Microbial profiling and single-cell transcriptomics reveal probiotic mechanisms of coral thermal resilience

We conducted three sequential coral bleaching experiments to identify an effective probiotic and elucidate its protective mechanisms. These experiments included efficacy evaluation (efficacy screening), geographic validation, and molecular profiling. In the efficacy evaluation, two candidate probiotics were tested for their ability to enhance thermal tolerance in S. pistillata from Mao’ao, on the northeastern coast of Taiwan. After identifying a candidate with significant efficacy, we validated its effects in a geographically and ecologically distinct coral population from Kenting, southern Taiwan. In the first two experiments, we monitored coral bleaching responses and microbial community changes. For molecular profiling, we additionally assembled a S. pistillata clade 1 genome and profiled host transcriptomic responses at both bulk and single-cell resolution. Coral_probiotic_data_and_code/Sample_info.xlsx contains the NCBI accession numbers of raw sequences and their corresponding experimental information. Coral_probiotic_data_and_code/Transcriptome analyses/new_gene_id.csv contains the gene IDs used in the paper and their corresponding IDs in the StringTie-derived S. pistillata transcriptome annotation.