Skip to main content
SpringerLink
Log in

Flaviflexus equikiangi sp. nov. isolated from faeces of Equus kiang (Tibetan wild ass) and carrying a class 1 integron gene cassette in its genome

  • Microbial Systematics and Evolutionary Microbiology
  • Published:
Journal of Microbiology Aims and scope Submit manuscript

Abstract

Two Gram-stain-positive, catalase-negative, non-spore-forming, cocci-shaped strains (dk850T and JY899) were isolated from the feces of Equus kiang in the Qinghai-Tibet Plateau of China. 16S rRNA gene sequence-based phylogenetic analyses showed that strains dk850T and JY899 belong to the genus Flaviflexus, closest to F. salsibiostraticola KCTC 33148T, F. ciconiae KCTC 49253T and F. huanghaiensis H5T. The DNA G + C content of strain dk850T was 62.9%. The digital DNA-DNA hybridization values of strain dk850T with the closely related species were below the 70% threshold for species demarcation. The two strains grew best at 28°C on brain heart infusion (BHI) agar with 5% sheep blood. All strains had C18:1ω9c and C16:0 as the major cellular fatty acids. MK-9(H4) was the major menaquinone in strain dk850T. The major polar lipids included diphosphatidylglycerol and an unidentified phospholipid. Strains dk850T and JY899 were identified as carrying a class 1 integron containing the aminoglycoside resistance gene aadA11, both strains were resistant to spectinomycin and streptomycin. Based on several lines of evidence from phenotypic and phylogenetic analyses, strains dk850T and JY899 represent a novel species of the genus Flaviflexus, for which the name Flaviflexus equikiangi sp. nov. is proposed. The type strain is dk850T(= CGMCC 1.16593T = JCM 33598T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Aramaki, T., Blanc-Mathieu, R., Endo, H., Ohkubo, K., Kanehisa, M., Goto, S., and Ogata, H. 2020. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251–2252.

    Article  CAS  Google Scholar 

  • Berlin, K., Koren, S., Chin, C.S., Drake, J.P., Landolin, J.M., and Phillippy, A.M. 2015. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat. Biotechnol. 33, 623–630.

    Article  CAS  Google Scholar 

  • Chun, J., Oren, A., Ventosa, A., Christensen, H., Arahal, D.R., da Costa, M.S., Rooney, A.P., Yi, H., Xu, X.W., De Meyer, S., et al. 2018. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int. J. Syst. Evol. Microbiol. 68, 461–466.

    Article  CAS  Google Scholar 

  • Clinical and Laboratory Standards Institute, CLSI. 2012. Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Second Informational Supplement. Clinical and Laboratory Standards Institute, Wayne, Pennsylvania, USA.

    Google Scholar 

  • Clinical and Laboratory Standards Institute, CLSI. 2017. Methods for Antimicrobial Susceptibility Testing of Infrequently Isolated or Fastidious Bacteria Isolated From Animals. 1st edn. CLSI supplement VET06. Clinical and Laboratory Standards Institute, Wayne, Pennsylvania, USA.

    Google Scholar 

  • Delgado, S., Suárez, A., and Mayo, B. 2006. Identification of dominant bacteria in feces and colonic mucosa from healthy Spanish adults by culturing and by 16S rDNA sequence analysis. Dig. Dis. Sci. 51, 744–751.

    Article  Google Scholar 

  • Du, Z.J., Miao, T.T., Lin, X.Z., Liu, Q.Q., and Chen, G.J. 2013. Flaviflexus huanghaiensis gen. nov., sp. nov., an actinobacterium of the family Actinomycetaceae. Int. J. Syst. Evol. Microbiol. 63, 1863–1867.

    Article  CAS  Google Scholar 

  • Dong, W.L., Kong, L.C., Wang, Y., Gou, C.L., Xu, B., Ma, H.X., and Gao, Y.H. 2017. Aminoglycoside resistance of Trueperella pyogenes isolated from pigs in China. J. Vet. Med. Sci. 79, 1836–1839.

