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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.

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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.

Fig. 1 in Streptomyces gossypiisoli sp. nov., isolated from cotton soil in Xinjiang, PR China

Fig. 1. Scanning electron microscopy image of strain TRM 44567T grown on Gause's agar at 37 °C for 7 days. Bars, 5 µm (left) and 20 µm (right).

Fig. 1 in Emendation of the Genus Auritidibacter Yassin et al. 2011 and Auritidibacter ignavus Yassin et al. 2011 based on features observed from Canadian and Swiss clinical isolates and wholegenome sequencing analysis

Fig. 1. Phylogenetic consensus tree based on nearly full-length 16S rRNA gene sequences. Phylogeny reconstructed with neighbourjoining (NJ), maximum-likelihood (ML) and maximum parsimony algorithms with NJ/ML/MP data respectively shown at nodes for type strains of type species of genera assigned to the family Micrococcaceae. The tree was calculated using MEGA X based on 1000 resamplings (bootstrap analysis, with only values ≥70% shown). Bar, 0.01 (NJ) or 0.02 (ML) substitutions per nucleotide position. The type strain of Cellulomonas flavigena was included as an unrelated outlier.

Fig. 1 in Nocardioides vastitatis sp. nov., isolated from Taklamakan desert soil

Fig. 1. Neighbour-joining phylogenic tree on the basis of 16S rRNA gene sequences showing the phylogenic position of strain 21Sc5- 5T and related species. Luedemannella helvata 3-9(24)T was used as an outgroup. Numbers at nodes refer to bootstrap values (based on 1000 replicates; only values>50 % are shown). Bar, 1 nt substitution per 1000 nt.

Fig. 1 in Blautia argi sp. nov., a new anaerobic bacterium isolated from dog faeces

Fig. 1. Phylogenetic consensus tree based on 16S rRNA gene sequences, reconstructed with the neighbour-joining (NJ), maximumparsimony (MP) and maximum-likelihood (ML) algorithms, indicating the taxonomic positions of isolates and close relatives. Bootstrap values (>70 %, NJ/MP/ML) calculated for 1000 subsets are shown at branch nodes. Atopobium minutum served as an outgroup. Bar, 0.02 subsitutions per nucleotide position.

Fig. 1 in Nocardioides sambongensis sp. nov., isolated from Dokdo Islands soil

Fig. 1. Neighbour-joining phylogenetic tree reconstructed based on a comparative analysis of 16S rRNA gene sequences showing the relationships between strain KUDC5002T and related species. Numbers at the nodes indicate the levels of bootstrap support (%) based on 1000 resampled datasets. The 16S rRNA gene sequence of Kribbella flavida DSM 17836T was used as an outgroup. Solid circles indicate that the corresponding nodes were also obtained in both the maximum-likelihood and maximum-parsimony trees. Open circles indicate that the corresponding nodes were also obtained from the maximum-likelihood tree. Bar, 0.01 nucleotide substitutions per position.

Fig. 1 in Arenibacillus arenosus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from sea sand

Fig. 1. Maximum-likelihood phylogenetic tree based on nearly complete 16S rRNA gene sequences showing the relationships of strain CAU 1304T to members of related genera of the family Rhodobacteraceae. Filled circles indicate that the corresponding nodes were also recovered in the trees generated with the neighbour-joining and maximum-parsimony algorithms. The numbers at nodes indicate levels of bootstrap support based on a maximum-likelihood analysis of 1000 resampled datasets; only values>70 % are given. Bar, 0.01 substitutions per nucleotide position. Pelagicola litoralis CL-ES2T (EF192392) was used as an outgroup organism.

Fig. 2 in Actinomyces qiguomingii sp. nov., isolated from the Pantholops hodgsonii

Fig. 2. Neighbour-joining phylogenomic tree of Actinomyces qiguomingii sp. nov. and other available strains of the most closely related species based on 178 core genes from genome sequences. Numbers on the tree indicate each split in the tree with support values from the Shimodaira–Hasegawa test [34] calculated for 1000 resamples. Bifidobacterium bifidum ATCC 29521T was used as the outgroup.

Fig. 1 in Flavobacterium niveum sp. nov., isolated from a freshwater creek

Fig. 1. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showing the position of Flavobacterium niveum TAPW14T and other Flavobacterium species. Numbers at nodes are bootstrap percentages (>70 %) based on the neighbour-joining (above nodes) and maximum-parsimony (below nodes) tree-making algorithms. Filled circles indicate branches of the tree that were also recovered using the maximum-likelihood and maximum-parsimony tree-making algorithms. Open circles indicate that the corresponding nodes were also recovered in the tree generated with the maximum-parsimony algorithm. Myroides odoratus ATCC 4651T was used as an outgroup. Bar, 0.01 substitutions per nucleotide position.

Fig. 1 in Flavobacterium tibetense sp. nov., isolated from a wetland

Fig. 1. Phylogenetic tree of strain YH5T and related type strains within the genus Flavobacterium based on almost-complete 16S rRNA gene sequences. The tree was calculated using the neighbour-joining algorithm in MEGA 5 software. Numbers at nodes indicate the percentages of bootstrap support based on 1000 resampled datasets; only values>50 % are shown. Zobellia galactanivorans DsijT (FP476056) was used as outgroup. Bar, 0.01 substitutions per nucleotide position.

Fig. 1 in Actinomyces qiguomingii sp. nov., isolated from the Pantholops hodgsonii

Fig. 1. Neighbour-joining phylogenetic tree based on nearly complete 16S rRNA gene sequences showing the relationships between Actinomyces qiguomingii sp. nov. and the type strains of the genus Actinomyces. Solid circles indicate the nodes supported by both maximum-likelihood and maximum-parsimony analyses. Bootstrap values (70%) based on 1000 replicates are shown at branch nodes. Bar, 0.020 changes per nucleotide position.