Bacterial diversity in the oral cavity of 10 healthy individuals (original) (raw)
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Defining the healthy "core microbiome" of oral microbial communities
BMC Microbiology, 2009
Background: Most studies examining the commensal human oral microbiome are focused on disease or are limited in methodology. In order to diagnose and treat diseases at an early and reversible stage an indepth definition of health is indispensible. The aim of this study therefore was to define the healthy oral microbiome using recent advances in sequencing technology (454 pyrosequencing).
Shehla Yousuf et al, Analysis Of Role Of Oral Microbiome In Health And Disease., Indo Am
Every human body contains a personalized set of foreign inhabitants essential to maintaining health, yet also capable of eliciting disease. The totality of these microorganisms, their genomes and ecosystems encompasses the microbiome. The basic aim of the study is to find the role of oral microbiome in health and disease. As the correlation between the human microbiome and health becomes more evident, microbiome research is becoming central to the advancement of disease diagnostics and therapeutics as well as the development of personalized medicine. There are several ways to sequence a metagenome or segments of a metagenome, each technique serving a unique purpose. The most common techniques include 16S ribosomal RNA sequencing, pyrosequencing, and shotgun sequencing. The bacterial flora in a healthy oral cavity vs a diseased one is distinctly different, suggesting there may be a profile for a core oral microbiome of health. According to various studies, identical bacterial sequences have been discovered in the oral cavities of unrelated healthy individuals.
Study of inter- and intra-individual variations in the salivary microbiota
BMC Genomics, 2010
Background: Oral bacterial communities contain species that promote health and others that have been implicated in oral and/or systemic diseases. Culture-independent approaches provide the best means to assess the diversity of oral bacteria because most of them remain uncultivable.
Genes
There is currently no criterion to select appropriate bioinformatics tools and reference databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study aims to determine the influence of multiple tools and reference databases on α-diversity measurements and β-diversity comparisons analyzing the human oral microbiome. We compared the results of taxonomical classification by Greengenes, the Human Oral Microbiome Database (HOMD), National Center for Biotechnology Information (NCBI) 16S, SILVA, and the Ribosomal Database Project (RDP) using Quantitative Insights Into Microbial Ecology (QIIME) and the Divisive Amplicon Denoising Algorithm (DADA2). There were 15 phyla present in all of the analyses, four phyla exclusive to certain databases, and different numbers of genera were identified in each database. Common genera found in the oral microbiome, such as Veillonella, Rothia, and Prevotella, are annotated by all databases; however, less common genera, such as B...
Frontiers in Microbiology
The oral cavity is an important window for microbial communication between the environment and the human body. The oral microbiome plays an important role in human health. However, compared to the gut microbiome, the oral microbiome has been poorly explored. Here, we analyzed 404 datasets from human oral saliva samples published by the Earth Microbiome Project (EMP) and compared them with 815 samples from the human gut, nose/pharynx, and skin. The diversity of the human saliva microbiome varied significantly among individuals, and the community compositions were complex and diverse. The saliva microbiome showed the lowest species diversity among the four environment types. Human oral habitats shared a small core bacterial community containing only 14 operational taxonomic units (OTUs) under 5 phyla, which occupied over 75% of the sequence abundance. For the four habitats, the core taxa of the saliva microbiome had the greatest impact on saliva habitats than other habitats and were m...
Future Prospective of Oral Microbiome Research
Applied Sciences, 2021
Oral microbiome has complex structure. It consisted of more than 700 species of bacteria. These bacteria contains pathogens for human health. In contrast, some beneficial bacteria were included. Perspective of oral microbiome is not still elucidated. In this paper, information regarding oral microbiome of health older adults and oral diseases are included. Additionally, concise review of oral microbiome are presented.
NPJ biofilms and microbiomes, 2017
Oral microbes form a complex and dynamic biofilm community, which is subjected to daily host and environmental challenges. Dysbiosis of the oral biofilm is correlated with local and distal infections and postulating a baseline for the healthy core oral microbiota provides an opportunity to examine such shifts during the onset and recurrence of disease. Here we quantified the daily, weekly, and monthly variability of the oral microbiome by sequencing the largest oral microbiota time-series to date, covering multiple oral sites in ten healthy individuals. Temporal dynamics of salivary, dental, and tongue consortia were examined by high-throughput 16S rRNA gene sequencing over 90 days, with four individuals sampled additionally 1 year later. Distinct communities were observed between dental, tongue, and salivary samples, with high levels of similarity observed between the tongue and salivary communities. Twenty-six core OTUs that classified within Streptococcus, Fusobacterium, Haemophi...
Diversity of the oral microbiome between dentate and edentulous individuals
Oral Diseases, 2019
BackgroundMeasurement of saliva microbes is promoted as a way to detect oral and systemic disease, yet there is a multitude of factors that affect the oral microbiome. The salivary microbiome is influenced by oral biofilm of shedding (epithelial) and non‐shedding (tooth) surfaces.MethodsTo gauge the ability of salivary microbial analytics to distinguish between edentulous and dentate oral conditions, we looked for differences in the saliva microbiome of subjects with and without teeth. Fifty‐two dentate and 49 edentulous subjects provided stimulated saliva samples. 16S rRNA gene sequencing, QIIME‐based data processing, and statistical analysis were done using several different analytical approaches to detect differences in the salivary microbiome between the two groups.ResultsBacteria diversity was lower in the edentulous group. Remarkably, all 31 of the most significant differences in taxa were deficits that occur in the edentulous group. As one might expect many of these taxa are ...
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing
Journal of Microbiological Methods, 2009
To date, metagenomic studies have relied on the utilization and analysis of reads obtained using 454 pyrosequencing to replace conventional Sanger sequencing. After extensively scanning the 16S ribosomal RNA (rRNA) gene, we identified the V5 hypervariable region as a short region providing reliable identification of bacterial sequences available in public databases such as the Human Oral Microbiome Database. We amplified samples from the oral cavity of three healthy individuals using primers covering an ~82-base segment of the V5 loop, and sequenced using the Illumina technology in a single orientation. We identified 135 genera or higher taxonomic ranks from the resulting 1,373,824 sequences. While the abundances of the most common phyla (Firmicutes, Proteobacteria, Actinobacteria, Fusobacteria and TM7) are largely comparable to previous studies, Bacteroidetes were less present. Potential sources for this difference include classification bias in this region of the 16S rRNA gene, human sample variation, sample preparation and primer bias. Using an Illumina sequencing approach, we achieved a much greater depth of coverage than previous oral microbiota studies, allowing us to identify several taxa not yet discovered in these types of samples, and to assess that at least 30,000 additional reads would be required to identify only one additional phylotype. The evolution of high-throughput sequencing technologies, and their subsequent improvements in read length enable the utilization of different platforms for studying communities of complex flora. Access to large amounts of data is already leading to a better representation of sample diversity at a reasonable cost.