Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China Author Teng, Chao Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, Author Zhou, Zhengfu Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, Author Molnár, István Natural Products Center, School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, United States of America, Author Li, Xinna Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, Author Tang, Ran Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, Author Chen, Ming Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, Author Wang, Lin Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, & Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, P. R. China Author Su, Shiyou Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, Author Zhang, Wei Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, Author Lin, Min Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China, text PLoS ONE 2015 e 0122254 2015-04-01 10 4 1 16 journal article 10.1371/journal.pone.0122254 1932-6203 PMC4382152 25830331 12802690
Table 2. Fatty acid composition of strain ZW T and related members of the genus Sphingobacterium.
Fatty acid1 2 3 4 5 6 7 8 9
doi:10.1371/journal.pone.0122254.g002
C 14:01.7 - 1.0 1.4 1.3 0.7 2.0 - 1.2
C 16:05.0 2.2 3.5 7.3 3.5 4.5 1.8 3.4 3.2
C 16:0 3-OH5.4 1.2 2.7 4.8 2.4 3.3 15.2 - 6.7
Iso-C 15:0 Iso-C 15:0 3-OH Iso-C 17:0 3-OH Summed feature 327.9 29.5 30.1 27.2 28.6 33.3 22.4 45.6 27.8 3.0 2.3 2.2 3.1 2.5 2.2 5.8 1.5 1.2 15.2 19.7 12.5 15.4 13.5 13.4 12.8 16.6 12.5 39.2 37.5 42.7 37.8 37.0 35.0 34.4 - 29.6
Strains: 1, Sphingobacterium deserti sp. nov. ZW T; 2, S. composti 4M24T (data from this study); 3, S. spiritivorum JCM 1277 T (data from this study); 4, S. arenae H-12T (data from this study); 5, S. shayense HS 39T [30]; 6, S. nematocida M-SX103T [31]; 7, S. bambusae IBFC2009 T [32]; 8, S. daejeonense TR 6-04T [33]; 9, S. kyonggiense KEMC 2241 -005T [34]. Numbers represent percentages of the total fatty acids.–, not detected (<1%). Summed feature 3: C16:1ω7c / C16:1ω6c, or C16:1ω6c / C16:1ω7c.
doi:10.1371/journal.pone.0122254.t002
similarities that are lower than 97% and DNA–DNA relatedness values below 70% support the identification of bacterial isolates as belonging to a new species. The average nucleotide identity (ANI) of the genome sequence (see below) of strain ZW T against the four other Sphingobacterium species for which genome sequences are publicly available ranged from 84.40% (with strain S. thalpophilum DSM 11723) to 84.94% (with strain S. paucimobilis HER1398). These ANI values are also considerably lower than the 95 to 96% threshold used to identify isolates as
belonging to the same bacterial species [38, 39] (S1 Table). Thus, rDNA phylogeny (S3 Fig, S4 Fig), genome relatedness and chemotaxonomic characteristics all indicate that strain ZW T rep-
resents a novel species within the genus Sphingobacterium (S5 Fig). We propose the name S. deserti sp. nov. (de.ser’ ti. L. gen. n. deserti of a desert), with ZW T (= KCTC 32092T = ACCC 05744T) as the type strain.
Genome organization of strain ZW T To further characterize this novel species, we sequenced the genome of strain ZW T using WGM technology. The resulting whole genome optical map allowed the assembly of the first
Fig 2. Neighbor-joining phylogenetic tree indicating the relationships between the strain ZW T and other Sphingobacterium spp. Bootstrap values (expressed as percentages of 1,000 replications) of> 70% are shown at branch points. Bar, 0.01 substitutions per nucleotide position.