Antonie van Leeuwenhoek

, Volume 112, Issue 10, pp 1533–1544 | Cite as

Hymenobacter oligotrophus sp. nov., isolated from a contaminated agar plate

  • Yingchao Geng
  • Yumin Zhang
  • Jin Tian
  • Jia Liu
  • Kun Qin
  • Yao Huang
  • Ziyan Wei
  • Fang PengEmail author
Original Paper


A taxonomic study of a Gram-stain negative, rod-shaped, motile, asporogenous, catalase- and oxidase-positive bacterium, sh-6T, forming pink-red colonies, isolated from a contaminated R2A plate in the laboratory was performed. Its optimum growth temperature was determined to be 28 °C in the absence of NaCl on R2A plates. On the basis of 16S rRNA gene sequence analysis, strain sh-6T belongs to the genus Hymenobacter and is closely related to Hymenobacter deserti ZLB-3T (95.05%), Hymenobacter paludis KBP-30T (94.96%), Hymenobacter coalescens WW84T (94.04%), Hymenobacter gummosus ANT-18T (93.38%), Hymenobacter ocellatus Myx2105T (93.70%), Hymenobacter jeollabukensis 1-3-3-8T (93.48%) and Hymenobacter koreensis GYR3077T (93.21%). Comparison of the genome of strain sh-6T and that of H. gummosus ANT-18T gave digital DNA–DNA hybridization and Average Nucleotide Identity values of 20.6% and 78.4%, respectively. The respiratory isoprenoid quinone and polyamine component were identified as MK-7 and sym-homospermidine, respectively. The major cellular fatty acids identified as iso-C15:0, summed feature 4 (iso-C17:1 I/anteiso B), iso-C16:0, iso-C17:0 3-OH and iso-C17:0. The major polar lipid of strain sh-6T determined to be phosphatidylethanolamine. The DNA G+C content was determined to be 60.5 mol%. On the basis of the evidence presented in this study, a novel species of the genus Hymenobacter, Hymenobacter oligotrophus sp. nov., is proposed, with the type strain sh-6T (= CCTCC AB 2016064T = KCTC 62345T).


Hymenobacter oligotrophus Novel species Phylogenetic analysis Taxonomy 


Author’s contribution

YG performed the laboratory experiments, analysed the data, and drafted the manuscript. YZ contributed to the polyphasic taxonomy. JT contributed to the biochemical characterisation. KQ contributed to the fatty acids determination. JL contributed to strains activation and preservation. YH and ZW contributed to the morphological analyses. FP designed the experiments and supervised the manuscript.


This work was supported by the National Key R&D Program of China (2018YFC1406701), the R&D Infrastructure and Facility Development Program of the Ministry of Science and Technology of the People’s Republic of China (Grant No. NIMR-2017-8), the National Natural Science Foundation of China (Grant No. 31270538), and the Chinese Polar Scientific Strategy Research Fund IC201706.

Compliance with ethical standards

Conflicts of interest

The authors declare that there are no conflicts of interest.

Ethical approval

This article does not contain any studies with human participants and/or animals performed by any of the authors. The formal consent is not required in this study.

Supplementary material

10482_2019_1279_MOESM1_ESM.doc (1.4 mb)
Supplementary material 1 (DOC 1436 kb)


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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.China Center for Type Culture Collection (CCTCC), College of Life SciencesWuhan UniversityWuhanChina

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