Oral Microbiome

Chronic hepatitis C virus (HCV) infection can cause severe hepatic affectation such as liver cirrhosis and hepatocellular carcinoma (H. C. Li & Lo, 2015). Therefore, chronic HCV represents a major physical and economic burden to patients (Abdel-Razek et al., 2019). Recently, the introduction of direct-acting antiviral (DAA) therapy has reformed HCV management. It provides promising results of chronic HCV elimination after its short-term use with less side effects when compared to the previously used interferon-based regimens (El Kassas et al., 2018; Raad et al., 2018). Proper understanding of the pathophysiology of liver disease has led to the discovery of the presence of a distant active player in the disease process, namely gut microbiota (Konturek et al., 2018). In chronic liver diseases, dysbiosis was reported in the gut microbiome in the form of an increase in the levels of pathogenic bacteria and their endotoxins. Furthermore, the intestinal wall was proven to acquire higher permeability allowing for the dysbiotic bacteria and its endotoxins to translocate to distant organs. The endotoxins, then, induce inflammatory reactions causing cytokine storm. Together with the chronic inflammation and immune dysfunction caused primarily by liver disease, the inflammatory changes caused by the gut

The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unpre- cedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.

Ancient dental pulps are highly precious samples because they conserve DNA from humans and blood-borne pathogens for ages. However, little is known about the microbial communities that are present in the dental pulps.  Here we analyzed ancient and modern dental pulp samples from different time periods and geographic regions and found that they are colonized by distinct microbial communities, which can be differentiated from other oral cavity samples. We found that despite the presence of environmental bacteria, ancient dental pulps conserve a good record of oral microbes. We were able to detect several different oral pathogens in ancient and modern dental pulps, which are commonly associated with periodontal diseases. We thus showed that ancient dental pulp are not only valuable sources of DNA from humans and systemic infections, but also an open window for the study of ancient oral microbiomes.

This paper critiques a study on the placental microbiome and specifically, recommendations it makes to women for preventing premature births, which were exaggerated and embellished in the media coverage it received. We contend that these preventative recommendations contribute to a pernicious, growing trend of policing women’s bodies and argue that the study provides no empirical evidence to justify them. Finally, we emphasize how the recommendations ignore important social and environmental risk factors for preterm birth that lie beyond individual choices and bodies. Future research on the placental microbiome, and especially media reports of it, ought to take these problems into account.

The extracts from the root, bark and seed of Garcinia kola are currently used in traditional medicine in
Nigeria. The aim of this study was to evaluate the inhibitory activity of crude extracts of G. kola on
Fusobacterium nucleatum isolated from the oral cavity. Methanol and aqueous extracts were prepared
from the seed and the minimal inhibitory concentration was evaluated by the agar dilution method,
using a Wilkins-Chalgren agar supplemented with horse blood (5%), hemin (5 μg/ml) and menadione (1
μg/ml). Antimicrobial activity of plant extracts on microbial biofilms was determined in microtiter plates.
The seed of G. kola demonstrated significant inhibitory action on F. nucleatum isolates at a
concentration of 1.25 and 12.5 mg/ml for amoxicillin resistant strain. It was able to inhibit the microbial
biofilm formed by the association of F. nucleatum with Porphyromonas gingivalis ATCC 33277,
Aggregatibacter actinomycetemcomitans ATCC 33384 and Prevotella intermedia ATCC 2564 at a
concentration of 25 mg/ml. The in-vitro inhibitory effect of G. kola on F. nucleatum population suggests
a potential role for its use in oral hygiene.

The concept of the human oral microbiome was applied to understand health and disease, lifestyles, and dietary habits throughout part of human history. In the present study, we augment the understanding of ancient oral microbiomes by characterizing human dental calculus samples recovered from the ancient Abbey of Badia Pozzeveri (central Italy), with differences in socioeconomic status, time period, burial type, and sex. Samples dating from the Middle Ages (11th century) to the Industrial Revolution era (19th century) were characterized using high-throughput sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. Consistent with previous studies, individuals from Badia Pozzeveri possessed commensal oral bacteria that resembled modern oral microbiomes. These results suggest that members of the oral microbiome are ubiquitous despite differences in geographical regions, time period, sex, and socioeconomic status. The presence of fecal bacteria could be in agreement with poor hygiene practices, consistent with the time period. Respiratory tract, nosocomial, and other rare pathogens detected in the dental calculus samples are intriguing and could suggest subject-specific comorbidities that could be reflected in the oral microbiome.

