Oral Biofilm Sampling for Microbiome Analysis in Healthy Children

Abstract

Oral biofilm and its molecular analysis provide a basis for investigating various dental research and clinical questions. Knowledge of biofilm composition leads to a better understanding of cariogenic and periopathogenic mechanisms. Microbial changes taking place in the oral cavity during childhood are of interest for several reasons. The evolution of the child oral microbiota and shifts in its composition need to be analyzed further to understand and possibly prevent the onset of disease. At the same time, advanced knowledge of the natural composition of oral biofilm is needed. Early stages of caries-free permanent dentition with healthy gums provide a widely unaffected subgingival habitat that can serve as an in situ baseline for studying features of oral health and disease. Analysis of children's oral biofilm during different stages in life is thus an important theme in the field. Modern molecular analysis methods can provide comprehensive information about the bacterial diversity of such biofilms. To enable microbiota data comparison, it is important to standardize each step in the procedure for molecular data generation. This procedure spans from clinical sampling, Next Generation Sequencing (NGS), bioinformatic data processing, to taxonomic interpretation. One of the most critical factors here is biofilm sampling. Sampling in children is even more challenging in particular due to limited space in subgingival areas. We thus focus on the use of paper points for subgingival sampling. This article provides a detailed protocol for oral biofilm sampling of the subgingival sulcus, the mucosa, and saliva in children.

Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body

“…Nasal swabs ( n = 7) were obtained from healthy adult volunteers (18–40 years old) and were taken from the olfactory mucosa located at the ceiling of the nasal cavity using ultra minitip nylon flocked swabs (Copan, Brescia, Italy) (Koskinen et al, 2018). Oral samples ( n = 7) were obtained using a standardized protocol for paper point sampling from healthy children (10 years old) who participated in a microbiome study investigating the subgingival biofilm formation (Santigli et al, 2016, 2017). Appendix samples ( n = 6) were obtained during pediatric appendectomies from children (7–12 years old) with either acute or ulcerous appendicitis.…”

Exploring the archaeome: detection of archaeal signatures in the human body

“…The nose swabs were obtained from healthy volunteers and were taken from the olfactory mucosa located at the ceiling of the nasal cavity using ultra minitip nylon flocked swabs (Copan, Brescia, Italy; n=7) (Koskinen et al, 2018). The oral samples have been obtained by standardized protocol for paper point sampling (Santigli et al, 2017) from healthy volunteers who participated in a microbiome study investigating the subgingival biofilm formation in children (n=7) (Santigli et al, 2016). Appendix samples have been obtained from collaboration partners at the Department of Pediatric and Adolescent Surgery and the Institute of Pathology, both Medical University of Graz (appendix specimens were obtained during pediatric appendectomies from either acute or ulcerous appendicitis; n=6).…”

Interaction of Oral and Toothbrush Microbiota Affects Oral Cavity Health

“…Here, we compared the microbiota between oral cavities and toothbrushes, and explored the potential risk of bacteria in toothbrushes, which provides useful data on oral health. However, sampling by gargling carries a risk of contamination from the throat or upper aerodigestive ways; therefore, a more suitable sampling method for oral bacteria should be used (Santigli et al, 2017).…”