    Article  CAS  Google Scholar 

  • Hasegawa, T., Takizawa M., and Tanida, S. 1983. A rapid analysis for chemical grouping of aerobic actinomycetes. J. Gen. Appl. Microbiol. 29, 319–322.

    Article  CAS  Google Scholar 

  • Huang, Y., Wang, X., Yang, J., Lu, S., Lai, X.H., Jin, D., Pu, J., Huang, Y., Ren, Z., Zhu, W., et al. 2019. Nocardioides yefusunii sp. nov., isolated from Equus kiang (Tibetan wild ass) faeces. Int. J. Syst. Evol. Microbiol. 69, 3629–3635.

    Article  CAS  Google Scholar 

  • Huson, D.H. and Scornavacca, C. 2012. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst. Biol. 61, 1061–1067.

    Article  Google Scholar 

  • Jin, D., Chen, C., Li, L., Lu, S., Li, Z., Zhou, Z., Jing, H., Xu, Y., Du, P., Wang, H., et al. 2013. Dynamics of fecal microbial communities in children with diarrhea of unknown etiology and genomic analysis of associated Streptococcus lutetiensis. BMC Microbiol. 13, 141.

    Article  CAS  Google Scholar 

  • Jin, L., Ko, S.R., Lee, H.G., Kim, B.H., Kim, H.S., Ahn, C.Y., and Oh, H.M. 2014. Flaviflexus salsibiostraticola sp. nov., an actinobacterium isolated from a biofilm reactor. Int. J. Syst. Evol. Microbiol. 64, 3293–3296.

    Article  CAS  Google Scholar 

  • Kanehisa, M. and Sato, Y. 2020. KEGG Mapper for inferring cellular functions from protein sequences. Protein Sci. 29, 28–35.

    Article  CAS  Google Scholar 

  • Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111–120.

    Article  CAS  Google Scholar 

  • Kumar, S., Stecher, G., and Tamura, K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874.

    Article  CAS  Google Scholar 

  • Kwiecień, E., Stefańska, I., Chrobak-Chmiel, D., Sałamaszyńska-Guz, A., and Rzewuska, M. 2020. New determinants of aminoglycoside resistance and their association with the class 1 integron gene cassettes in Trueperella pyogenes. Int. J. Mol. Sci. 21, 4230.

    Article  Google Scholar 

  • Lee, J.Y., Kang, W., Kim, P.S., Lee, S.Y., Shin, N.R., Sung, H., Lee, J.Y., Yun, J.H., Jeong, Y.S., Han, J.E., et al. 2020. Flaviflexus ciconiae sp. nov., isolated from the faeces of the oriental stork. Int. J. Syst. Evol. Microbiol. 70, 5439–5444.

    Article  CAS  Google Scholar 

  • Llanes, C., Neuwirth, C., El Garch, F., Hocquet, D., and Plésiat, P. 2006. Genetic analysis of a multiresistant strain of Pseudomonas aeruginosa producing PER-1 β-lactamase. Clin. Microbiol. Infect. 12, 270–278.

    Article  CAS  Google Scholar 

  • Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P.M., and Henrissat, B. 2014. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490–D495.

    Article  CAS  Google Scholar 

  • Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.P., and Göker, M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14, 60.

    Article  Google Scholar 

  • Overbeek, R., Olson, R., Pusch, G.D., Olsen, G.J., Davis, J.J., Disz, T., Edwards, R.A., Gerdes, S., Parrello, B., Shukla, M., et al. 2014. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 42, D206–D214.

    Article  CAS  Google Scholar 

  • Price, M.N., Dehal, P.S. and Arkin, A.P. 2009. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26, 1641–1650.

    Article  CAS  Google Scholar 

  • Richter, M. and Rosselló-Móra, R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106, 19126–19131.

