Nature 388, 539-547 (7 August 1997) | ; Received 16 May 1997; Accepted 1 July 1997

The complete genome sequence of the gastric pathogen Helicobacter pylori

Jean-F. Tomb1, Owen White1, Anthony R. Kerlavage1, Rebecca A. Clayton1, Granger G. Sutton1, Robert D. Fleischmann1, Karen A. Ketchum1, Hans Peter Klenk1, Steven Gill1, Brian A. Dougherty1, Karen Nelson1, John Quackenbush1, Lixin Zhou1, Ewen F. Kirkness1, Scott Peterson1, Brendan Loftus1, Delwood Richardson1, Robert Dodson1, Hanif G. Khalak1, Anna Glodek1, Keith McKenney1, Lisa M. Fitzegerald1, Norman Lee1, Mark D. Adams1, Erin K. Hickey1, Douglas E. Berg2, Jeanine D. Gocayne1, Teresa R. Utterback1, Jeremy D. Peterson1, Jenny M. Kelley1, Matthew D. Cotton1, Janice M. Weidman1, Claire Fujii1, Cheryl Bowman1, Larry Watthey1, Erik Wallin3, William S. Hayes4, Mark Borodovsky4, Peter D. Karp5, Hamilton O. Smith6, Claire M. Fraser1 and J. Craig Venter1

  1. The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
  2. Department of Molecular Biology, School of Medicine, Washington University St Louis, 660 S. Euclid Avenue, St Louis, Missouri 63110, USA
  3. Department of Biochemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
  4. School of Biology, Georgia Tech, Atlanta, Georgia 30332, USA
  5. SRI International, Artificial Intelligence Center, 333 Ravenswood Avenue, Menlo Park, California 94025, USA
  6. Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, 725 N. Wolfe Street, Baltimore, Maryland 21205, USA

Correspondence to: Jean-F. Tomb1 Correspondence and requests for materials should be addressed to J.-F.T. (e-mail: Email: The annotated genome sequence and gene family alignments are available on the World-Wide Website at The sequence has been deposited with GenBank under accession number AE000511.


Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified, underscoring the potential complexity of host–pathogen interaction. Based on the large number of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric tracts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal pathogens, probably uses recombination and slipped-strand mispairing within repeats as mechanisms for antigenic variation and adaptive evolution. Consistent with its restricted niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH.