Amplicon-based microbiome study highlights the loss of diversity and the establishment of a set of species in patients with dentin caries

Wolff, Diana; Frese, Cornelia; Schoilew, Kyrill; Dalpke, Alexander H.; Wolff, Björn; Boutin, Sébastien

doi:10.1371/journal.pone.0219714

Cited by 26 publications

(18 citation statements)

References 43 publications

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“…( Gueimonde et al, 2012 ). Consistent with our results, Wolff et al (2019) also reported P. denticolens enriched in carious dentin samples. A previous study by de Matos BM and colleagues demonstrated that S. mutans and P. denticolens have a synergistic effect that promotes a higher pH drop than the individual pH drops, which means that the presence of both species may indicate a higher cariogenic potential ( de Matos et al, 2017 ).…”

Section: Discussionsupporting

confidence: 92%

Metagenomic Analysis of Dental Plaque on Pit and Fissure Sites With and Without Caries Among Adolescents

Pang¹,

Wang²,

Ye³

et al. 2021

Front. Cell. Infect. Microbiol.

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Caries is one of the most prevalent infectious diseases worldwide and is driven by the dysbiosis of dental biofilms adhering to tooth surfaces. The pits and fissured surfaces are the most susceptible sites of caries. However, information on the taxonomic composition and functional characteristics of the plaque microbiota in the pit and fissure sites is very limited. This study aimed to use metagenomic sequencing analyses to investigate the relationship between the plaque microbiome in the pit and fissure site and caries in adolescents. A total of 20 adolescents with active pit and fissure surface caries were involved as well as 20 age-matched, caries-free teenagers for control tests. Plaque samples were collected from the pit and fissure site and were subjected to metagenomic analyses, in which the microbial communities were investigated. Our results showed that the microbiota diversity was similar between those two groups. At the species level, the relative abundances of A. gerencseriae, P. acidifaciens, P. multisaccharivorax, S. oralis, S. mutans, and P. denticolens were higher in the caries-active group. N. elongata, C. hominis, and A. johnsonii were relatively more abundant in the caries-free groups. Functional analysis suggested that the metabolic pathway was the most abundant pathway, and the functional traits of the level 2 pathways included amino acid metabolism, metabolism of cofactors, and vitamins and carbohydrate metabolism. Our results also revealed that the caries group displayed several alterations in metabolic pathways, including enriched functions in carbohydrate digestion and absorption. This study suggested that in addition to the specific anatomical structures of the pit and fissured surfaces, the fundamental differences in the plaque microbiome may also be related to the susceptibility of pit and fissure caries.

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Section: Discussionsupporting

confidence: 92%

Metagenomic Analysis of Dental Plaque on Pit and Fissure Sites With and Without Caries Among Adolescents

Pang¹,

Wang²,

Ye³

et al. 2021

Front. Cell. Infect. Microbiol.

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“…The richness indexes Shannon-Wiener, Simpson, and Pielou-Shannon revealed similar alpha diversity among sites from CA subjects and from INCL from CA and CI subjects. However, sound sites from CA subjects were less diverse and presented less evenness than from CF-S. Higher diversity has been described in healthy sites by several ecological studies [Gross et al, 2010;Benítez-Páez et al, 2014;Simón-Soro et al, 2014;Xiao et al, 2016;Schoilew et al, 2019;Wolff et al, 2019]. The lowering of the pH, from lactate produced by acid-producing species, could lead to suppression of acid-sensitive species and overgrowth of acidtolerant species, resulting in decreased bacterial diversity in supragingival plaques as caries progresses, as well as a decreasing number of species capable of surviving harsh conditions [Gross et al, 2010].…”

Section: Discussion/conclusionmentioning

confidence: 82%

“…The functional redundancy feature of microbiota, inherent to related species, may explain the human microbiome inter-individual variability. The interpersonal microbial composition variability extension, within and across varied dental plaque niches, is largely uncharacterized, but these factors are likely to directly contribute to the disparate results obtained from various studies examining dental caries [Benitéz-Páez et al, 2014;Simón-Soro et al, 2014;Mark Welch et al, 2016, Xiao et al, 2016Espinoza et al, 2018;Wolff et al, 2019].…”

