The Complete Genome of Emcibacter congregatus ZYLT, a Marine Bacterium Encoding a CRISPR-Cas 9 Immune System

  • Zhe Zhao
  • Rui-an Zhang
  • Ge-yi Fu
  • Ran Zhang
  • Yan-fang Nie
  • Cong SunEmail author
  • Min WuEmail author


Emcibacter congregatus ZYLT was isolated from a sediment sample cultured in situ in a coast located in the East China Sea. The genome of E. congregatus ZYLT was sequenced and assembled into one single circular chromosome with the size of 4,189,011 bp and G+C content of 52.6%. Genomic annotation showed that E. congregatus ZYLT had an intact Type II-C CRISPR-Cas system consists of three cas genes (cas 9, cas 1, and cas 2), 34 direct repeat sequences with the length of 36 bp, and 33 spacers. The predicted Cas 9 protein was smaller than most of existing genome editing tools. This structure might have potential in developing new gene editing system and uncovering the regulatory mechanisms of CRISPR-Cas system. Besides, the comparison between E. congregatus ZYLT and its relative species living in neritic environments unraveled some common traits of the defective strategies of these bacteria to face inshore challenges including the motility, multidrug resistance, and universal efflux pumps.



This work was supported by Zhejiang Provincial Natural Science Foundation of China under Grant No. LQ19C010005, China Postdoctoral Science Foundation (Grant No. 2018M642382), and the Science & Technology Basic Resources Investigation Program of China (Grant No. 2017FY100300).

Compliance with Ethical Standards

Conflicts of interest

The authors declare that they have no conflict of interest.

Supplementary material

284_2019_1867_MOESM1_ESM.docx (403 kb)
Supplementary file1 (DOCX 402 kb)


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© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.College of Life SciencesZhejiang UniversityHangzhouPeople’s Republic of China
  2. 2.College of Life Sciences and MedicineZhejiang Sci-Tech UniversityHangzhouPeople’s Republic of China
  3. 3.School of Materials Science and EngineeringZhejiang UniversityHangzhouPeople’s Republic of China
  4. 4.Ocean CollegeZhejiang UniversityHangzhouPeople’s Republic of China

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