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Carbohydrates are the main source of nutrition for <i>B. coli</i>, supplying energy for cell growth and development. The research aimed at investigating the mechanism of starch on the growth and replication of <i>B. coli</i>. Single-cell separation was used to isolate single trophozoites of <i>B. coli</i> under a stereomicroscope, transcriptomic profiling was conducted based on the SMART-seq2 single-cell RNA-seq method. Comparative genomic analysis was performed on <i>B. coli</i> and eight other ciliates to obtain specific and expanded gene families of <i>B. coli</i>. GO and KEGG enrichment analysis were used to analyze the key genes of <i>B. coli</i> under the action of starch in the present study. The results of single-cell RNA-seq depicts starch affected the growth and replication of <i>B. coli</i> in two ways: (1) the cell cycle was positively promoted by the activation of the cAMP/PKA signaling pathway via glycolysis; (2) the cell autophagy was suppressed through the PI3K/AKT/mTOR pathway. Genes involved in endocytosis, carbohydrate utilization, and the cAMP/PKA signaling pathway were highly enriched in both specific and expanded gene families of <i>B. coli</i>. Starch can be ingested and hydrolyzed into glucose, in turn affecting various biological processes of <i>B. coli</i>. The molecular mechanism of the effect of starch on the growth and proliferation of <i>B. coli</i> by promoting cell cycle and inhibiting the autophagy of trophozoites has been elucidated in our study.