This review presents literature that highlights saliva’s utility as a biofluid in the diagnosis and monitoring of COVID-19. A systematic search was performed in 5 electronic databases (PubMed, Embase, LILACS, Scopus, and Web of Science). Studies were eligible for inclusion if they assessed the potential diagnostic value and/or other discriminatory properties of biological markers in the saliva of patients with COVID-19. As of July 22, 2020, a total of 28 studies have investigated the presence of SARS-CoV-2 RNA in saliva. Several of those studies confirmed reliable detection of SARS-CoV-2 in the saliva of patients with COVID-19. Saliva offered sensitivity and specificity for SARS-CoV-2 detection comparable to that of the current standard of nasopharyngeal and throat swabs. However, the utility of saliva in diagnosing COVID-19 infection remains understudied. Clinical studies with larger patient populations that measure recordings at different stages during the disease are still necessary to confirm the accuracy of COVID-19 diagnosis with saliva. Nevertheless, the utility of saliva as a diagnostic tool opens the possibility of using rapid and less invasive diagnostic strategies by targeting bioanalytes rather than the pathogen.

Research on the human microbiome has mainly been restricted to the identification of most abundant microbiota associated with health or disease. Their abundance may reflect their capacity to exploit their niche, however, metabolic functions exerted by low-abundant microrganisms can impact the dysbiotic signature of local microbial habitats. This scoping review aims to map the literature regarding the management of low-abundant microorganisms in studies investigating human microbiome samples. A systematic literature search was performed in 5 electronic databases, as well as grey literature. We selected clinical microbiome studies targeting human participants of any age, from any body site. We also included studies with secondary data which originated from human biofilm samples. All of the papers used next-generation sequencing (NGS) techniques in their methodology. A total of 826 manuscripts were retrieved, of which 42 were included in this review and 22 reported low-abundant bacteria (LB) in samples taken from 7 body sites (breast, gut, oral cavity, skin, stomach, upper respiratory tract (URT), and vagina). Four studies reported microbes at abundance levels between 5 and 20%, 8 studies reported between 1 and 5%, and 18 studies reported below 1%. Fifteen papers mentioned fungi and/or archaea, and from those only 4 (fungi) and 2 (archaea) produced data regarding the abundance of these domains. While most studies were directed towards describing the taxonomy, diversity and abundance of the highly abundant species, low-abundant species have largely been overlooked. Indeed, most studies select a cut-off value at <1% for low-abundant organisms to be excluded in their analyses. This practice may compromise the true diversity and influence of all members of the human microbiota. Despite their low abundance and signature in biofilms, they may generate important markers contributing to dysbiosis, in a sort of ‘butterfly effect’. A detailed snapshot of the physiological, biological mechanisms at play, including virulence determinants in the context of a dysbiotic community, may help better understand the health-disease transition.

Actinomyces spp. gene expression in root caries lesions

Following gingival recession, which increases with age, the root surface becomes exposed, creating new environments for microbial colonization and biofilm formation. The formation of root surface biofilms is influenced by the availability and composition of saliva and gingival crevicular fluid; they provide components for the conditioning film (acquired root surface pellicle) and also act as a source of nutrients. The early bacterial colonizers of the root surface are similar to those found on the enamel, and Gram-positive species such as Streptococcus sanguinis, S. oralis, S. mitis, and Actinomyces species predominate. The root surface has a lower mineral and higher organic content than enamel, and so is more vulnerable to demineralization. The characterization of the microbiota associated with root surface lesions is still ongoing. Traditional culture-based studies have implicated species such as mutans streptococci, lactobacilli, bifidobacteria, and Actinomyces species, while molecular-based studies have provided evidence for a more complex microbiota with many Gram-negative and anaerobic bacteria being detected in addition to the more conventional cariogenic organisms. Ecological concepts have been applied to explain the microbial etiology of root caries. The acidic environment generated from the fermentation of dietary sugars selects saccharolytic bacteria that can preferentially grow and metabolize under low pH conditions, and then proteolytic Gram-negative species are selected when the dentin is exposed and collagen and other proteins become accessible to be catabolized. These species act in concert to degrade the inorganic and organic components of the dental tissues.