Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8

Background: The Mongolian gerbils are a good model to mimic the
Helicobacter pylori-associated pathogenesis of the human stomach.
In the current study the gerbil-adapted strain B8 was completely
sequenced, annotated and compared to previous genomes, including
the 73 supercontigs of the parental strain B128. Results: The
complete genome of H. pylori B8 was manually curated gene by gene,
to assign as much function as possible. It consists of a circular
chromosome of 1,673,997 bp and of a small plasmid of 6,032 bp
carrying nine putative genes. The chromosome contains 1,711 coding
sequences, 293 of which are strain-specific, coding mainly for
hypothetical proteins, and a large plasticity zone containing a
putative type-IV-secretion system and coding sequences with unknown
function. The cag-pathogenicity island is rearranged such that the
cagA-gene is located 13,730 bp downstream of the inverted gene
cluster cagB-cag1. Directly adjacent to the cagA-gene, there are
four hypothetical genes and one variable gene with a different
codon usage compared to the rest of the H. pylori B8-genome. This
indicates that these coding sequences might be acquired via
horizontal gene transfer. The genome comparison of strain B8 to its
parental strain B128 delivers 425 unique B8-proteins. Due to the
fact that strain B128 was not fully sequenced and only
automatically annotated, only 12 of these proteins are definitive
singletons that might have been acquired during the
gerbil-adaptation process of strain B128. Conclusion: Our sequence
data and its analysis provide new insight into the high genetic
diversity of H. pylori-strains. We have shown that the
gerbil-adapted strain B8 has the potential to build, possibly by a
high rate of mutation and recombination, a dynamic pool of genetic
variants (e. g. fragmented genes and repetitive regions) required
for the adaptation-processes. We hypothesize that these variants
are essential for the colonization and persistence of strain B8 in
the gerbil stomach during in ammation.