title: Fallacy of the Unique Genome: Sequence Diversity within SingleHelicobacter pyloriStrains.
abstract: Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passagedHelicobacter pyloristrain SS1 and its parent PMSS1 to assess intra- and intergenomic variability. Using high sequence coverage depth and experimental validation, we detected extensive genome plasticity within theseH. pyloriisolates, including movement of the transposable element IS607, large and small inversions, multiple single nucleotide polymorphisms, and variation incagAcopy number. ThecagAgene was found as 1 to 4 tandem copies located off thecagisland in both SS1 and PMSS1; this copy number variation correlated with protein expression. To gain insight into the changes that occurred during mouse adaptation, we also compared SS1 and PMSS1 and observed 46 differences that were distinct from the within-genome variation. The most substantial was an insertion incagY, which encodes a protein required for a type IV secretion system function. We detected modifications in genes coding for two proteins known to affect mouse colonization, the HpaA neuraminyllactose-binding protein and the FutB α-1,3 lipopolysaccharide (LPS) fucosyltransferase, as well as genes predicted to modulate diverse properties. In sum, our work suggests that data from consensus genome assemblies from single colonies may be misleading by failing to represent the variability present. Furthermore, we show that high-depth genomic sequencing data of a population can be analyzed to gain insight into the normal variation within bacterial strains.IMPORTANCEAlthough it is well known that many bacterial genomes are highly variable, it is nonetheless traditional to refer to, analyze, and publish "the genome" of a bacterial strain. Variability is usually reduced ("only sequence from a single colony"), ignored ("just publish the consensus"), or placed in the "too-hard" basket ("analysis of raw read data is more robust"). Now that whole-genome sequences are regularly used to assess virulence and track outbreaks, a better understanding of the baseline genomic variation present within single strains is needed. Here, we describe the variability seen in typical working stocks and colonies of pathogenHelicobacter pylorimodel strains SS1 and PMSS1 as revealed by use of high-coverage mate pair next-generation sequencing (NGS) and confirmed by traditional laboratory techniques. This work demonstrates that reliance on a consensus assembly as "the genome" of a bacterial strain may be misleading.
authors.affiliation: Institute of Environmental Science and Research, Porirua, New Zealand jenny.draper@esr.cri.nz jvsolnick@ucdavis.edu karplus@soe.ucsc.edu ottemann@ucsc.edu.|Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, California, USA.|Department of Microbiology & Environmental Toxicology, UC Santa Cruz, Santa Cruz, California, USA.
authors.forename: Jenny L
authors.identifier: 0000-0002-6916-6442
authors.initials: JL
authors.lastname: Draper
authors.affiliation: Departments of Medicine and Microbiology & Immunology, Center for Comparative Medicine, UC Davis, California, USA.
authors.forename: Lori M
authors.initials: LM
authors.lastname: Hansen
authors.affiliation: Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, California, USA.
authors.forename: David L
authors.initials: DL
authors.lastname: Bernick
authors.affiliation: Department of Microbiology & Environmental Toxicology, UC Santa Cruz, Santa Cruz, California, USA.
authors.forename: Samar
authors.initials: S
authors.lastname: Abedrabbo
authors.affiliation: Pacific Biosciences, Menlo Park, California, USA.
authors.forename: Jason G
authors.initials: JG
authors.lastname: Underwood
authors.affiliation: Department of Population Health and Reproduction, 100K Pathogen Genome Project, UC Davis, Davis, California, USA.
authors.forename: Nguyet
authors.initials: N
authors.lastname: Kong
authors.affiliation: Department of Population Health and Reproduction, 100K Pathogen Genome Project, UC Davis, Davis, California, USA.
authors.forename: Bihua C
authors.initials: BC
authors.lastname: Huang
authors.affiliation: Department of Population Health and Reproduction, 100K Pathogen Genome Project, UC Davis, Davis, California, USA.
authors.forename: Allison M
authors.initials: AM
authors.lastname: Weis
authors.affiliation: Department of Population Health and Reproduction, 100K Pathogen Genome Project, UC Davis, Davis, California, USA.
authors.forename: Bart C
authors.identifier: 0000-0002-7471-1978
authors.initials: BC
authors.lastname: Weimer
authors.affiliation: Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom.
authors.forename: Arnoud H M
authors.identifier: 0000-0003-0203-1305
authors.initials: AH
authors.lastname: van Vliet
authors.affiliation: Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, California, USA.
authors.forename: Nader
authors.initials: N
authors.lastname: Pourmand
authors.affiliation: Departments of Medicine and Microbiology & Immunology, Center for Comparative Medicine, UC Davis, California, USA jenny.draper@esr.cri.nz jvsolnick@ucdavis.edu karplus@soe.ucsc.edu ottemann@ucsc.edu.
authors.forename: Jay V
authors.initials: JV
authors.lastname: Solnick
authors.affiliation: Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, California, USA jenny.draper@esr.cri.nz jvsolnick@ucdavis.edu karplus@soe.ucsc.edu ottemann@ucsc.edu.
authors.forename: Kevin
authors.initials: K
authors.lastname: Karplus
authors.affiliation: Department of Microbiology & Environmental Toxicology, UC Santa Cruz, Santa Cruz, California, USA jenny.draper@esr.cri.nz jvsolnick@ucdavis.edu karplus@soe.ucsc.edu ottemann@ucsc.edu.
authors.forename: Karen M
authors.identifier: 0000-0001-6265-7401
authors.initials: KM
authors.lastname: Ottemann
mesh_terms: D000818:Animals; D014644:Genetic Variation; D016680:Genome, Bacterial; D016480:Helicobacter pylori / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D009154:Mutation