Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data.

Understanding the function of the human microbiome is important but the development of statistical methods specifically for the microbial gene expression (i.e. metatranscriptomics) is in its infancy. Many currently employed differential expression analysis methods have been designed for different data types and have not been evaluated in metatranscriptomics settings. To address this gap, we undertook a comprehensive evaluation and benchmarking of 10 differential analysis methods for metatranscriptomics data. We used a combination of real and simulated data to evaluate performance (i.e. type I error, false discovery rate and sensitivity) of the following methods: log-normal (LN), logistic-beta (LB), MAST, DESeq2, metagenomeSeq, ANCOM-BC, LEfSe, ALDEx2, Kruskal-Wallis and two-part Kruskal-Wallis. The simulation was informed by supragingival biofilm microbiome data from 300 preschool-age children enrolled in a study of childhood dental disease (early childhood caries, ECC), whereas validations were sought in two additional datasets from the ECC study and an inflammatory bowel disease study. The LB test showed the highest sensitivity in both small and large samples and reasonably controlled type I error. Contrarily, MAST was hampered by inflated type I error. Upon application of the LN and LB tests in the ECC study, we found that genes C8PHV7 and C8PEV7, harbored by the lactate-producing Campylobacter gracilis, had the strongest association with childhood dental disease. This comprehensive model evaluation offers practical guidance for selection of appropriate methods for rigorous analyses of differential expression in metatranscriptomics. Selection of an optimal method increases the possibility of detecting true signals while minimizing the chance of claiming false ones.

Understanding the Predictive Potential of the Oral Microbiome in the Development and Progression of Early Childhood Caries.

BACKGROUND: Early childhood caries (ECC) is the most common chronic disease in young children and a public health problem worldwide. It is characterized by the presence of atypical and fast progressive caries lesions. The aggressive form of ECC, severe early childhood caries (S-ECC), can lead to the destruction of the whole crown of most of the deciduous teeth and cause pain and sepsis, affecting the child's quality of life. Although the multifactorial etiology of ECC is known, including social, environmental, behavioral, and genetic determinants, there is a consensus that this disease is driven by an imbalance between the oral microbiome and host, or dysbiosis, mediated by high sugar consumption and poor oral hygiene. Knowledge of the microbiome in healthy and caries status is crucial for risk monitoring, prevention, and development of therapies to revert dysbiosis and restore oral health. Molecular biology tools, including next-generation sequencing methods and proteomic approaches, have led to the discovery of new species and microbial biomarkers that could reveal potential risk profiles for the development of ECC and new targets for anti-caries therapies. This narrative review summarized some general aspects of ECC, such as definition, epidemiology, and etiology, the influence of oral microbiota in the development and progression of ECC based on the current evidence from genomics, transcriptomic, proteomic, and metabolomic studies and the effect of antimicrobial intervention on oral microbiota associated with ECC. CONCLUSION: The evaluation of genetic and proteomic markers represents a promising approach to predict the risk of ECC before its clinical manifestation and plan efficient therapeutic interventions for ECC in its initial stages, avoiding irreversible dental cavitation.

The bacterial microbiome and metabolome in caries progression and arrest.

Aim: This in vivo experimental study investigated bacterial microbiome and metabolome longitudinal changes associated with enamel caries lesion progression and arrest. Methods: We induced natural caries activity in three caries-free volunteers prior to four premolar extractions for orthodontic reasons. The experimental model included placement of a modified orthodontic band on smooth surfaces and a mesh on occlusal surfaces. We applied the caries-inducing protocol for 4- and 6-weeks, and subsequently promoted caries lesion arrest via a 2-week toothbrushing period. Lesions were verified clinically and quantitated via micro-CT enamel density measurements. The biofilm microbial composition was determined via 16S rRNA gene Illumina sequencing and NMR spectrometry was used for metabolomics. Results: Biofilm maturation and caries lesion progression were characterized by an increase in Gram-negative anaerobes, including Veillonella and Prevotella. Streptococcus was associated caries lesion progression, while a more equal distribution of Streptococcus, Bifidobacterium, Atopobium, Prevotella, Veillonella, and Saccharibacteria (TM7) characterized arrest. Lactate, acetate, pyruvate, alanine, valine, and sugars were more abundant in mature biofilms compared to newly formed biofilms. Conclusions: These longitudinal bacterial microbiome and metabolome results provide novel mechanistic insights into the role of the biofilm in caries progression and arrest and offer promising candidate biomarkers for validation in future studies.

