Complete genome sequence of a commensal bacterium, Hafnia alvei CBA7124, isolated from human feces

Hye Seon Song, Joon Yong Kim, Yeon Bee Kim, Myeong Seon Jeong, Jisu Kang, Jin Kyu Rhee, Joseph Kwon, Ju Suk Kim, Jong Soon Choi, Hak Jong Choi, Young Do Nam, Seong Woon Roh

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


Background: Members of the genus Hafnia have been isolated from the feces of mammals, birds, reptiles, and fish, as well as from soil, water, sewage, and foods. Hafnia alvei is an opportunistic pathogen that has been implicated in intestinal and extraintestinal infections in humans. However, its pathogenicity is still unclear. In this study, we isolated H. alvei from human feces and performed sequencing as well as comparative genomic analysis to better understand its pathogenicity. Results: The genome of H. alvei CBA7124 comprised a single circular chromosome with 4,585,298 bp and a GC content of 48.8%. The genome contained 25 rRNA genes (9 5S rRNA genes, 8 16S rRNA genes, and 8 23S rRNA genes), 88 tRNA genes, and 4043 protein-coding genes. Using comparative genomic analysis, the genome of this strain was found to have 72 strain-specific singletons. The genome also contained genes for antibiotic and antimicrobial resistance, as well as toxin-antitoxin systems. Conclusions: We revealed the complete genome sequence of the opportunistic gut pathogen, H. alvei CBA7124. We also performed comparative genomic analysis of the sequences in the genome of H. alvei CBA7124, and found that it contained strain-specific singletons, antibiotic resistance genes, and toxin-antitoxin systems. These results could improve our understanding of the pathogenicity and the mechanism behind the antibiotic resistance of H. alvei strains.

Original languageEnglish
Article number41
JournalGut Pathogens
Issue number1
StatePublished - 27 Jul 2017

Bibliographical note

Funding Information:
This research was supported by the Korean Food Research Institute (E0131600‑04); the World Institute of Kimchi funded by the Ministry of Science, ICT and Future Planning, Republic of Korea (KE1702‑2); the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science, and Technology (2015R1D1A1A09061039); and the Ewha Womans University scholarship of 2016.

Publisher Copyright:
© 2017 The Author(s).


  • Comparative genomics
  • Complete genome sequence
  • Gut microbiota
  • Hafnia alvei CBA7124


Dive into the research topics of 'Complete genome sequence of a commensal bacterium, Hafnia alvei CBA7124, isolated from human feces'. Together they form a unique fingerprint.

Cite this