    Article  CAS  Google Scholar 

  • Thompson, J.D., Gibson, T.J., and Higgins, D.G. 2002. Multiple sequence alignment using ClustalW and ClustalX. Curr. Protoc. Bioinformatics 2.3.1–2.3.22.

  • Wang, X., Yang, J., Lu, S., Lai, X.H., Jin, D., Pu, J., Niu, L., Zhu, W., Liang, J., Huang, Y., et al. 2019. Paraliobacillus zengyii sp. nov., a slightly halophilic and extremely halotolerant bacterium isolated from Tibetan antelope faeces. Int. J. Syst. Evol. Microbiol. 69, 1426–1432.

    Article  CAS  Google Scholar 

  • Wargo, M.J., Szwergold, B.S., and Hogan, D.A. 2008. Identification of two gene clusters and a transcriptional regulator required for Pseudomonas aeruginosa glycine betaine catabolism. J. Bacteriol. 190, 2690–2699.

    Article  CAS  Google Scholar 

  • Wayne, L.G. 1988. International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Zentralbl. Bakteriol. Mikrobiol. Hyg. A 268, 433–434.

    CAS  PubMed  Google Scholar 

  • Xu, L., Dong, Z., Fang, L., Luo, Y., Wei, Z., Guo, H., Zhang, G., Gu, Y.Q., Coleman-Derr, D., Xia, Q., et al. 2019. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res. 47, W52–W58.

    Article  CAS  Google Scholar 

  • Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., and Chun, J. 2017a. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613–1617.

    Article  CAS  Google Scholar 

  • Yoon, S.H., Ha, S.M., Lim, J., Kwon, S. and Chun, J. 2017b. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek. 110, 1281–1286.

    Article  CAS  Google Scholar 

  • Zhang, H., Yohe, T., Huang, L., Entwistle, S., Wu, P., Yang, Z., Busk, P.K., Xu, Y. and Yin, Y. 2018. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 46, W95–W101.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by grants from National Key R&D Program of China (2019YFC1200500 and 2019YFC1200505) and Research Units of Discovery of Unknown Bacteria and Function (2018RU010).

Author information

Authors and Affiliations

  1. Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, P. R. China

    Caixin Yang, Xingxing Lian, Yanpeng Cheng, Yifan Jiao, Kui Dong, Suping Wang & Jianguo Xu

  2. State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, P. R. China

    Caixin Yang, Xingxing Lian, Yanpeng Cheng, Yifan Jiao, Jing Yang, Kui Dong, Shan Lu, Dong Jin, Han Zheng, Ji Pu, Liyun Liu & Jianguo Xu

  3. Shenzhen Center for Disease Control and Prevention, Shenzhen, 518000, PR China

    Yanpeng Cheng

  4. Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, 201508, P. R. China

    Jing Yang, Shan Lu, Dong Jin, Han Zheng & Jianguo Xu

  5. Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 102206, P. R. China

    Jing Yang, Shan Lu, Dong Jin, Liyun Liu & Jianguo Xu

  6. Shanxi Eye Hospital, Taiyuan, Shanxi, 030001, P. R. China

    Kui Dong

  7. Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, 476000, P. R. China

    Xin-He Lai

  8. Institute of Public Health, Nankai University, Tianjin, 300305, P. R. China

    Jianguo Xu

Authors
  1. Caixin Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xingxing Lian
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yanpeng Cheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yifan Jiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jing Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Kui Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Shan Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Xin-He Lai
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Dong Jin
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Han Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Ji Pu
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Suping Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Liyun Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Jianguo Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jianguo Xu.

Additional information

Conflict of Interest

The authors declare that they have no conflict of interest.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yang, C., Lian, X., Cheng, Y. et al. Flaviflexus equikiangi sp. nov. isolated from faeces of Equus kiang (Tibetan wild ass) and carrying a class 1 integron gene cassette in its genome. J Microbiol. 60, 585–593 (2022). https://doi.org/10.1007/s12275-022-1673-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12275-022-1673-3

Keywords

Search

Navigation