Defining the healthy "core microbiome" of oral microbial communities (original) (raw)
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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...
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...
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.
OTUs clustering should be avoided for defining oral microbiome
2021
ABSTRACTThis in silico investigation aimed to: 1) evaluate a set of primer pairs with high coverage, including those most commonly used in the literature, to find the different oral species with 16S rRNA gene amplicon similarity/identity (ASI) values ≥97%; and 2) identify oral species that may be erroneously clustered in the same operational taxonomic unit (OTU) and ascertain whether they belong to distinct genera or other higher taxonomic ranks.Thirty-nine primer pairs were employed to obtain amplicon sequence variants (ASVs) from the complete genomes of 186 bacterial and 135 archaeal species. For each primer, ASVs without mismatches were aligned using BLASTN and their similarity values were obtained. Finally, we selected ASVs from different species with an ASI value ≥97% that were covered 100% by the query sequences. For each primer, the percentage of species-level coverage with no ASI≥97% (SC-NASI≥97%) was calculated.Based on the SC-NASI≥97% values, the best primer pairs were OP_...
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.
CORE: A Phylogenetically-Curated 16S rDNA Database of the Core Oral Microbiome
PLoS ONE, 2011
Comparing bacterial 16S rDNA sequences to GenBank and other large public databases via BLAST often provides results of little use for identification and taxonomic assignment of the organisms of interest. The human microbiome, and in particular the oral microbiome, includes many taxa, and accurate identification of sequence data is essential for studies of these communities. For this purpose, a phylogenetically curated 16S rDNA database of the core oral microbiome, CORE, was developed. The goal was to include a comprehensive and minimally redundant representation of the bacteria that regularly reside in the human oral cavity with computationally robust classification at the level of species and genus. Clades of cultivated and uncultivated taxa were formed based on sequence analyses using multiple criteria, including maximumlikelihood-based topology and bootstrap support, genetic distance, and previous naming. A number of classification inconsistencies for previously named species, especially at the level of genus, were resolved. The performance of the CORE database for identifying clinical sequences was compared to that of three publicly available databases, GenBank nr/nt, RDP and HOMD, using a set of sequencing reads that had not been used in creation of the database. CORE offered improved performance compared to other public databases for identification of human oral bacterial 16S sequences by a number of criteria. In addition, the CORE database and phylogenetic tree provide a framework for measures of community divergence, and the focused size of the database offers advantages of efficiency for BLAST searching of large datasets. The CORE database is available as a searchable interface and for download at http://microbiome.osu.edu.
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 ...
The salivary microbiome, assessed by a high-throughput and culture-independent approach
2011
The lack of cultivation of a significant fraction of bacteria found in the oral cavity means that culture-independent approaches are needed for the study of the salivary bacterial community composition and diversity. Saliva is easily obtained and could provide an alternative to blood in diagnostics, forensics, epidemiology and population studies. Our goal in this review is to put together the findings from the handful of recent studies of human salivary bacteria derived from culture-independent high-throughput sequencing of the 16S rRNA gene and look for emerging trends in the resulting larger dataset. Differences in phyla and genera abundances between studies of the salivary microbiome may be due to individual (genetic and lifestyle) variations, geographic variations and biases introduced during the experimental steps. Nevertheless, seven major phyla found in all relevant studies may be arbitrarily assigned into three major categories according to their abundance: (i) Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were very abundant; (ii) TM7 and Fusobacteria were moderately abundant and (iii) Spirochaetes had the lowest abundance. The frequency of genera varied among the studies but many had a relatively consistent presence. Genera found in all of the four reported salivary microbiomes were generally present at a high frequency and contributed to 71-80% of all sequences in the corresponding datasets. Conversely, genera identified in only one available salivary microbiome generally showed a low abundance. Improvements in high-throughput sequencing technology will enable random metagenome fragment sequencing to become a powerful tool to study bacterial, archaeal, fungal, phage and human viral components of the salivary microbiome in parallel.
Bacterial diversity in the oral cavity of 10 healthy individuals
The ISME …, 2010
The composition of the oral microbiota from 10 individuals with healthy oral tissues was determined using culture-independent techniques. From each individual, 26 specimens, each from different oral sites at a single point in time, were collected and pooled. An 11th pool was constructed using portions of the subgingival specimens from all 10 individuals. The 16S ribosomal RNA gene was amplified using broad-range bacterial primers, and clone libraries from the individual and subgingival pools were constructed. From a total of 11 368 high-quality, nonchimeric, near full-length sequences, 247 species-level phylotypes (using a 99% sequence identity threshold) and 9 bacterial phyla were identified. At least 15 bacterial genera were conserved among all 10 individuals, with significant interindividual differences at the species and strain level. Comparisons of these oral bacterial sequences with near full-length sequences found previously in the large intestines and feces of other healthy individuals suggest that the mouth and intestinal tract harbor distinct sets of bacteria. Co-occurrence analysis showed significant segregation of taxa when community membership was examined at the level of genus, but not at the level of species, suggesting that ecologically significant, competitive interactions are more apparent at a broader taxonomic level than species. This study is one of the more comprehensive, high-resolution analyses of bacterial diversity within the healthy human mouth to date, and highlights the value of tools from macroecology for enhancing our understanding of bacterial ecology in human health.