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Additional file 7 Section S1. In this section, we conducted association analysis at the ASV level (i.e., 0% dissimilarity) using the same analysis strategies as described in the main texts for the bacterial vaginosis (BV) and the preterm birth (PTB) association studies.

Additional file 6 Table S2. OTUs significantly associated with preterm birth at FDR level of 0.05. TF: TreeFDR; SO: Single-OTU test implemented by POST with c=0; DE: DESeq2; WR-P: Wilcoxon rank-sum test using proportional data; WR-R: Wilcoxon rank-sum test using CLR transformed data.

Additional file 8 Table S3. The AUC using different pseudo-counts in Simulation A. The AUCs based on pseudo-count 0.5 are very close to the AUCs based on pseudo-count 1 across different scenarios and effect sizes.

Background: RhCMV/SIV vaccines protect ∼59% of vaccinated rhesus macaques against repeated limiting-dose intra-rectal exposure with highly pathogenic SIVmac239M, but the exact mechanism responsible for the vaccine efficacy is not known. It is becoming evident that complex interactions exist between gut microbiota and the host immune system. Here we aimed to investigate if the rhesus gut microbiome impacts RhCMV/SIV vaccine-induced protection., Methods: Three groups of 15 rhesus macaques naturally pre-exposed to RhCMV were vaccinated with RhCMV/SIV vaccines. Rectal swabs were collected longitudinally both before SIV challenge (after vaccination) and post challenge and were profiled using 16S rRNA based microbiome analysis., Results: We identified ∼2,400 16S rRNA amplicon sequence variants (ASVs), representing potential bacterial species/strains. Global gut microbial profiles were strongly associated with each of the three vaccination groups, and all animals tended to maintain consistent profiles throughout the pre-challenge phase. Despite vaccination group differences, using newly developed compositional data analysis techniques we identified a common gut microbial signature predictive of vaccine protection outcome across the three vaccination groups. Part of this microbial signature persisted even after SIV challenge. We also observed a strong correlation between this microbial signature and an early signature derived from whole blood transcriptomes in the same animals., Conclusions: Our findings indicate that changes in gut microbiomes are associated with RhCMV/SIV vaccine-induced protection and early host response to vaccination in rhesus macaques.