reuteri subspecies. ANI values within the same subspecies and between different subspecies were calculated for 33 L. reuteri genomes available in public databases (n=6 for L. reuteri subsp. kinnaridis, n=2 for L. reuteri subsp. porcinus, n=5 for L. reuteri subsp. murium, n=10 for L. reuteri subsp. reuteri, n=5 for L. reuteri subsp. suis and n=5 for L. reuteri subsp. rodentium). Further information on the involved genome sequences is listed in Table S1.

Fig. 2 in Streptomyces gossypiisoli sp. nov., isolated from cotton soil in Xinjiang, PR China

Fig. 2. Neighbour-joining phylogenetic tree based on nearly complete 16S rRNA gene sequences. The relationships between strain TRM 44567T and the type strains of phylogenetically closely related species of the genus Streptomyces were analysed. Actinomadura hibisca JCM 9627T (AF163115) was used as the outgroup. *, Branches that were also found using the maximum- likelihood method; +, branches that were also found using the maximum-parsimony method; *+, branches that were found using all three methods. Numbers at nodes are percentage bootstrap values based on 1000 replicates; only values>50% are given. Bar, 0.0100 substitutions per nucleotide position.