The etiology of periodontitis has traditionally been associated to a consortium of three bacterial species—the so-called “red-complex” of periodontal disease—which has been the target for most diagnostic and therapeutic strategies. However, other species have also been found to correlate with disease severity. In addition, the influence of smoking on periodontal microbiota is poorly understood. In the current manuscript, the composition of the subgingival microbiota in healthy individuals vs. patients with chronic periodontitis has been investigated using 16S pyrosequencing and the influence of smoking on periodontal composition has been examined. Subgingival bacterial communities were sampled from 82 patients: 22 non-smoking healthy controls, 28 non-smoking periodontal patients, and 32 smoking periodontal patients. Bacterial diversity was higher in periodontal patients than in healthy subjects, which could be interpreted as the consequence of a nutritionally richer environment or a reduced immune competence. Periodontal patients showed a significantly higher prevalence/relative abundance of “established” periopathogens but also other taxa whose role is not well-established and that should be targets for future research. These include Anaeroglobus, Bulleidia, Desulfobulbus, Filifactor, Mogibacterium, Phocaeicola, Schwartzia or TM7. The microbial community of smoking-associated periodontitis is less diverse and distinct from that of non-smokers, indicating that smoking has an influence on periodontal ecology. Interestingly, the high sequencing coverage allowed the detection at low proportions of periodontal pathogens in all healthy individuals, indicating that chronic periodontitis cannot be strictly considered an infectious disease but the outcome of a polymicrobial dysbiosis, where changes in the proportions of microbial consortia trigger the inflammatory and tissue-degradation responses of the host.

Over the last 5–10 years, optical coherence tomography (OCT) and atomic force microscopy (AFM) have been individually applied to monitor the morphological and mechanical properties of various single-species biofilms respectively. This investigation looked to combine OCT and AFM as a multi-scale approach to understand the role sucrose concentration and age play in the morphological and mechanical properties of oral, microcosm biofilms, in-vitro. Biofilms with low (0.1% w/v) and high (5% w/v) sucrose concentrations were grown on hydroxyapatite (HAP) discs from pooled human saliva and incubated for 3 and 5 days. Distinct mesoscale features of biofilms such as regions of low and high extracellular polymeric substances (EPS) were identified through observations made by OCT. Mechanical analysis revealed increasing sucrose concentration decreased Young's modulus and increased cantilever adhesion (p < 0.0001), relative to the biofilm. Increasing age was found to decrease adhesion only (p < 0.0001). This was due to mechanical interactions between the indenter and the biofilm increasing as a function of increased EPS content, due to increasing sucrose. An expected decrease in EPS cantilever contact decreased adhesion due to bacteria proliferation with biofilm age. The application OCT and AFM revealed new structure-property relationships in oral biofilms, unattainable if the techniques were used independently. Oral biofilms are complex microbial communities 1 , embedded in a matrix of extracellular polymeric substances (EPS) 2,3. EPS accounts for up to 90% of a biofilms' total mass 4,5 , consisting of polymers, mainly extracellular DNA (eDNA), polysaccharides, proteins and lipids of bacterial and salivary origin 2,6. Its' role is to provide a protective sheath 7 , encapsulating the multi-species bacterial complex, proliferating into distinct morphotypes, such as bulbous micro-colonies, maintaining its structural integrity 7. Oral biofilm formation is a hierarchical process 8 , consisting of surface attachment by primary bacterial colonizers, such as streptococci 9. This is followed by subsequent attachment of secondary, later and bridging colonizers, such as Actinomyces, Veillonella and fuso-bacterium respectively 8,9. A biofilms hierarchical nature 8 is an important feature to consider when contemplating how to analysis of their morphological and mechanical properties. During formation and proliferation, a biofilms' structural range extends from single molecular EPS constituents to bulbous micro-colonies and finally, fully formed mesoscale surface coverings 4. Applying techniques that span a range of length scales, are capable of in-vitro analysis and preserve biofilm structural and mechanical integrity are vital in the development of structure-property relationships. Traditionally, binding assays such as fluorescence staining have enabled researchers to extensively investigate a biofilms microbiology with increasing detail since the 1980′s 10,11. Since then, characterizing this multi-layered and multi-colonial bacterial community has led to the biological mapping of this complex, hierarchical structure 12. From a structural perspective, common characterization methods include scanning electron microscopy (SEM) 13–15 and confocal laser scanning microscopy (CLSM) 15,16. These techniques only provide basic morphology and quantitative live – dead ratios respectively 16. While these techniques can yield 3D structural information, they can be damaging to the specimen 17 and do not provide any mechanical information. Over the last 5 years, investigators have increasingly utilized atomic force microscopy (AFM) to obtain mechanical information from a variety of single-species biofilms, under several in-vitro conditions 18–20. Through non-destructive indentation, low applied force and known indenter geometry, mechanical properties such as elastic modulus, Young's modulus and adhesion can be obtained from generated force-displacement curves 21 .