The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization

Cabral, Damien J.; Wurster, Jenna I.; Flokas, Myrto Eleni; Alevizakos, Michail; Zabat, Michelle A.; Korry, Benjamin J.; Rowan, Aislinn D.; Sano, William H.; Andreatos, Nikolaos; Ducharme, Robert; Chan, Philip A.; Mylonakis, Eleftherios; Fuchs, Beth Burgwyn; Belenky, Peter

doi:10.1038/s41598-017-11427-2

Cited by 35 publications

(28 citation statements)

References 73 publications

(86 reference statements)

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“…This high-resolution amplicon sequence processing pipeline, DADA2, uses a statistical error modeling approach to denoise raw sequencing reads to infer true “biological variants” and can distinguish sequences with up to single nucleotide differences. The DADA2 approach has been shown to improve the resolution of 16S amplicon sequencing in several microbiome studies [ 8 , 34 – 36 ].…”

Section: Introductionmentioning

confidence: 99%

High-resolution ISR amplicon sequencing reveals personalized oral microbiome

et al. 2018

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BackgroundSequencing of the 16S rRNA gene has been the standard for studying the composition of microbial communities. While it allows identification of bacteria at the level of species, this method does not usually provide sufficient information to resolve communities at the sub-species level. Species-level resolution is not adequate for studies of transmission or stability or for exploring subspecies variation in disease association. Strain level analysis using whole metagenome shotgun sequencing has significant limitations that can make it unsuitable for large-scale studies. Achieving sufficient depth of sequencing can be cost-prohibitive, and even with adequate coverage, deconvoluting complex communities such as the oral microbiota is computationally very challenging. Thus, there is a need for high-resolution, yet cost-effective, high-throughput methods for characterizing microbial communities.ResultsSignificant improvement in resolution for amplicon-based bacterial community analysis was achieved by combining amplicon sequencing of a high-diversity marker gene, the ribosomal 16-23S intergenic spacer region (ISR), with a probabilistic error modeling based denoising algorithm, DADA2. The resolving power of this new approach was compared to that of both standard and high-resolution 16S-based approaches using a set of longitudinal subgingival plaque samples. The ISR strategy resulted in a 5.2-fold increase in community resolution compared to reference-based 16S rRNA gene analysis and showed 100% accuracy in predicting the correct source of a clinical sample. Individuals’ microbial communities were highly personalized, and although they exhibited some drift in membership and levels over time, that difference was always smaller than the differences between any two subjects, even after 1 year. The construction of an ISR database from publicly available genomic sequences allowed us to explore genomic variation within species, resulting in the identification of multiple variants of the ISR for most species.ConclusionsThe ISR approach resulted in significantly improved resolution of communities and revealed a highly personalized human oral microbiota that was stable over 1 year. Multiple ISR types were observed for all species examined, demonstrating a high level of subspecies variation in the oral microbiota. The approach is high-throughput, high-resolution yet cost-effective, allowing subspecies-level community fingerprinting at a cost comparable to that of 16S rRNA gene amplicon sequencing. It will be useful for a range of applications that require high-resolution identification of organisms, including microbial tracking, community fingerprinting, and potentially for identification of virulence-associated strains.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0535-z) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

High-resolution ISR amplicon sequencing reveals personalized oral microbiome

et al. 2018

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“…In this study, we show that Prevotella, Porphyromonas, Streptococcus, Veillonella, Haemophilus, Gemella, and Neisseria were the most common members of the Qatari salivary microbiome, with Prevotella being the most predominant genus. In contrast, Streptococcus is the most abundant genus in the UK, South Korea, Japan and US populations [46,[48][49][50][51][52][53]. The differences observed in the Qatari salivary microbiome compared to other populations, may be influenced by various factors, including host genetics, diet and environmental factors [49].…”