Rare Condition of Dens Invaginatus in a Maxillary Primary Molar and a Birooted Maxillary Primary Canine diagnosed during Routine Examination.

Congenital morphological dental alterations are related to the physiological phase of tooth development. Since the etiology of the dens invaginatus and supernumerary roots has yet to be fully determined, a rare presentation of dens invaginatus in a primary molar and a birooted deciduous maxillary canine were incidentally detected in routine radiographic examinations. Essential clinical considerations and treatment options are presented. CLINICAL SIGNIFICANCE: This study highlights the importance of a deep and comprehensive anamnesis and clinical examination, with radiographs taken when necessary. The negligence of these stages in an initial consultation could cause irreversible future damage to the patient, since rare dental anomalies or other lesions that require treatment may not be detected. HOW TO CITE THIS ARTICLE: Brandão ECB, Ribeiro AAA, Seabra LMA. Rare Condition of Dens Invaginatus in a Maxillary Primary Molar and a Birooted Maxillary Primary Canine diagnosed during Routine Examination. Int J Clin Pediatr Dent 2017;10(2): 193-195.

Influence of Caregiver's Sociodemographic Background on the Oral Health Status and Care of HIV-infected Children.

PURPOSE: The purpose of this study was to evaluate the relationship between socio-demographic characteristics of caregivers and the oral health of their children infected with human immunodeficiency virus (HIV+) compared to a group of HIV-children and their caregivers. METHODS: One hundred forty HIV+ and 140 healthy two- to five-year-old children and their caregivers who sought care at hospitals in Rio de Janeiro, Brazil, participated. Caregivers were interviewed for sociodemographic characteristics, and knowledge and attitudes regarding oral health. The decayed, missing and filled primary teeth (dmft) index was obtained for the children. Chi-square and Mann-Whitney tests were used (five percent significance level). Content analysis method was used for qualitative evaluation. RESULTS: Most interviewees were mothers (83.6 percent), did no work outside the home (69.3 percent), had low educational status (47.1 percent), and were born in the South/Southeast regions of Brazil (83.6 percent). The mean dmft was 3.48±3.14 for the HIV+ group and 1.02±1.00 for the healthy children. Oral care was reported as important by 54.1 percent of the caregivers. Those who didn't consider oral care important had never received information about oral health (P<0.01). Caregivers born in the North/Northeast regions took their children to the dentist less frequently than mothers born in other areas (P=0.02). Low educational status influenced the attitudes about oral health (P<0.01), irregular dental visits for the children (P<0.01), and the dmft index (P<0.01). CONCLUSION: Caregivers' low educational status and birthplace influenced the importance given to HIV+ children's oral health as well as the oral health knowledge and practices for both HIV+ and healthy children.

The oral health of HIV-infected Brazilian children.

BACKGROUND: The number of HIV-infected people has increased almost continuously. Paediatric dentists should be concerned about the oral findings in HIV-infected children and their aetiologic factors, to promote adequate treatment. AIM: To present the oral health aspects of Brazilian HIV-infected children and to verify the aetiological factors. DESIGN: A cross-sectional study was conducted with HIV-infected children. During the medical appointments, children were submitted to visual-tactile exams of oral soft tissues and teeth. All parents answered questions in a structured interview. Data were analysed using the SPSS, release 10.0 (Chicago, IL, USA). RESULTS: Of the 57 children examined, 39 (69.6%) presented one or more oral soft tissue manifestations. More than a half suffered from gingivitis and only 12.5% had no visible dental biofilm. A high prevalence of dental surfaces with active carious lesions was observed; mean DMFS-m and dmfs-m scores were 5.41 ± 5.61 and 16.77 ± 19.52, respectively. Caries activity and gingivitis were correlated with the presence of mature dental biofilm. CONCLUSIONS: Prevalence of soft tissue lesions, dental caries and gingivitis in HIV-infected children was high and correlated to lack of satisfactory oral hygiene habits, suggesting the need of therapeutic programmes that allow these children to recover their oral health.