Neonatal infection with <i>Helicobacter pylori</i> affects stomach and colon microbiome composition and gene expression in mice

The stomach bacterium <i>Helicobacter pylori</i> is estimated to infect half of the world's population, and the health implications are affected by the age at infection. Neonatal <i>H. pylori</i> infection of mice is a relevant model to investigate metabolic and immunological effects. We performed an explorative study at the dynamic 1st month of life to compare the composition of the gastrointestinal tract microbiome and stomach gene expression of mice neonatally infected with <i>H. pylori</i> with that of uninfected mice. We found that <i>H. pylori</i> was present only in the stomach, and that <i>H. pylori</i> loads increase with age from 1 week after infection and onward, especially after weaning. Stomach and colon microbiome composition was strikingly similar between sites at the same sampling time but changed significantly over 1 week, with increased diversity at both sites. Despite the fact that the relative abundance of <i>H. pylori</i> in the stomach was low and never exceeded 3%, the composition and alpha diversity of the gastrointestinal microbiome was significantly affected by infection. In a pathway enrichment analysis, we found that stomach gene expression related to the extracellular matrix, muscle contraction, and metabolism was affected by infection. Expression of these key processes was, in infected mice, shifted away from that of control mice toward that of all mice sampled the subsequent week, which we speculate represents accelerated development in infected mice.