Section: Discussion/conclusionmentioning

confidence: 99%

Functionally Active Microbiome in Supragingival Biofilms in Health and Caries

Corralo¹,

Ev²,

Damé‐Teixeira³

et al. 2021

Caries Res

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The oral microbiome is unique at inter and intra-individual levels at various sites due to physical and biological factors. This study aimed to compare the bacterial composition of supragingival biofilms collected from enamel sites with different caries activity, from active and inactive-caries subjects, and from caries-free (CF) subjects. Twenty-two individuals (aged between 13 and 76 years old; med = 23.5 years old) were allocated into 3 groups: caries-active (CA) (n = 10), caries-inactive (CI) (n = 6), and CF (n = 6). From the CA group, 3 sites were sampled: CA (active non-cavitated lesion), CI (inactive non-cavitated lesion), and sound enamel surface (S). From the subjects of the CI group, biofilm from a CI lesion was collected (INCL), while for the CF subjects, a pool of biofilm from sound enamel surfaces was sampled. The total RNA was extracted, and cDNA libraries were prepared and paired-end sequenced (Illumina HiSeq 3,000). Final dental biofilm samples analysed from CA was 16 (ANCL-CA = 6, INCL-CA = 4, S-CA = 6); from CI, 3 (INCL-CI = 3); and from CF, 6 (S-CF = 6) (some samples were lost by insufficient genetic material). Read sequences were processed and analysed using the Metagenomics RAST server. High-quality sequences (3,542,190) were clustered into operational taxonomic units (97% identity; SILVA SSU), representing 915 genera belonging to 29 phyla (higher abundant: Actinobacteria, Firmicutes, Bacteroidetes, and Fusobacteria). The presence of a core microbiome was observed (123 shared genera). The alpha diversity analysis showed less bacterial diversity in disease (S-CA) compared to health (S-CF). The dominant genera included Actinomyces, Corynebacterium, Capnocytophaga, Leptotrichia, Veillonella, Prevotella, Streptococcus, Eubacterium, and Neisseria. Veillonella and Leptotrichia were related with disease and Prevotella with health. Corynebacterium, Capnocytophaga, and Actinomyces clustered together presenting high abundance in health and disease. The Metric Multidimensional Scaling Ordination analysis shows that sites from active subjects (ANCL-CA, INCL-CA, and S-CA) are closer to each other than either INCL-CI subjects or S-CF subjects. In conclusion, supragingival bacterial communities presented intra-individual similarities, but inter-individual diversity and difference in bacterial composition reveal that the subject’s caries activity status matters more than sites.

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“…At the species level, Propionibacterium acidifaciens not only was more abundant in healthy children than children with caries in terms of deciduous teeth plaque but was also identi ed as a caries-speci c bacterium, absent in healthy children, and was detected in 13 children with caries in this study. Propionibacterium acidifaciens showed a higher abundance in individuals with caries in previous studies [46][47][48]. In 2009, Downes and Wade isolated Propionibacterium acidifaciens from the human oral cavity for the rst time [49].…”

Section: Discussionmentioning

confidence: 90%

Microbiome Analysis of Three Sample Types Obtained From Mixed Dentition Children With Different Caries Statuses: A Cross-Sectional Survey

Yang¹,

He²,

Yan³

et al. 2020

Preprint

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Background: Both supragingival plaque and saliva are commonly sampled for analysis of microbial communities. However, it remains unclear whether saliva can replace supragingival plaque for microbial studies of caries. There are limited studies on whether the microbiota of healthy first permanent molar (FPM) differs in different caries statuses of deciduous teeth. Herein, the PacBio Sequel platform was used to identify microbiome between three types of oral samples. Additionally, we compared the microbia between children with caries and healthy children in the same kind of microhabitat.Methods: In total, 30 children (aged 7–9 years) were enrolled in this study; 15 of them had dental caries. DNA was extracted from supragingival plaques of deciduous molars, supragingival plaques of maxillary FPMs, and saliva, and the v1–v9 regions of 16S rRNA was amplified. Additionally, PacBio sequencing and bioinformatic analyses were performed.Results: The salivary microbial alpha diversity were lower than that of the supragingival plaque on the teeth, but three was no difference between deciduous teeth and FPMs. Nonmetric multidimensional scaling analysis showed that the saliva samples were mainly scattered in the left side, whereas most plaque samples were distributed on the right. In the same microhabitat , there was no difference in microbial alpha and beta diverty between children with caries and healthy children. For the samples of the deciduous teeth, Streptococcus mutans, Propionibacterium acidifaciens, and Veillonella dispar were more abundant in the children with caries than healthy children, and the first two bacteria showed a positive correlation. For the samples of the FPMs, Selenomonas noxia was more abundant in healthy children than children with caries. But no differentially abundant microorganism were identified between the saliva subgroups. Conclusion:The microbial composition and struction of supragingival plaque was different from that of saliva, and supragingival plaque was found to be the best candidate for studying caries etiology. Streptococcus mutans, Veillonella dispar, and Propionibacterium acidifaciens are highly associated with the existence of deciduous caries. The microbia of the supragingival plaque on the healthy FPMs resemble when the caries status of the deciduous teeth was different, except for the abundance of Selenomonas noxia.

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Amplicon-based microbiome study highlights the loss of diversity and the establishment of a set of species in patients with dentin caries

Cited by 26 publications

References 43 publications

Metagenomic Analysis of Dental Plaque on Pit and Fissure Sites With and Without Caries Among Adolescents

Metagenomic Analysis of Dental Plaque on Pit and Fissure Sites With and Without Caries Among Adolescents

Functionally Active Microbiome in Supragingival Biofilms in Health and Caries

Microbiome Analysis of Three Sample Types Obtained From Mixed Dentition Children With Different Caries Statuses: A Cross-Sectional Survey

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