Background and aimsSurface modifications of titanium implants play essential role in facilitating osteointegration and enhancing their antimicrobial properties, while the latter is critical for preventing infectious diseases caused by the biofilm. However, it remains unknown about how the surface modifications could affect the composition and functional gene expression of oral microbiota deposited on the titanium implants. In this study, we aimed to investigate the impact of different nanostructured surfaces on the biofilm in vivo.ResultsNanophase calcium phosphate were successfully deposited into or between the TiO2 nanotubes with a diameter of 70–90 nm. NT and NTN surfaces showed increased roughness than the MP surface. XPS spectra showed that the O 1s was mainly divided into two bands in MP and NT samples, including Ti-O and -OH, while the surface modification of TiO2 nanotube in NT accounted for the increased intensity of Ti-O with the reference to that in MP samples. After the deposition of calcium phosphate, two new elemental peaks of Ca and P can be identified from the XPS survey spectrum of NTN. Moreover, the O 1s of NTN sample could be differentiated into three peaks, while the new one represented the -PO band. The 16S rDNA sequencing results showed that NT and NTN had minimal impact on the diversity and community structure of oral microbiota. Metatranscriptomic sequencing revealed that differentially expressed genes (DEGs) mostly differed in the terms of the biological process and cellular component on different surfaces. Gene Ontology (GO) terms enrichment indicated that NTN down-regulate the genes associated in localization and locomotion. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that the DEGs were associated with microbial metabolism, protein synthesis and bacterial invasion of epithelial cells.ConclusionTiO2 nanotube and calcium phosphate-coated TiO2 nanotube despite improving the antimicrobial properties of implant surfaces, had unexpectedly minimal impact on the microbiome composition and diversity. Notably, nanostructured titanium surfaces could inhibit the bacterial migration and colonization, down-regulate the pathogen invasion pathways, and further destruct bacterial cellular membrane, all in all, conferred the bactericidal properties.