BackgroundMalaria, caused by Plasmodium infection, is a global life-threatening infection disease especially during the COVID-19 pandemic. However, it is still unclear about the dynamic change and the interactions of the intestinal microbiota and immunity during the whole parasite infection. Here, we investigated the change of intestinal microbiome and transcriptome during the whole Plasmodium infection process in mice to analyze the dynamic landscape of parasitaemia dependent intestinal microbiota shifting and related to host immunity.ResultsThere were significant parasitaemia dependent changes of intestinal microbiota and transcriptome, and the microbiota was significantly correlated to the intestinal immunity. We found that (i) the diversity and composition of the intestinal microbiota represented a significant correlation along with the Plasmodium infection in family, genus and species level; (ii) particularly, Erysipelotrichaceae bacterium canine oral taxon 255, Sutterella*, Ruminococcus 1* and Eubacterium plexicaudatum ASF492 were specific during the parasitaemia rising state, while Eubacterium nodatum group* was specific in the recovering phase at species level; (iii) the up-regulated genes from the intestinal transcriptome were mainly enriched in immune cell differentiation pathways along with the malaria development, particularly, naive CD4+ T cells differentiated into Th1, Th2 and Tfh cells in the early immune response and into Th17 cells in the later response, while B cells were activated during the whole Plasmodium infection process; (iv) the abundance of the parasitaemia phase-specific microbiota represented a high correlation with the phase-specific immune cells development, particularly, Th1 cell with family Bacteroidales BS11 gut group, genera Prevotella 9, Ruminococcaceae UCG 008, Moryella and specie Sutterella* , Th2 cell with specie Sutterella*, Th17 cell with family Peptococcaceae , genus Lachnospiraceae FCS020 group and spices Ruminococcus 1*, Ruminococcus UGG 014* and Eubacterium plexicaudatum ASF492, Tfh and B cell with genera Moryella and species Erysipelotrichaceae bacterium canine oral taxon 255.ConclusionThere were a remarkable dynamic landscape of the parasitaemia dependent shifting of intestinal microbiota and immunity, and a notable correlation between the abundance of intestinal microbiota, especially at species level, and immune cells.