Section: Discussionmentioning

confidence: 99%

Profiling the Salivary microbiome of the Qatari population

et al. 2020

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Background: The role of the human microbiome in human health and disease has been studied in various body sites. However, compared to the gut microbiome, where most of the research focus is, the salivary microbiome still bears a vast amount of information that needs to be revealed. This study aims to characterize the salivary microbiome composition in the Qatari population, and to explore specific microbial signatures that can be associated with various lifestyles and different oral conditions. Materials and methods: We characterized the salivary microbiome of 997 Qatari adults using high-throughput sequencing of the V1-V3 region of the 16S rRNA gene. Results: In this study, we have characterized the salivary microbiome of 997 Qatari participants. Our data show that Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria are the common phyla isolated from the saliva samples, with Bacteroidetes being the most predominant phylum. Bacteroidetes was also more predominant in males versus females in the study cohort, although differences in the microbial diversity were not statistically significant. We also show that, a lower diversity of the salivary microbiome is observed in the elderly participants, with Prevotella and Treponema being the most significant genera. In participants with oral conditions such as mouth ulcers, bleeding or painful gum, our data show that Prevotella and Capnocytophaga are the most dominant genera as compared to the controls. Similar patterns were observed in participants with various smoking habits as compared to the non-smoking participants. Our data show that Streptococcus and Neisseria are more dominant among denture users, as compared to the non-denture users. Our data also show that, abnormal oral conditions are associated with a reduced microbial diversity and microbial richness. Moreover, in this study we show that frequent coffee drinkers have higher microbial diversity compared to the non-drinkers, indicating that coffee may cause changes to the salivary microbiome. Furthermore, tea drinkers show higher microbial richness as compared to the non-tea drinkers. Conclusion: This is the first study to assess the salivary microbiome in an Arab population, and one of the largest population-based studies aiming to the characterize the salivary microbiome composition and its association with age, oral health, denture use, smoking and coffee-tea consumption.

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“…In the sucrose phase its abundance in these two participants increased substantially and it was detected in samples of two more participants, yet altogether with abundances mostly below 0.01%. Some authors have found that amplifying the V1-V2 region of the 16S rDNA resulted in poorer detection of S. mutans compared to other primers 47 , 48 , while still achieving a better detection of the whole genus Streptococcus 49 . This is a possible reason for the low detection, yet even with culture technique, this species has not been detected frequently in our study participants (data not shown).…”

Section: Discussionmentioning

confidence: 99%

In-vivo shift of the microbiota in oral biofilm in response to frequent sucrose consumption

Anderson

Rothballer

Altenburger

et al. 2018

Sci Rep

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Caries is associated with shifts of microbiota in dental biofilms and primarily driven by frequent sucrose consumption. Data on environmentally induced in vivo microbiota shifts are scarce therefore we investigated the influence of frequent sucrose consumption on the oral biofilm. Splint systems containing enamel slabs were worn for 3 × 7 days with 7-day intervals to obtain oral biofilm samples. After a three-month dietary change of sucking 10 g of sucrose per day in addition to the regular diet, biofilm was obtained again at the end of the second phase. The microbiota was analysed using Illumina MiSeq amplicon sequencing (v1-v2 region). In addition, roughness of the enamel surface was measured with laser scanning microscopy. The sucrose phase resulted in significant differences in beta-diversity and significantly decreased species richness. It was marked by a significant increase in abundance of streptococci, specifically Streptococcus gordonii, Streptococcus parasanguinis and Streptococcus sanguinis. Enamel surface roughness began to increase, reflecting initial impairment of dental enamel surface. The results showed that frequent sucrose consumption provoked compositional changes in the microbiota, leading to an increase of non-mutans streptococci, hence supporting the extended ecological plaque hypothesis and emphasizing the synergy of multiple bacterial species in the development of caries.

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The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization

Cited by 35 publications

References 73 publications

High-resolution ISR amplicon sequencing reveals personalized oral microbiome

High-resolution ISR amplicon sequencing reveals personalized oral microbiome

Profiling the Salivary microbiome of the Qatari population

In-vivo shift of the microbiota in oral biofilm in response to frequent sucrose consumption

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