The oral cavity, though not saliva in particular, has offered caregivers a direct, non-invasive source of genomic material. In recent years, genetic testing has moved away from reliance upon invasive blood sampling toward user-friendly buccal swabs (42, 43). From commercially available at-home genetic testing kits (e.g., http://23andme.com, http://Ancestry.com) to paternity testing in the NICU, the ease with which sufficient quality and quantity of DNA samples can be obtained has markedly improved (43). However, beyond cellular DNA which is best harvested through cells, saliva is likely a rich source of cell-free and exosomal DNA that may provide caregivers with specific opportunities to monitor the overall health of the individual and further explore cell-to-cell communication (44–46). While research in this area continues to emerge, it is easy to see its applicability to child health. Genomic analysis of plasma cell-free DNA is directly impacting the field of cancer biology (47). Oncologists may now monitor the genomes of cell-free tumor DNA in plasma samples in order to generate targeted and personal therapies, assess drug resistance, and monitor a patient’s response to therapy by quantitative analysis of tumor load. Analysis of salivary cell-free DNA may provide similar insight and be highly beneficial in children affected by cancer who are already undergoing countless needle sticks and invasive procedures. Indeed, Pu et al. have recently demonstrated the applicability of a salivary assay for the detection of a genomic deletion in the epidermal growth factor receptor in patients with non-small cell lung cancer (48). While future studies are needed to demonstrate the role of cell-free salivary DNA in child health, it nevertheless offers yet another opportunity to improve delivery of care in this vulnerable population.

Our laboratory was one of the first to publish real-time developmental information available at a transcriptomic (RNA or gene expression) level in the newborn (49–51). In our original article, we demonstrated that transcripts, indicative of all major organ systems, were readily detected in an infant’s mouth (49). Genes identified were known to play a role in the developing GI, nervous, and hematological systems. While the trafficking mechanisms of these gene transcripts remain largely unknown, these initial hypothesis discovery experiments led to a series of targeted assays aimed at better defining developmental milestones and phenotypes.

Using high-throughput screening tools, such as multiplexed reverse transcriptase-quantitative polymerase chain reaction, on total RNA extracted from as little as 5 µL of neonatal saliva, we have been able to identify a panel of genes whose combined expression profiles may help neonatal caregivers to objectively assess oral feeding skills (52, 53). Genes identified on the panel are involved in diverse biological functions including hunger signaling (AMPK, NYP2R), palate development (WNT3), and sensory integration (NPHP4, PLXNA1). In initial studies, the combined salivary expression profile of these biomarkers was shown to be up to 78% accurate in predicting mature oral feeding skills in the newborn. In addition, our laboratory has been the first to link expression levels of a well-described speech–language gene, FOXP2, to oral feeding success in the newborn (54, 55). These experiments have laid the foundation for future studies to non-invasively explore developmental biology in our youngest patients and offer caregivers an enormous opportunity to utilize salivary transcriptomics to further explore, diagnose, and potentially prevent other areas of neonatal pathology where disrupted development results in unique and often life-threatening diseases including bronchopulmonary dysplasia, necrotizing enterocolitis (NEC), or retinopathy of prematurity. However, as a newly emerging field, it is important to recognize the potential impact of growth and biology on assay applicability. As stated previously, defining normative values across the age spectrum, exploring sex differences in expression patterns, understanding the role of salivary gland development, microbial colonization patterns, diet, and tooth eruption on gene expression will take prospective, collaborative, multicenter trials. Failing to perform the necessary experiments, such as observational studies to examine developing microbial colonization patterns or to establish normative reference genes for appropriate gene expression analyses over time, will directly impact our ability to translate these exciting discoveries to the bedside.

Saliva has been estimated to contain approximately 2,000 peptides, comprising 40–50% of total secreted body proteins (56). Unlike nucleic acids (DNA and RNA) that traditionally require the additional step of extraction prior to analysis, salivary proteins may be detected and quantified directly after collection. This ease of processing, combined with their relative stability compared to either DNA or RNA, makes proteins ideal biomarkers. Recent advances in technology and bioinformatics has allowed for the comprehensive profiling of hundreds to thousands of proteins from a single sample source to improve our understanding of the physiological, as well as the pathological, status of the human being (57–61).

To date, salivary protein biomarkers have been described for multiple adult oral and systemic diseases, including breast, pancreatic, and oral cancers (62–65), as well as autoimmune diseases, such as Sjögren’s disease, diffuse systemic sclerosis, rheumatoid arthritis, and systemic lupus erythematosus (SLE) (66). Moreover, studies have investigated the role of salivary proteomic analyses to predict myocardial infarction, diabetes mellitus types 1 and 2, and pulmonary diseases (67–69). While the pediatric patient population is ripe for similar diagnostic advances, here too, an investigator must pay specific attention to unique circumstances, including ongoing and rapid development as well as hormonal changes associated with puberty, which may impact proteomic analyses in newborns, infants, and children.

