Abstract
ABSTRACTMany 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-passaged Helicobacter pylori strain 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 these H. pylori isolates, including movement of the transposable element IS607, large and small inversions, multiple single nucleotide polymorphisms, and variation in cagA copy number. The cagA gene was found as 1 to 4 tandem copies located off the cag island 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 in cagY, 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.
Highlights
Our results demonstrated that SRR5236049 (PMSS1) and SRP099088 (SS1) has substantial working stock population variability, so we assessed whether PMSS1 would show a similar degree of variability
We focused on the insertion elements, inversions, and copy number alterations but did not analyze single nucleotide polymorphisms (SNPs) because the Pacbio sequencing technology used for PMSS1 has a high error rate and did not allow confident SNP detection
We found that there was rather a collection of genomes that differed with regard to gene copy number, insertion sequences, inversions, and SNPs
Summary
Many bacterial genomes are highly variable but are typically published as a single assembled genome. We describe the variability seen in typical working stocks and colonies of pathogen Helicobacter pylori model strains SS1 and PMSS1 as revealed by use of high-coverage mate pair next-generation sequencing (NGS) and confirmed by traditional laboratory tech-. Numerous studies have examined within-strain bacterial variability over time or in response to specific conditions, from early observations involving sectored colony formation (1) to recent work monitoring E. coli genome rearrangements over time (2), less is known about the extent of the genetic changes to expect within a typical laboratory culture (3). H. pylori strains vary from each other by numerous gene rearrangements, inversions, sequence variation, and gene gain or loss (4, 5) Such changes have been observed to occur even within the same strain during the course of infection (5–7).
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