Host-derived small RNAs are emerging as critical regulators in the dynamic interactions between host tissues and the microbiome, with implications for microbial pathogenesis and host defense. Among these, transfer RNA-derived small RNAs (tsRNAs) have garnered attention for their roles in modulating microbial behavior. However, the bacterial factors mediating tsRNA interaction and functionality remain poorly understood. In this study, using RNA affinity pull-down assay in combination with mass spectrometry, we identified a putative membrane-bound protein, annotated as P-type ATPase transporter (PtaT) in Fusobacterium nucleatum (Fn), which binds Fn-targeting tsRNAs in a sequence-specific manner. Through targeted mutagenesis and phenotypic characterization, we showed that in both the Fn type strain and a clinical tumor isolate, deletion of ptaT led to reduced tsRNA intake and enhanced resistance to tsRNA-induced growth inhibition. Global RNA sequencing and label-free Raman spectroscopy revealed the phenotypic differences between Fn wild type and PtaT-deficient mutant, highlighting the functional significance of PtaT in purine and pyrimidine metabolism. Furthermore, AlphaFold 3 prediction provides evidence supporting the specific binding between PtaT and Fn-targeting tsRNA. By uncovering the first RNA-binding protein in Fn implicated in growth modulation through interactions with host-derived small RNAs (sRNAs), our study offers new insights into sRNA-mediated host-pathogen interplay within the context of microbiome-host interactions.
Fusobacterium nucleatum/growth & development* ; RNA-Binding Proteins/genetics* ; Bacterial Proteins/genetics* ; RNA, Bacterial/metabolism* ; Humans ; RNA, Transfer/metabolism*

Human oral bacteria live in multispecies communities in the biofilm called dental plaque. This review focuses on the interactions of seven species and the ability of each species individually and together with other species to grow on saliva as the sole source of nutrient. Community formation in biofilms in flow cells is monitored using species-specific fluorophore-conjugated immunoglobulin G, and images are captured by confocal microscopy. Early colonizing veillonellae emerge from this review of interspecies interactions in saliva as a critical genus that guides the development of multispecies communities. Highly selective interspecies recognition is evident as initial colonizers pair with early and middle colonizers to form multispecies communities that grow on saliva.
Actinomyces ; growth & development ; Aggregatibacter actinomycetemcomitans ; growth & development ; Animals ; Biofilms ; growth & development ; Dental Enamel ; microbiology ; Dental Plaque ; metabolism ; microbiology ; Fluorescent Dyes ; metabolism ; Fusobacterium nucleatum ; growth & development ; Humans ; Microbial Consortia ; physiology ; Microbial Interactions ; physiology ; Microscopy, Confocal ; Polysaccharides, Bacterial ; chemistry ; Saliva ; metabolism ; microbiology ; Streptococcus oralis ; growth & development ; Veillonella ; growth & development

AIMThe purpose of this study was to develop a mathematical model to quantitatively describe the passive transport of macromolecules within dental biofilms.

METHODOLOGYFluorescently labeled dextrans with different molecular mass (3 kD, 10 kD, 40 kD, 70 kD, 2000 kD) were used as a series of diffusion probes. Streptococcus mutans, Streptococcus sanguinis, Actinomyces naeslundii and Fusobacterium nucleatum were used as inocula for biofilm formation. The diffusion processes of different probes through the in vitro biofilm were recorded with a confocal laser microscope.

RESULTSMathematical function of biofilm penetration was constructed on the basis of the inverse problem method. Based on this function, not only the relationship between average concentration of steady-state and molecule weights can be analyzed, but also that between penetrative time and molecule weights.

CONCLUSIONThis can be used to predict the effective concentration and the penetrative time of anti-biofilm medicines that can diffuse through oral biofilm. Furthermore, an improved model for large molecule is proposed by considering the exchange time at the upper boundary of the dental biofilm.

Actinomyces ; growth & development ; Algorithms ; Biofilms ; growth & development ; Biological Transport ; Dental Plaque ; microbiology ; Dextrans ; pharmacokinetics ; Diffusion ; Fluorescent Dyes ; pharmacokinetics ; Fusobacterium nucleatum ; growth & development ; Macromolecular Substances ; pharmacokinetics ; Microscopy, Confocal ; Models, Biological ; Molecular Probe Techniques ; Streptococcus mutans ; growth & development ; Streptococcus sanguis ; growth & development