The salivary proteome varies from childhood to adolescence and is often dependent upon growth (70–72). For example, concentrations of salivary insulin growth factor (IGF-I) may vary and serve as an indicator of skeletal growth throughout childhood (71). Nutritional status of the child also affects salivary biomarkers. Malnourished children have specific salivary proteomic variations associated with protein energy under nutrition or PEU (73), and children affected with type 1 diabetes have been shown to have higher levels of salivary pro-inflammatory biomarkers compared to healthy controls. Conversely, there is a growing body of research examining salivary metabolomics that may predict metabolic syndrome, type 2 diabetes, and obesity in children. A recent study of 744 children (age 11) showed that salivary levels of c-reactive protein, salivary insulin, and leptin were higher and adiponectin levels lower in obese children compared to healthy normal weight children (74). Other studies tested the applicability and reliability of using salivary glucose levels as a surrogate for blood levels (75–77). With the use of a regression equation, salivary glucose values could accurately be converted to blood glucose levels, providing patients, especially children with type 1 diabetes, with a non-invasive tool for self-monitoring (78).

Beyond assessing the nutritional and metabolic status of children, there have been a limited number of studies utilizing salivary proteins for disease detection in this population. Salivary biomarkers for familial juvenile SLE, a more aggressive form of the disease known to causes widespread tissue damage and inflammation, have been described (79). Interestingly, there have also been recent studies showing aberrant protein expression in the saliva of children affected with autism spectrum disorder. Research has shown that there are decreased levels of three proteins, statherin, histatin 1, and acidic proline-rich protein, in the saliva of autistic children compared to healthy controls (80, 81). In addition, Wormwood and colleagues have recently demonstrated that salivary proteomic analyses of children can inform caregivers about developing cognitive functions (82). The ability of saliva to provide a window into disrupted neurodevelopment holds enormous promise for the field, allowing caregivers insight into areas of the body once believed only to be accessible though costly neuroimaging (e.g., MRI, CT) or invasive procedures (e.g., cerebral spinal fluid, blood).

According to the World Health Organization, infectious diseases are the leading cause of death of children and adolescents worldwide (83). Improved methods for earlier detection of infections, particularly in developing nations where blood sampling is not only invasive but also impractical, holds the potential for significantly improving outcomes. While the healthy human mouth contains as many as 500 million bacterial cells with more than 700 different colony species (84–86), it can also harbor and shed pathological infections. Upper respiratory infections, such as the influenza virus and human bocavirus HboV-1, a mild respiratory disease, can be detected in the saliva up to 1 year after primary infection (87, 88). In addition, cytomegalovirus (CMV), Epstein–Barr virus, human herpes virus (HHV) 6, and HHV7 can all be detected in human saliva (89–91). CMV, the most common cause of congenital hearing loss in children in developed countries (92), was one of the first viruses to be successfully detected through salivary analysis in the newborn (93). These initial reports showed not only that the virus was as readily detectable in saliva compared to more traditional assays using urine but also that saliva had a higher sensitivity for CMV detection compared to blood (94). Most recently, saliva has been shown to be an important biofluid for monitoring infectious Zika virus particles (95, 96). Salivary assays aimed at Zika RNA detection may prove to be a valuable tool for caregivers who are tracking exposure rates, transmission, and shedding of the virus.

In addition to the specific microbial detection, saliva also contains IgA, IgM, and IgG, which can assess immunological status and response to infection (97). For instance, studies have reported both the detection of specific antibodies to rotavirus infection in saliva (98), as well as the immunological response after administration of the vaccine (99). Similarly, rubella-specific IgM antibodies are detectable in children’s saliva (100), as are IgG levels of children who are seropositive for mumps, measles, and the herpes simplex virus (101, 102). Moreover, the hepatitis B virus, human immunodeficiency viruses, and Salmonella typhi can all be identified through the use of advanced technological approaches for Ig detection in the salivary fluid of children (103–105).

One of the more interesting aspects of working with saliva as a biofluid for clinical assessment is the fact that it harbors hundreds of organisms. In recent years, the field of metagenomics, defined as the genomes of all the organisms living in a specific environment in the human body, has emerged (106). Our ability to analyze not simply human gene and protein expression but also the organisms residing in the mouth that may be responsible for such a response, provides yet another opportunity to improve child health. Unique microbial colonization patterns have been shown to be associated with disease including childhood caries, NEC, and metabolic syndrome. Identifying aberrant microbial colonization patterns, while simultaneously monitoring an individual’s unique immune and inflammatory response, may allow for the development of preventative strategies to improve health outcomes (86, 107).

In 2014, the Centers for Disease Control reported that the prevalence of children ≥12 years old using illicit drug was 12% (107), and the use of non-medical psychotherapeutic drugs was 2.5%. Sadly, as drug abuse has become increasingly common, novel detection methods, including those that can be performed easily in the either home or office under direct visualization, are needed. Salivary drug screening assays have already been approved by the USFDA and are available for medical and commercial use (e.g., http://americanscreeningcorp.com). Cocaine, amphetamines, opioids, benzodiazepines, and tetra-hydro-cannabinoids, among others, can all be detected and quantified in saliva (108–111). Further, concentrations of drug metabolites of a variety of prescribed drugs are also measurable in saliva (112, 113), making ease of obtaining therapeutic levels without invasive, serial phlebotomy possible.